From f26cbf68d2a374d137d424b72f4fa4e09312beb4 Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Wed, 1 Apr 2026 11:14:21 -0500
Subject: [PATCH 01/16] update path for outputs

---
 src/permutation_analysis/prioritize_targets.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/permutation_analysis/prioritize_targets.R b/src/permutation_analysis/prioritize_targets.R
index 80f82e3..06aed6c 100644
--- a/src/permutation_analysis/prioritize_targets.R
+++ b/src/permutation_analysis/prioritize_targets.R
@@ -55,7 +55,7 @@ print(top_brainspan_coexpr)
 
 write_csv(
   rbind(top_gtex_coexpr, top_brainspan_coexpr),
-  paste0(indir, "setbp1_target_coexpression.csv")
+  paste0(outdir, "top_target_coexpression.csv")
 )
 
 ### gene functional pathway annotations ###
@@ -88,7 +88,7 @@ setbp1_pathways <- pathway_df %>%
   filter(!is.na(Target_Gene)) %>%
   filter(Target_Gene %in% setbp1_targets)
 
-write_csv(setbp1_pathways, paste0(indir, "setbp1_target_pathways.csv"))
+write_csv(setbp1_pathways, paste0(outdir, "setbp1_target_pathways.csv"))
 
 print(str(setbp1_pathways))
 print(unique(stringr::str_sort(setbp1_pathways$Target_Gene)))
@@ -98,6 +98,6 @@ prioritized_targets <- top_gtex_coexpr %>%
   select(Target_Gene, Method) %>%
   bind_rows(setbp1_pathways)
 
-write_csv(prioritized_targets, paste0(indir, "setbp1_targets_prioritized.csv"))
+write_csv(prioritized_targets, paste0(outdir, "setbp1_targets_prioritized.csv"))
 
 print(table(prioritized_targets$Target_Gene))

From 8401a97148070a4da14a0b4513857e783a5a7c5b Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Wed, 1 Apr 2026 11:39:39 -0500
Subject: [PATCH 02/16] update prioritization script names

---
 src/permutation_analysis/04_job_prioritize.sh |  17 +++
 .../04_prioritize_targets.R                   | 103 ++++++++++++++++++
 2 files changed, 120 insertions(+)
 create mode 100644 src/permutation_analysis/04_job_prioritize.sh
 create mode 100644 src/permutation_analysis/04_prioritize_targets.R

diff --git a/src/permutation_analysis/04_job_prioritize.sh b/src/permutation_analysis/04_job_prioritize.sh
new file mode 100644
index 0000000..e9f4f63
--- /dev/null
+++ b/src/permutation_analysis/04_job_prioritize.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+#SBATCH --ntasks=1
+#SBATCH --mem-per-cpu=64G
+#SBATCH --partition=short
+
+#### DATASETS ####
+
+cap_container -c singularity "lizzyr/lw_dea:0.3.1"
+
+singularity exec --cleanenv \
+                 --containall \
+                 -B "${CAP_PROJECT_PATH}" \
+                 "${CAP_CONTAINER_PATH}"/lw_dea_0.3.1.sif \
+                  Rscript --vanilla "${CAP_PROJECT_PATH}"/src/permutation_analysis/prioritize_targets.R \
+                  -i "${CAP_DATA_PATH}/" \
+                  -o "${CAP_RESULTS_PATH}"/permutation_analysis/
diff --git a/src/permutation_analysis/04_prioritize_targets.R b/src/permutation_analysis/04_prioritize_targets.R
new file mode 100644
index 0000000..06aed6c
--- /dev/null
+++ b/src/permutation_analysis/04_prioritize_targets.R
@@ -0,0 +1,103 @@
+##### Prioritization of SETBP1 Targets #####
+## GOAL: Prioritize SETBP1 targets by coexpression and pathway annotations
+
+suppressPackageStartupMessages({
+  library(argparse)
+  library(readr)
+  library(gprofiler2)
+  library(ggplot2)
+  library(tidyverse)
+  library(vroom)
+})
+###### SET UP ######
+# create parser object
+parser <- ArgumentParser()
+
+parser$add_argument("-i", "--indir",
+  type = "character",
+  help = "Path to the input data directory to access expression data"
+)
+parser$add_argument("-o", "--outdir",
+  type = "character",
+  help = "Path to the directory to write results"
+)
+# get command line options, if help option encountered print help and exit
+args <- parser$parse_args()
+indir <- args$indir
+outdir <- args$outdir
+
+# create output dir if needed
+if (!dir.exists(outdir)) dir.create(outdir, recursive = TRUE)
+# SETBP1 targets
+setbp1_targets_table <- read_csv(paste0(indir, "260303_setbp1_targets.csv"))
+setbp1_targets <- unique(setbp1_targets_table$Target)
+gtex_coexpr <- read_csv(paste0(outdir, "gtex_target_coexpression.csv"))
+brainspan_coexpr <- read_csv(
+  paste0(
+    outdir, "SETBP1_target_coexpression_brainspan.csv"
+  )
+)
+
+### TOP COEXPRESSED TARGETS ###
+top_gtex_coexpr <- gtex_coexpr %>%
+  filter(FDR < 0.05) %>%
+  slice_max(abs(Spearman_Rho), prop = 0.25) %>%
+  mutate(Method = "GTEx_Coexpr")
+cat("\nTop quartile significantly coexpressed targets across tissues/ages:\n")
+print(top_gtex_coexpr)
+
+top_brainspan_coexpr <- brainspan_coexpr %>%
+  filter(FDR < 0.05) %>%
+  slice_max(abs(Spearman_Rho), prop = 0.25) %>%
+  mutate(Method = "Brainspan_Coexpr")
+cat("\nTop quartile significantly coexpressed targets across tissues/ages:\n")
+print(top_brainspan_coexpr)
+
+write_csv(
+  rbind(top_gtex_coexpr, top_brainspan_coexpr),
+  paste0(outdir, "top_target_coexpression.csv")
+)
+
+### gene functional pathway annotations ###
+pathway_map <- list(
+  "Chromatin_organization" = "GO:0006325",
+  "Chromatin_binding" = "GO:0003682",
+  "Prostaglandin_receptor_activity" = "GO:0004955",
+  "Synapse_assembly" = "GO:0007416",
+  "Gene_expression" = "GO:0010467",
+  "Translation" = "GO:0006412",
+  "Translation_regulator_activity" = "GO:0045182",
+  "Mitochondrion" = "GO:0005739",
+  "Mitochondrion_organization" = "GO:0007005"
+)
+
+target_pathway_ids <- unlist(pathway_map)
+
+pathway_df <- gconvert(
+  query = target_pathway_ids,
+  organism = "hsapiens",
+  target = "HGNC",
+  mthreshold = Inf,
+  filter_na = TRUE
+)
+cat(str(pathway_df))
+
+setbp1_pathways <- pathway_df %>%
+  dplyr::select(input, target) %>%
+  rename("Method" = input, "Target_Gene" = target) %>%
+  filter(!is.na(Target_Gene)) %>%
+  filter(Target_Gene %in% setbp1_targets)
+
+write_csv(setbp1_pathways, paste0(outdir, "setbp1_target_pathways.csv"))
+
+print(str(setbp1_pathways))
+print(unique(stringr::str_sort(setbp1_pathways$Target_Gene)))
+
+### COMBINED TARGET PRIORITIZATION ###
+prioritized_targets <- top_gtex_coexpr %>%
+  select(Target_Gene, Method) %>%
+  bind_rows(setbp1_pathways)
+
+write_csv(prioritized_targets, paste0(outdir, "setbp1_targets_prioritized.csv"))
+
+print(table(prioritized_targets$Target_Gene))

From 47805ffde2e262f5011d40e1c32a14e4d97ebf2d Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Wed, 1 Apr 2026 11:51:02 -0500
Subject: [PATCH 03/16] fix filenames and output filepaths

---
 .../setbp1_target_pathways.csv                | 168 ++++++++++++++
 .../setbp1_targets_prioritized.csv            | 214 ++++++++++++++++++
 .../top_target_coexpression.csv               |  88 +++++++
 src/permutation_analysis/04_job_prioritize.sh |   3 +-
 4 files changed, 472 insertions(+), 1 deletion(-)
 create mode 100644 results/permutation_analysis/setbp1_target_pathways.csv
 create mode 100644 results/permutation_analysis/setbp1_targets_prioritized.csv
 create mode 100644 results/permutation_analysis/top_target_coexpression.csv

diff --git a/results/permutation_analysis/setbp1_target_pathways.csv b/results/permutation_analysis/setbp1_target_pathways.csv
new file mode 100644
index 0000000..d814406
--- /dev/null
+++ b/results/permutation_analysis/setbp1_target_pathways.csv
@@ -0,0 +1,168 @@
+Method,Target_Gene
+GO:0006325,BRCA1
+GO:0006325,KMT2A
+GO:0006325,SET
+GO:0006325,EPC2
+GO:0006325,KAT7
+GO:0006325,CHEK1
+GO:0006325,DPY30
+GO:0006325,PBRM1
+GO:0006325,PHF8
+GO:0006325,EED
+GO:0006325,ZZEF1
+GO:0006325,SUPT5H
+GO:0006325,KAT6A
+GO:0006325,MECOM
+GO:0003682,KMT2A
+GO:0003682,SET
+GO:0003682,NCOA5
+GO:0003682,KAT7
+GO:0003682,MEIS1
+GO:0003682,ZEB1
+GO:0003682,PBRM1
+GO:0003682,PHF8
+GO:0003682,SUPT5H
+GO:0003682,EED
+GO:0003682,KAT6A
+GO:0003682,PAF1
+GO:0007416,EPHA7
+GO:0007416,MEF2C
+GO:0007416,RAP2A
+GO:0010467,SARS2
+GO:0010467,RPS16
+GO:0010467,ZNF862
+GO:0010467,NDUFAB1
+GO:0010467,ZNHIT6
+GO:0010467,KMT2A
+GO:0010467,SET
+GO:0010467,NCOA5
+GO:0010467,CDKN1A
+GO:0010467,FOXP2
+GO:0010467,MRPS12
+GO:0010467,NSUN5
+GO:0010467,CTNNBL1
+GO:0010467,CDK8
+GO:0010467,ELP3
+GO:0010467,ZC3H10
+GO:0010467,EPC2
+GO:0010467,KAT7
+GO:0010467,RIOK2
+GO:0010467,MRPL15
+GO:0010467,NAA30
+GO:0010467,EIF4B
+GO:0010467,MED29
+GO:0010467,PIGK
+GO:0010467,HAX1
+GO:0010467,MEIS1
+GO:0010467,ZMAT2
+GO:0010467,ABT1
+GO:0010467,CDKN2A
+GO:0010467,ZEB1
+GO:0010467,TAF5
+GO:0010467,CHEK1
+GO:0010467,ZC3H15
+GO:0010467,ANK3
+GO:0010467,CWF19L2
+GO:0010467,HS2ST1
+GO:0010467,TSEN2
+GO:0010467,SFR1
+GO:0010467,UTP14A
+GO:0010467,CNOT11
+GO:0010467,DPY30
+GO:0010467,GNL3
+GO:0010467,PBRM1
+GO:0010467,NOL6
+GO:0010467,BAG5
+GO:0010467,LEO1
+GO:0010467,E4F1
+GO:0010467,RNF139
+GO:0010467,AFF1
+GO:0010467,PAF1
+GO:0010467,PHF8
+GO:0010467,PTGS2
+GO:0010467,EED
+GO:0010467,EIF3K
+GO:0010467,MRPS16
+GO:0010467,RBM33
+GO:0010467,HOXA9
+GO:0010467,TCEA1
+GO:0010467,SUPT5H
+GO:0010467,MEF2C
+GO:0010467,DDI2
+GO:0010467,TAF13
+GO:0010467,CEP290
+GO:0010467,KAT6A
+GO:0010467,MECOM
+GO:0010467,CHERP
+GO:0010467,DNAJC19
+GO:0010467,MT-TL1
+GO:0010467,MT-TF
+GO:0010467,MT-TT
+GO:0010467,MCTS1
+GO:0010467,MZF1
+GO:0010467,SNORD13
+GO:0010467,NSUN6
+GO:0010467,HOXA10
+GO:0010467,EEF1G
+GO:0010467,EIF3D
+GO:0010467,HM13
+GO:0010467,PPP5C
+GO:0010467,NDFIP2
+GO:0010467,BRCA1
+GO:0006412,SARS2
+GO:0006412,RPS16
+GO:0006412,EIF4B
+GO:0006412,MRPS12
+GO:0006412,NSUN5
+GO:0006412,ZC3H15
+GO:0006412,ELP3
+GO:0006412,MRPL15
+GO:0006412,CNOT11
+GO:0006412,RNF139
+GO:0006412,EIF3K
+GO:0006412,MRPS16
+GO:0006412,TCEA1
+GO:0006412,MT-TL1
+GO:0006412,MT-TF
+GO:0006412,MT-TT
+GO:0006412,MCTS1
+GO:0006412,EEF1G
+GO:0006412,EIF3D
+GO:0005739,DLAT
+GO:0005739,PDSS2
+GO:0005739,NDUFAB1
+GO:0005739,NOL6
+GO:0005739,BAG5
+GO:0005739,NDUFS5
+GO:0005739,NUDT9
+GO:0005739,ETFDH
+GO:0005739,MRPS16
+GO:0005739,NBR1
+GO:0005739,TOMM7
+GO:0005739,MT-ND6
+GO:0005739,MT-ND1
+GO:0005739,TIMM23B
+GO:0005739,DNAJC19
+GO:0005739,PARG
+GO:0005739,TIMM23
+GO:0005739,CRLS1
+GO:0005739,USP48
+GO:0005739,PDPR
+GO:0005739,NDFIP2
+GO:0005739,SARS2
+GO:0005739,MRPS12
+GO:0005739,COX4I1
+GO:0005739,DCAF8
+GO:0005739,MRPL15
+GO:0005739,PSMB6
+GO:0005739,HAX1
+GO:0005739,TMEM177
+GO:0005739,MPC1
+GO:0005739,CDKN2A
+GO:0007005,CDKN2A
+GO:0007005,NDUFS5
+GO:0007005,TOMM7
+GO:0007005,MT-ND6
+GO:0007005,MT-ND1
+GO:0007005,NEURL4
+GO:0007005,NDUFAB1
diff --git a/results/permutation_analysis/setbp1_targets_prioritized.csv b/results/permutation_analysis/setbp1_targets_prioritized.csv
new file mode 100644
index 0000000..1f6a52f
--- /dev/null
+++ b/results/permutation_analysis/setbp1_targets_prioritized.csv
@@ -0,0 +1,214 @@
+Target_Gene,Method
+MYO9A,GTEx_Coexpr
+UBR1,GTEx_Coexpr
+EPC2,GTEx_Coexpr
+RALGAPA1,GTEx_Coexpr
+DCAF8,GTEx_Coexpr
+PBRM1,GTEx_Coexpr
+IPO8,GTEx_Coexpr
+TBC1D23,GTEx_Coexpr
+ESYT1,GTEx_Coexpr
+KAT7,GTEx_Coexpr
+KMT2A,GTEx_Coexpr
+ZEB1,GTEx_Coexpr
+GGCX,GTEx_Coexpr
+TTC23,GTEx_Coexpr
+CWF19L2,GTEx_Coexpr
+ZZEF1,GTEx_Coexpr
+CHERP,GTEx_Coexpr
+NBR1,GTEx_Coexpr
+TMTC3,GTEx_Coexpr
+TIMM23B,GTEx_Coexpr
+ZC3H10,GTEx_Coexpr
+CDK8,GTEx_Coexpr
+RAD52,GTEx_Coexpr
+NUDT9,GTEx_Coexpr
+NAALADL2,GTEx_Coexpr
+BAG5,GTEx_Coexpr
+PDPR,GTEx_Coexpr
+FAF1,GTEx_Coexpr
+RIOK2,GTEx_Coexpr
+PARG,GTEx_Coexpr
+BET1L,GTEx_Coexpr
+SUPT5H,GTEx_Coexpr
+PKN2,GTEx_Coexpr
+E4F1,GTEx_Coexpr
+UTP14A,GTEx_Coexpr
+RNF139,GTEx_Coexpr
+EIF4B,GTEx_Coexpr
+NAA30,GTEx_Coexpr
+USP48,GTEx_Coexpr
+AFF1,GTEx_Coexpr
+PHF8,GTEx_Coexpr
+CCDC174,GTEx_Coexpr
+PPP5C,GTEx_Coexpr
+TCEA1,GTEx_Coexpr
+ZEB1-AS1,GTEx_Coexpr
+AASDH,GTEx_Coexpr
+BRCA1,GO:0006325
+KMT2A,GO:0006325
+SET,GO:0006325
+EPC2,GO:0006325
+KAT7,GO:0006325
+CHEK1,GO:0006325
+DPY30,GO:0006325
+PBRM1,GO:0006325
+PHF8,GO:0006325
+EED,GO:0006325
+ZZEF1,GO:0006325
+SUPT5H,GO:0006325
+KAT6A,GO:0006325
+MECOM,GO:0006325
+KMT2A,GO:0003682
+SET,GO:0003682
+NCOA5,GO:0003682
+KAT7,GO:0003682
+MEIS1,GO:0003682
+ZEB1,GO:0003682
+PBRM1,GO:0003682
+PHF8,GO:0003682
+SUPT5H,GO:0003682
+EED,GO:0003682
+KAT6A,GO:0003682
+PAF1,GO:0003682
+EPHA7,GO:0007416
+MEF2C,GO:0007416
+RAP2A,GO:0007416
+SARS2,GO:0010467
+RPS16,GO:0010467
+ZNF862,GO:0010467
+NDUFAB1,GO:0010467
+ZNHIT6,GO:0010467
+KMT2A,GO:0010467
+SET,GO:0010467
+NCOA5,GO:0010467
+CDKN1A,GO:0010467
+FOXP2,GO:0010467
+MRPS12,GO:0010467
+NSUN5,GO:0010467
+CTNNBL1,GO:0010467
+CDK8,GO:0010467
+ELP3,GO:0010467
+ZC3H10,GO:0010467
+EPC2,GO:0010467
+KAT7,GO:0010467
+RIOK2,GO:0010467
+MRPL15,GO:0010467
+NAA30,GO:0010467
+EIF4B,GO:0010467
+MED29,GO:0010467
+PIGK,GO:0010467
+HAX1,GO:0010467
+MEIS1,GO:0010467
+ZMAT2,GO:0010467
+ABT1,GO:0010467
+CDKN2A,GO:0010467
+ZEB1,GO:0010467
+TAF5,GO:0010467
+CHEK1,GO:0010467
+ZC3H15,GO:0010467
+ANK3,GO:0010467
+CWF19L2,GO:0010467
+HS2ST1,GO:0010467
+TSEN2,GO:0010467
+SFR1,GO:0010467
+UTP14A,GO:0010467
+CNOT11,GO:0010467
+DPY30,GO:0010467
+GNL3,GO:0010467
+PBRM1,GO:0010467
+NOL6,GO:0010467
+BAG5,GO:0010467
+LEO1,GO:0010467
+E4F1,GO:0010467
+RNF139,GO:0010467
+AFF1,GO:0010467
+PAF1,GO:0010467
+PHF8,GO:0010467
+PTGS2,GO:0010467
+EED,GO:0010467
+EIF3K,GO:0010467
+MRPS16,GO:0010467
+RBM33,GO:0010467
+HOXA9,GO:0010467
+TCEA1,GO:0010467
+SUPT5H,GO:0010467
+MEF2C,GO:0010467
+DDI2,GO:0010467
+TAF13,GO:0010467
+CEP290,GO:0010467
+KAT6A,GO:0010467
+MECOM,GO:0010467
+CHERP,GO:0010467
+DNAJC19,GO:0010467
+MT-TL1,GO:0010467
+MT-TF,GO:0010467
+MT-TT,GO:0010467
+MCTS1,GO:0010467
+MZF1,GO:0010467
+SNORD13,GO:0010467
+NSUN6,GO:0010467
+HOXA10,GO:0010467
+EEF1G,GO:0010467
+EIF3D,GO:0010467
+HM13,GO:0010467
+PPP5C,GO:0010467
+NDFIP2,GO:0010467
+BRCA1,GO:0010467
+SARS2,GO:0006412
+RPS16,GO:0006412
+EIF4B,GO:0006412
+MRPS12,GO:0006412
+NSUN5,GO:0006412
+ZC3H15,GO:0006412
+ELP3,GO:0006412
+MRPL15,GO:0006412
+CNOT11,GO:0006412
+RNF139,GO:0006412
+EIF3K,GO:0006412
+MRPS16,GO:0006412
+TCEA1,GO:0006412
+MT-TL1,GO:0006412
+MT-TF,GO:0006412
+MT-TT,GO:0006412
+MCTS1,GO:0006412
+EEF1G,GO:0006412
+EIF3D,GO:0006412
+DLAT,GO:0005739
+PDSS2,GO:0005739
+NDUFAB1,GO:0005739
+NOL6,GO:0005739
+BAG5,GO:0005739
+NDUFS5,GO:0005739
+NUDT9,GO:0005739
+ETFDH,GO:0005739
+MRPS16,GO:0005739
+NBR1,GO:0005739
+TOMM7,GO:0005739
+MT-ND6,GO:0005739
+MT-ND1,GO:0005739
+TIMM23B,GO:0005739
+DNAJC19,GO:0005739
+PARG,GO:0005739
+TIMM23,GO:0005739
+CRLS1,GO:0005739
+USP48,GO:0005739
+PDPR,GO:0005739
+NDFIP2,GO:0005739
+SARS2,GO:0005739
+MRPS12,GO:0005739
+COX4I1,GO:0005739
+DCAF8,GO:0005739
+MRPL15,GO:0005739
+PSMB6,GO:0005739
+HAX1,GO:0005739
+TMEM177,GO:0005739
+MPC1,GO:0005739
+CDKN2A,GO:0005739
+CDKN2A,GO:0007005
+NDUFS5,GO:0007005
+TOMM7,GO:0007005
+MT-ND6,GO:0007005
+MT-ND1,GO:0007005
+NEURL4,GO:0007005
+NDUFAB1,GO:0007005
diff --git a/results/permutation_analysis/top_target_coexpression.csv b/results/permutation_analysis/top_target_coexpression.csv
new file mode 100644
index 0000000..cd22751
--- /dev/null
+++ b/results/permutation_analysis/top_target_coexpression.csv
@@ -0,0 +1,88 @@
+Target_Gene,Spearman_Rho,P_Value,FDR,Method
+MYO9A,0.8390821820084338,0,0,GTEx_Coexpr
+UBR1,0.8236870308086461,0,0,GTEx_Coexpr
+EPC2,0.816869184030563,0,0,GTEx_Coexpr
+RALGAPA1,0.8104387281195069,0,0,GTEx_Coexpr
+DCAF8,0.8012994667679644,0,0,GTEx_Coexpr
+PBRM1,0.7847282679214185,0,0,GTEx_Coexpr
+IPO8,0.7796582882643719,0,0,GTEx_Coexpr
+TBC1D23,0.7715737178414818,0,0,GTEx_Coexpr
+ESYT1,0.7715601969412416,0,0,GTEx_Coexpr
+KAT7,0.7687530389441259,0,0,GTEx_Coexpr
+KMT2A,0.7670202217905395,0,0,GTEx_Coexpr
+ZEB1,0.7619917916837197,0,0,GTEx_Coexpr
+GGCX,0.756490182916181,0,0,GTEx_Coexpr
+TTC23,0.7507166573294056,0,0,GTEx_Coexpr
+CWF19L2,0.7391402818207754,0,0,GTEx_Coexpr
+ZZEF1,0.7379008632291393,0,0,GTEx_Coexpr
+CHERP,0.7344391458096833,0,0,GTEx_Coexpr
+NBR1,0.7245617593047815,0,0,GTEx_Coexpr
+TMTC3,0.7226914832831698,0,0,GTEx_Coexpr
+TIMM23B,0.7181462446481214,0,0,GTEx_Coexpr
+ZC3H10,0.7180324747959462,0,0,GTEx_Coexpr
+CDK8,0.7159809072200963,0,0,GTEx_Coexpr
+RAD52,0.7136436441109464,0,0,GTEx_Coexpr
+NUDT9,0.7083930145296485,0,0,GTEx_Coexpr
+NAALADL2,0.7049563171171831,0,0,GTEx_Coexpr
+BAG5,0.7049074964618852,0,0,GTEx_Coexpr
+PDPR,0.7021572429222492,0,0,GTEx_Coexpr
+FAF1,0.697608819191427,0,0,GTEx_Coexpr
+RIOK2,0.6971399082050161,0,0,GTEx_Coexpr
+PARG,0.6898706050987761,0,0,GTEx_Coexpr
+BET1L,0.6841960228971125,0,0,GTEx_Coexpr
+SUPT5H,0.6834033866980204,0,0,GTEx_Coexpr
+PKN2,0.6827336547886925,0,0,GTEx_Coexpr
+E4F1,0.6802659037190822,0,0,GTEx_Coexpr
+UTP14A,0.6716843489426706,0,0,GTEx_Coexpr
+RNF139,0.6707941030803772,0,0,GTEx_Coexpr
+EIF4B,0.670426056616079,0,0,GTEx_Coexpr
+NAA30,0.6684199360192891,0,0,GTEx_Coexpr
+USP48,0.6664224211523371,0,0,GTEx_Coexpr
+AFF1,0.6650660374207301,0,0,GTEx_Coexpr
+PHF8,0.6645806548466711,0,0,GTEx_Coexpr
+CCDC174,0.6639564331476699,0,0,GTEx_Coexpr
+PPP5C,0.6616582280872436,0,0,GTEx_Coexpr
+TCEA1,0.6557145709940534,0,0,GTEx_Coexpr
+ZEB1-AS1,0.6550246155788777,0,0,GTEx_Coexpr
+AASDH,0.6547870254691704,0,0,GTEx_Coexpr
+PBRM1,0.8996528291815317,5.193292567810596e-190,9.659524176127708e-188,Brainspan_Coexpr
+EPC2,0.8762826658548637,1.1355972204798998e-167,1.0561054150463067e-165,Brainspan_Coexpr
+KAT6A,0.8672590603243179,3.1127564134570265e-160,1.9299089763433566e-158,Brainspan_Coexpr
+EPHA7,0.8350026342237999,1.554269060737794e-137,7.227351132430745e-136,Brainspan_Coexpr
+CHERP,0.8332364869232324,1.9505681581718096e-136,7.256113548399131e-135,Brainspan_Coexpr
+LEO1,0.8284393994049094,1.6228175973952227e-133,5.030734551925189e-132,Brainspan_Coexpr
+NCOA5,0.8238664195116253,8.140169847519039e-131,2.162959416626488e-129,Brainspan_Coexpr
+EPRS,0.8214159148107448,2.1167805269964606e-129,4.921514725266771e-128,Brainspan_Coexpr
+TAF5,0.807397303118699,1.0549756973773712e-121,2.1802831079132336e-120,Brainspan_Coexpr
+COX4I1,-0.7988146566553582,2.6920388850845556e-117,5.0071923262572733e-116,Brainspan_Coexpr
+DIEXF,0.795646457085308,1.0071212605623211e-115,1.7029504951326522e-114,Brainspan_Coexpr
+RP11-277P12.6,-0.7931057016452419,1.756225695962438e-114,2.7221498287417787e-113,Brainspan_Coexpr
+ETFDH,-0.7918503891857853,7.104770329187421e-114,1.0165286778683539e-112,Brainspan_Coexpr
+EIF4B,0.7879218750977395,5.300302652475869e-112,7.041830666860798e-111,Brainspan_Coexpr
+ANP32A,0.7743391348044478,8.017808306260882e-106,9.942082299763495e-105,Brainspan_Coexpr
+KLHDC9,-0.7738174402772361,1.357569109536665e-105,1.578174089836373e-104,Brainspan_Coexpr
+C4orf46,0.7566507294757406,2.1494242026551718e-98,2.3517229511403643e-97,Brainspan_Coexpr
+MTND5P11,-0.7551099905913948,8.894982566998288e-98,9.191481985898231e-97,Brainspan_Coexpr
+ARL5B,0.7492345769624533,1.819002104942758e-95,1.7807073237860682e-94,Brainspan_Coexpr
+UTP14A,0.7407309978711025,3.107612509634212e-92,2.8900796339598174e-91,Brainspan_Coexpr
+C4orf36,-0.7385191702621436,2.0534979010351325e-91,1.8188124266311175e-90,Brainspan_Coexpr
+FAF1,0.7270254028953836,2.776396577490415e-87,2.3473171064237153e-86,Brainspan_Coexpr
+MED29,-0.7267797769349299,3.384179617567856e-87,2.67505396089962e-86,Brainspan_Coexpr
+CDK8,0.7267552560410849,3.451682530193058e-87,2.67505396089962e-86,Brainspan_Coexpr
+NSUN6,0.7221188053987667,1.390728602196525e-85,1.0347020800342149e-84,Brainspan_Coexpr
+SET,0.7193114966711217,1.2571274056587338e-84,8.993296055866328e-84,Brainspan_Coexpr
+ASB7,0.7172030334180581,6.454081713678158e-84,4.446145180533841e-83,Brainspan_Coexpr
+TAF13,-0.7166272928391065,1.0062464156349854e-83,6.68435118957526e-83,Brainspan_Coexpr
+EIF3D,0.7060276777504164,2.94843652392418e-80,1.891066184309991e-79,Brainspan_Coexpr
+CTNNBL1,0.6997359833691623,2.8511815086808275e-78,1.767732535382113e-77,Brainspan_Coexpr
+RNF111,0.6964448457122839,2.9718333970820386e-77,1.7831000382492228e-76,Brainspan_Coexpr
+ZC3H10,0.6950595820188451,7.895542075076033e-77,4.5892838311379446e-76,Brainspan_Coexpr
+SOX2-OT,-0.6899719135680192,2.7250559448783583e-75,1.5359406234768928e-74,Brainspan_Coexpr
+MIR4461,-0.6854989312355636,5.77388982814577e-74,3.158657376573862e-73,Brainspan_Coexpr
+DNAJC19,-0.6838761361243224,1.7245614069128133e-73,9.164812048165236e-73,Brainspan_Coexpr
+GNL3,0.6793224226476309,3.5789750460865523e-72,1.849137107144719e-71,Brainspan_Coexpr
+ZZEF1,0.6641655910974141,5.895870184580735e-68,2.9638698765730184e-67,Brainspan_Coexpr
+VAMP8,-0.6637569095333314,7.600243107522766e-68,3.720118994734827e-67,Brainspan_Coexpr
+KLRC2,-0.6598509159233871,8.435331365720325e-67,4.0230041898050785e-66,Brainspan_Coexpr
+CDKN1A,-0.6524821911270686,7.176834216478372e-65,3.337227910662443e-64,Brainspan_Coexpr
+EEF1G,0.6446092608076465,7.229510823490885e-63,3.2797293004129377e-62,Brainspan_Coexpr
diff --git a/src/permutation_analysis/04_job_prioritize.sh b/src/permutation_analysis/04_job_prioritize.sh
index e9f4f63..dcebf2b 100644
--- a/src/permutation_analysis/04_job_prioritize.sh
+++ b/src/permutation_analysis/04_job_prioritize.sh
@@ -7,11 +7,12 @@
 #### DATASETS ####
 
 cap_container -c singularity "lizzyr/lw_dea:0.3.1"
+script="${CAP_PROJECT_PATH}"/src/permutation_analysis/04_prioritize_targets.R
 
 singularity exec --cleanenv \
                  --containall \
                  -B "${CAP_PROJECT_PATH}" \
                  "${CAP_CONTAINER_PATH}"/lw_dea_0.3.1.sif \
-                  Rscript --vanilla "${CAP_PROJECT_PATH}"/src/permutation_analysis/prioritize_targets.R \
+                  Rscript --vanilla "${script}" \
                   -i "${CAP_DATA_PATH}/" \
                   -o "${CAP_RESULTS_PATH}"/permutation_analysis/

From 0fbf54f3ce7939cbb96685995c84e90730c039e5 Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Wed, 1 Apr 2026 14:09:35 -0500
Subject: [PATCH 04/16] filter for top 10% instead of top 25% coexpressed genes

---
 .../setbp1_targets_prioritized.csv            | 28 ----------
 .../top_target_coexpression.csv               | 53 -------------------
 .../04_prioritize_targets.R                   | 14 ++---
 3 files changed, 8 insertions(+), 87 deletions(-)

diff --git a/results/permutation_analysis/setbp1_targets_prioritized.csv b/results/permutation_analysis/setbp1_targets_prioritized.csv
index 1f6a52f..9de2d0b 100644
--- a/results/permutation_analysis/setbp1_targets_prioritized.csv
+++ b/results/permutation_analysis/setbp1_targets_prioritized.csv
@@ -17,34 +17,6 @@ CWF19L2,GTEx_Coexpr
 ZZEF1,GTEx_Coexpr
 CHERP,GTEx_Coexpr
 NBR1,GTEx_Coexpr
-TMTC3,GTEx_Coexpr
-TIMM23B,GTEx_Coexpr
-ZC3H10,GTEx_Coexpr
-CDK8,GTEx_Coexpr
-RAD52,GTEx_Coexpr
-NUDT9,GTEx_Coexpr
-NAALADL2,GTEx_Coexpr
-BAG5,GTEx_Coexpr
-PDPR,GTEx_Coexpr
-FAF1,GTEx_Coexpr
-RIOK2,GTEx_Coexpr
-PARG,GTEx_Coexpr
-BET1L,GTEx_Coexpr
-SUPT5H,GTEx_Coexpr
-PKN2,GTEx_Coexpr
-E4F1,GTEx_Coexpr
-UTP14A,GTEx_Coexpr
-RNF139,GTEx_Coexpr
-EIF4B,GTEx_Coexpr
-NAA30,GTEx_Coexpr
-USP48,GTEx_Coexpr
-AFF1,GTEx_Coexpr
-PHF8,GTEx_Coexpr
-CCDC174,GTEx_Coexpr
-PPP5C,GTEx_Coexpr
-TCEA1,GTEx_Coexpr
-ZEB1-AS1,GTEx_Coexpr
-AASDH,GTEx_Coexpr
 BRCA1,GO:0006325
 KMT2A,GO:0006325
 SET,GO:0006325
diff --git a/results/permutation_analysis/top_target_coexpression.csv b/results/permutation_analysis/top_target_coexpression.csv
index cd22751..8b00193 100644
--- a/results/permutation_analysis/top_target_coexpression.csv
+++ b/results/permutation_analysis/top_target_coexpression.csv
@@ -17,34 +17,6 @@ CWF19L2,0.7391402818207754,0,0,GTEx_Coexpr
 ZZEF1,0.7379008632291393,0,0,GTEx_Coexpr
 CHERP,0.7344391458096833,0,0,GTEx_Coexpr
 NBR1,0.7245617593047815,0,0,GTEx_Coexpr
-TMTC3,0.7226914832831698,0,0,GTEx_Coexpr
-TIMM23B,0.7181462446481214,0,0,GTEx_Coexpr
-ZC3H10,0.7180324747959462,0,0,GTEx_Coexpr
-CDK8,0.7159809072200963,0,0,GTEx_Coexpr
-RAD52,0.7136436441109464,0,0,GTEx_Coexpr
-NUDT9,0.7083930145296485,0,0,GTEx_Coexpr
-NAALADL2,0.7049563171171831,0,0,GTEx_Coexpr
-BAG5,0.7049074964618852,0,0,GTEx_Coexpr
-PDPR,0.7021572429222492,0,0,GTEx_Coexpr
-FAF1,0.697608819191427,0,0,GTEx_Coexpr
-RIOK2,0.6971399082050161,0,0,GTEx_Coexpr
-PARG,0.6898706050987761,0,0,GTEx_Coexpr
-BET1L,0.6841960228971125,0,0,GTEx_Coexpr
-SUPT5H,0.6834033866980204,0,0,GTEx_Coexpr
-PKN2,0.6827336547886925,0,0,GTEx_Coexpr
-E4F1,0.6802659037190822,0,0,GTEx_Coexpr
-UTP14A,0.6716843489426706,0,0,GTEx_Coexpr
-RNF139,0.6707941030803772,0,0,GTEx_Coexpr
-EIF4B,0.670426056616079,0,0,GTEx_Coexpr
-NAA30,0.6684199360192891,0,0,GTEx_Coexpr
-USP48,0.6664224211523371,0,0,GTEx_Coexpr
-AFF1,0.6650660374207301,0,0,GTEx_Coexpr
-PHF8,0.6645806548466711,0,0,GTEx_Coexpr
-CCDC174,0.6639564331476699,0,0,GTEx_Coexpr
-PPP5C,0.6616582280872436,0,0,GTEx_Coexpr
-TCEA1,0.6557145709940534,0,0,GTEx_Coexpr
-ZEB1-AS1,0.6550246155788777,0,0,GTEx_Coexpr
-AASDH,0.6547870254691704,0,0,GTEx_Coexpr
 PBRM1,0.8996528291815317,5.193292567810596e-190,9.659524176127708e-188,Brainspan_Coexpr
 EPC2,0.8762826658548637,1.1355972204798998e-167,1.0561054150463067e-165,Brainspan_Coexpr
 KAT6A,0.8672590603243179,3.1127564134570265e-160,1.9299089763433566e-158,Brainspan_Coexpr
@@ -61,28 +33,3 @@ ETFDH,-0.7918503891857853,7.104770329187421e-114,1.0165286778683539e-112,Brainsp
 EIF4B,0.7879218750977395,5.300302652475869e-112,7.041830666860798e-111,Brainspan_Coexpr
 ANP32A,0.7743391348044478,8.017808306260882e-106,9.942082299763495e-105,Brainspan_Coexpr
 KLHDC9,-0.7738174402772361,1.357569109536665e-105,1.578174089836373e-104,Brainspan_Coexpr
-C4orf46,0.7566507294757406,2.1494242026551718e-98,2.3517229511403643e-97,Brainspan_Coexpr
-MTND5P11,-0.7551099905913948,8.894982566998288e-98,9.191481985898231e-97,Brainspan_Coexpr
-ARL5B,0.7492345769624533,1.819002104942758e-95,1.7807073237860682e-94,Brainspan_Coexpr
-UTP14A,0.7407309978711025,3.107612509634212e-92,2.8900796339598174e-91,Brainspan_Coexpr
-C4orf36,-0.7385191702621436,2.0534979010351325e-91,1.8188124266311175e-90,Brainspan_Coexpr
-FAF1,0.7270254028953836,2.776396577490415e-87,2.3473171064237153e-86,Brainspan_Coexpr
-MED29,-0.7267797769349299,3.384179617567856e-87,2.67505396089962e-86,Brainspan_Coexpr
-CDK8,0.7267552560410849,3.451682530193058e-87,2.67505396089962e-86,Brainspan_Coexpr
-NSUN6,0.7221188053987667,1.390728602196525e-85,1.0347020800342149e-84,Brainspan_Coexpr
-SET,0.7193114966711217,1.2571274056587338e-84,8.993296055866328e-84,Brainspan_Coexpr
-ASB7,0.7172030334180581,6.454081713678158e-84,4.446145180533841e-83,Brainspan_Coexpr
-TAF13,-0.7166272928391065,1.0062464156349854e-83,6.68435118957526e-83,Brainspan_Coexpr
-EIF3D,0.7060276777504164,2.94843652392418e-80,1.891066184309991e-79,Brainspan_Coexpr
-CTNNBL1,0.6997359833691623,2.8511815086808275e-78,1.767732535382113e-77,Brainspan_Coexpr
-RNF111,0.6964448457122839,2.9718333970820386e-77,1.7831000382492228e-76,Brainspan_Coexpr
-ZC3H10,0.6950595820188451,7.895542075076033e-77,4.5892838311379446e-76,Brainspan_Coexpr
-SOX2-OT,-0.6899719135680192,2.7250559448783583e-75,1.5359406234768928e-74,Brainspan_Coexpr
-MIR4461,-0.6854989312355636,5.77388982814577e-74,3.158657376573862e-73,Brainspan_Coexpr
-DNAJC19,-0.6838761361243224,1.7245614069128133e-73,9.164812048165236e-73,Brainspan_Coexpr
-GNL3,0.6793224226476309,3.5789750460865523e-72,1.849137107144719e-71,Brainspan_Coexpr
-ZZEF1,0.6641655910974141,5.895870184580735e-68,2.9638698765730184e-67,Brainspan_Coexpr
-VAMP8,-0.6637569095333314,7.600243107522766e-68,3.720118994734827e-67,Brainspan_Coexpr
-KLRC2,-0.6598509159233871,8.435331365720325e-67,4.0230041898050785e-66,Brainspan_Coexpr
-CDKN1A,-0.6524821911270686,7.176834216478372e-65,3.337227910662443e-64,Brainspan_Coexpr
-EEF1G,0.6446092608076465,7.229510823490885e-63,3.2797293004129377e-62,Brainspan_Coexpr
diff --git a/src/permutation_analysis/04_prioritize_targets.R b/src/permutation_analysis/04_prioritize_targets.R
index 06aed6c..6a3f3dd 100644
--- a/src/permutation_analysis/04_prioritize_targets.R
+++ b/src/permutation_analysis/04_prioritize_targets.R
@@ -37,18 +37,19 @@ brainspan_coexpr <- read_csv(
     outdir, "SETBP1_target_coexpression_brainspan.csv"
   )
 )
+cat("\nTotal number of unique SETBP1 targets: ", length(setbp1_targets))
 
 ### TOP COEXPRESSED TARGETS ###
 top_gtex_coexpr <- gtex_coexpr %>%
   filter(FDR < 0.05) %>%
-  slice_max(abs(Spearman_Rho), prop = 0.25) %>%
+  slice_max(abs(Spearman_Rho), prop = 0.10) %>%
   mutate(Method = "GTEx_Coexpr")
 cat("\nTop quartile significantly coexpressed targets across tissues/ages:\n")
 print(top_gtex_coexpr)
 
 top_brainspan_coexpr <- brainspan_coexpr %>%
   filter(FDR < 0.05) %>%
-  slice_max(abs(Spearman_Rho), prop = 0.25) %>%
+  slice_max(abs(Spearman_Rho), prop = 0.10) %>%
   mutate(Method = "Brainspan_Coexpr")
 cat("\nTop quartile significantly coexpressed targets across tissues/ages:\n")
 print(top_brainspan_coexpr)
@@ -80,6 +81,7 @@ pathway_df <- gconvert(
   mthreshold = Inf,
   filter_na = TRUE
 )
+cat("\npathway_df structure:\n")
 cat(str(pathway_df))
 
 setbp1_pathways <- pathway_df %>%
@@ -90,14 +92,14 @@ setbp1_pathways <- pathway_df %>%
 
 write_csv(setbp1_pathways, paste0(outdir, "setbp1_target_pathways.csv"))
 
-print(str(setbp1_pathways))
-print(unique(stringr::str_sort(setbp1_pathways$Target_Gene)))
-
 ### COMBINED TARGET PRIORITIZATION ###
 prioritized_targets <- top_gtex_coexpr %>%
   select(Target_Gene, Method) %>%
   bind_rows(setbp1_pathways)
 
 write_csv(prioritized_targets, paste0(outdir, "setbp1_targets_prioritized.csv"))
+cat("\nSaved final prioritized targets to: setbp1_targets_prioritized.csv\n\n")
+cat("\nNumber of top prioritized targets: ", length(unique(prioritized_targets$Target_Gene)))
+cat("\nFrequency of targets by prioritization method:\n")
 
-print(table(prioritized_targets$Target_Gene))
+print(sort(table(prioritized_targets$Target_Gene)))

From 893c69a45757a85249bf401b7bfd9953f04b3c24 Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Mon, 6 Apr 2026 11:47:57 -0500
Subject: [PATCH 05/16] update prioritization with updated SETBP1 targets

---
 .../setbp1_target_pathways.csv                | 66 +++++++++++++++++++
 .../setbp1_targets_prioritized.csv            | 66 +++++++++++++++++++
 .../04_prioritize_targets.R                   |  7 +-
 3 files changed, 137 insertions(+), 2 deletions(-)

diff --git a/results/permutation_analysis/setbp1_target_pathways.csv b/results/permutation_analysis/setbp1_target_pathways.csv
index d814406..3b963be 100644
--- a/results/permutation_analysis/setbp1_target_pathways.csv
+++ b/results/permutation_analysis/setbp1_target_pathways.csv
@@ -1,13 +1,22 @@
 Method,Target_Gene
 GO:0006325,BRCA1
+GO:0006325,ZMYND11
+GO:0006325,INO80D
 GO:0006325,KMT2A
+GO:0006325,HDAC9
 GO:0006325,SET
+GO:0006325,EPC1
+GO:0006325,BAZ2B
 GO:0006325,EPC2
 GO:0006325,KAT7
 GO:0006325,CHEK1
 GO:0006325,DPY30
 GO:0006325,PBRM1
+GO:0006325,BMI1
+GO:0006325,BPTF
+GO:0006325,JMJD1C
 GO:0006325,PHF8
+GO:0006325,CHD2
 GO:0006325,EED
 GO:0006325,ZZEF1
 GO:0006325,SUPT5H
@@ -20,84 +29,133 @@ GO:0003682,KAT7
 GO:0003682,MEIS1
 GO:0003682,ZEB1
 GO:0003682,PBRM1
+GO:0003682,BMI1
+GO:0003682,JMJD1C
 GO:0003682,PHF8
+GO:0003682,CHD2
 GO:0003682,SUPT5H
 GO:0003682,EED
+GO:0003682,MLLT10
 GO:0003682,KAT6A
 GO:0003682,PAF1
 GO:0007416,EPHA7
+GO:0007416,PTPN13
+GO:0007416,PTEN
+GO:0007416,ERBB4
 GO:0007416,MEF2C
 GO:0007416,RAP2A
 GO:0010467,SARS2
 GO:0010467,RPS16
+GO:0010467,ZMYND11
 GO:0010467,ZNF862
+GO:0010467,TRDMT1
+GO:0010467,ACTA2
+GO:0010467,PITRM1
+GO:0010467,HGF
+GO:0010467,CDKN1B
+GO:0010467,BMP5
+GO:0010467,PDE4D
+GO:0010467,INO80D
 GO:0010467,NDUFAB1
+GO:0010467,WDR75
+GO:0010467,NFE2L2
 GO:0010467,ZNHIT6
 GO:0010467,KMT2A
 GO:0010467,SET
+GO:0010467,EPC1
+GO:0010467,BAZ2B
 GO:0010467,NCOA5
 GO:0010467,CDKN1A
+GO:0010467,HDAC9
 GO:0010467,FOXP2
 GO:0010467,MRPS12
 GO:0010467,NSUN5
 GO:0010467,CTNNBL1
 GO:0010467,CDK8
 GO:0010467,ELP3
+GO:0010467,CCNH
 GO:0010467,ZC3H10
 GO:0010467,EPC2
 GO:0010467,KAT7
+GO:0010467,DNAJC1
 GO:0010467,RIOK2
 GO:0010467,MRPL15
+GO:0010467,FGF5
+GO:0010467,BMPR1B
 GO:0010467,NAA30
 GO:0010467,EIF4B
 GO:0010467,MED29
+GO:0010467,PRKACB
 GO:0010467,PIGK
 GO:0010467,HAX1
 GO:0010467,MEIS1
+GO:0010467,RBMS3
 GO:0010467,ZMAT2
 GO:0010467,ABT1
 GO:0010467,CDKN2A
 GO:0010467,ZEB1
 GO:0010467,TAF5
 GO:0010467,CHEK1
+GO:0010467,ARID5B
 GO:0010467,ZC3H15
 GO:0010467,ANK3
 GO:0010467,CWF19L2
+GO:0010467,MBNL1
 GO:0010467,HS2ST1
 GO:0010467,TSEN2
 GO:0010467,SFR1
 GO:0010467,UTP14A
 GO:0010467,CNOT11
+GO:0010467,SNF8
+GO:0010467,RUNX1
 GO:0010467,DPY30
 GO:0010467,GNL3
 GO:0010467,PBRM1
+GO:0010467,PITX2
 GO:0010467,NOL6
 GO:0010467,BAG5
 GO:0010467,LEO1
 GO:0010467,E4F1
+GO:0010467,BMI1
+GO:0010467,ZFPM2
 GO:0010467,RNF139
+GO:0010467,BPTF
+GO:0010467,PTEN
+GO:0010467,JMJD1C
 GO:0010467,AFF1
 GO:0010467,PAF1
 GO:0010467,PHF8
 GO:0010467,PTGS2
+GO:0010467,CHD2
 GO:0010467,EED
+GO:0010467,NR2F1
+GO:0010467,ERBB4
+GO:0010467,CSRNP3
 GO:0010467,EIF3K
+GO:0010467,ALX1
 GO:0010467,MRPS16
 GO:0010467,RBM33
 GO:0010467,HOXA9
+GO:0010467,MLLT10
 GO:0010467,TCEA1
+GO:0010467,LIN28B
 GO:0010467,SUPT5H
 GO:0010467,MEF2C
 GO:0010467,DDI2
+GO:0010467,PTPRC
 GO:0010467,TAF13
 GO:0010467,CEP290
 GO:0010467,KAT6A
 GO:0010467,MECOM
 GO:0010467,CHERP
+GO:0010467,RBM20
+GO:0010467,BMPR2
 GO:0010467,DNAJC19
+GO:0010467,ZFHX4
 GO:0010467,MT-TL1
 GO:0010467,MT-TF
 GO:0010467,MT-TT
+GO:0010467,DENND1B
 GO:0010467,MCTS1
 GO:0010467,MZF1
 GO:0010467,SNORD13
@@ -116,6 +174,7 @@ GO:0006412,MRPS12
 GO:0006412,NSUN5
 GO:0006412,ZC3H15
 GO:0006412,ELP3
+GO:0006412,DNAJC1
 GO:0006412,MRPL15
 GO:0006412,CNOT11
 GO:0006412,RNF139
@@ -129,6 +188,7 @@ GO:0006412,MCTS1
 GO:0006412,EEF1G
 GO:0006412,EIF3D
 GO:0005739,DLAT
+GO:0005739,RPIA
 GO:0005739,PDSS2
 GO:0005739,NDUFAB1
 GO:0005739,NOL6
@@ -136,6 +196,8 @@ GO:0005739,BAG5
 GO:0005739,NDUFS5
 GO:0005739,NUDT9
 GO:0005739,ETFDH
+GO:0005739,METAP1D
+GO:0005739,ERBB4
 GO:0005739,MRPS16
 GO:0005739,NBR1
 GO:0005739,TOMM7
@@ -150,6 +212,8 @@ GO:0005739,USP48
 GO:0005739,PDPR
 GO:0005739,NDFIP2
 GO:0005739,SARS2
+GO:0005739,PITRM1
+GO:0005739,PPP3CC
 GO:0005739,MRPS12
 GO:0005739,COX4I1
 GO:0005739,DCAF8
@@ -159,8 +223,10 @@ GO:0005739,HAX1
 GO:0005739,TMEM177
 GO:0005739,MPC1
 GO:0005739,CDKN2A
+GO:0007005,HGF
 GO:0007005,CDKN2A
 GO:0007005,NDUFS5
+GO:0007005,ERBB4
 GO:0007005,TOMM7
 GO:0007005,MT-ND6
 GO:0007005,MT-ND1
diff --git a/results/permutation_analysis/setbp1_targets_prioritized.csv b/results/permutation_analysis/setbp1_targets_prioritized.csv
index 9de2d0b..5375a7f 100644
--- a/results/permutation_analysis/setbp1_targets_prioritized.csv
+++ b/results/permutation_analysis/setbp1_targets_prioritized.csv
@@ -18,14 +18,23 @@ ZZEF1,GTEx_Coexpr
 CHERP,GTEx_Coexpr
 NBR1,GTEx_Coexpr
 BRCA1,GO:0006325
+ZMYND11,GO:0006325
+INO80D,GO:0006325
 KMT2A,GO:0006325
+HDAC9,GO:0006325
 SET,GO:0006325
+EPC1,GO:0006325
+BAZ2B,GO:0006325
 EPC2,GO:0006325
 KAT7,GO:0006325
 CHEK1,GO:0006325
 DPY30,GO:0006325
 PBRM1,GO:0006325
+BMI1,GO:0006325
+BPTF,GO:0006325
+JMJD1C,GO:0006325
 PHF8,GO:0006325
+CHD2,GO:0006325
 EED,GO:0006325
 ZZEF1,GO:0006325
 SUPT5H,GO:0006325
@@ -38,84 +47,133 @@ KAT7,GO:0003682
 MEIS1,GO:0003682
 ZEB1,GO:0003682
 PBRM1,GO:0003682
+BMI1,GO:0003682
+JMJD1C,GO:0003682
 PHF8,GO:0003682
+CHD2,GO:0003682
 SUPT5H,GO:0003682
 EED,GO:0003682
+MLLT10,GO:0003682
 KAT6A,GO:0003682
 PAF1,GO:0003682
 EPHA7,GO:0007416
+PTPN13,GO:0007416
+PTEN,GO:0007416
+ERBB4,GO:0007416
 MEF2C,GO:0007416
 RAP2A,GO:0007416
 SARS2,GO:0010467
 RPS16,GO:0010467
+ZMYND11,GO:0010467
 ZNF862,GO:0010467
+TRDMT1,GO:0010467
+ACTA2,GO:0010467
+PITRM1,GO:0010467
+HGF,GO:0010467
+CDKN1B,GO:0010467
+BMP5,GO:0010467
+PDE4D,GO:0010467
+INO80D,GO:0010467
 NDUFAB1,GO:0010467
+WDR75,GO:0010467
+NFE2L2,GO:0010467
 ZNHIT6,GO:0010467
 KMT2A,GO:0010467
 SET,GO:0010467
+EPC1,GO:0010467
+BAZ2B,GO:0010467
 NCOA5,GO:0010467
 CDKN1A,GO:0010467
+HDAC9,GO:0010467
 FOXP2,GO:0010467
 MRPS12,GO:0010467
 NSUN5,GO:0010467
 CTNNBL1,GO:0010467
 CDK8,GO:0010467
 ELP3,GO:0010467
+CCNH,GO:0010467
 ZC3H10,GO:0010467
 EPC2,GO:0010467
 KAT7,GO:0010467
+DNAJC1,GO:0010467
 RIOK2,GO:0010467
 MRPL15,GO:0010467
+FGF5,GO:0010467
+BMPR1B,GO:0010467
 NAA30,GO:0010467
 EIF4B,GO:0010467
 MED29,GO:0010467
+PRKACB,GO:0010467
 PIGK,GO:0010467
 HAX1,GO:0010467
 MEIS1,GO:0010467
+RBMS3,GO:0010467
 ZMAT2,GO:0010467
 ABT1,GO:0010467
 CDKN2A,GO:0010467
 ZEB1,GO:0010467
 TAF5,GO:0010467
 CHEK1,GO:0010467
+ARID5B,GO:0010467
 ZC3H15,GO:0010467
 ANK3,GO:0010467
 CWF19L2,GO:0010467
+MBNL1,GO:0010467
 HS2ST1,GO:0010467
 TSEN2,GO:0010467
 SFR1,GO:0010467
 UTP14A,GO:0010467
 CNOT11,GO:0010467
+SNF8,GO:0010467
+RUNX1,GO:0010467
 DPY30,GO:0010467
 GNL3,GO:0010467
 PBRM1,GO:0010467
+PITX2,GO:0010467
 NOL6,GO:0010467
 BAG5,GO:0010467
 LEO1,GO:0010467
 E4F1,GO:0010467
+BMI1,GO:0010467
+ZFPM2,GO:0010467
 RNF139,GO:0010467
+BPTF,GO:0010467
+PTEN,GO:0010467
+JMJD1C,GO:0010467
 AFF1,GO:0010467
 PAF1,GO:0010467
 PHF8,GO:0010467
 PTGS2,GO:0010467
+CHD2,GO:0010467
 EED,GO:0010467
+NR2F1,GO:0010467
+ERBB4,GO:0010467
+CSRNP3,GO:0010467
 EIF3K,GO:0010467
+ALX1,GO:0010467
 MRPS16,GO:0010467
 RBM33,GO:0010467
 HOXA9,GO:0010467
+MLLT10,GO:0010467
 TCEA1,GO:0010467
+LIN28B,GO:0010467
 SUPT5H,GO:0010467
 MEF2C,GO:0010467
 DDI2,GO:0010467
+PTPRC,GO:0010467
 TAF13,GO:0010467
 CEP290,GO:0010467
 KAT6A,GO:0010467
 MECOM,GO:0010467
 CHERP,GO:0010467
+RBM20,GO:0010467
+BMPR2,GO:0010467
 DNAJC19,GO:0010467
+ZFHX4,GO:0010467
 MT-TL1,GO:0010467
 MT-TF,GO:0010467
 MT-TT,GO:0010467
+DENND1B,GO:0010467
 MCTS1,GO:0010467
 MZF1,GO:0010467
 SNORD13,GO:0010467
@@ -134,6 +192,7 @@ MRPS12,GO:0006412
 NSUN5,GO:0006412
 ZC3H15,GO:0006412
 ELP3,GO:0006412
+DNAJC1,GO:0006412
 MRPL15,GO:0006412
 CNOT11,GO:0006412
 RNF139,GO:0006412
@@ -147,6 +206,7 @@ MCTS1,GO:0006412
 EEF1G,GO:0006412
 EIF3D,GO:0006412
 DLAT,GO:0005739
+RPIA,GO:0005739
 PDSS2,GO:0005739
 NDUFAB1,GO:0005739
 NOL6,GO:0005739
@@ -154,6 +214,8 @@ BAG5,GO:0005739
 NDUFS5,GO:0005739
 NUDT9,GO:0005739
 ETFDH,GO:0005739
+METAP1D,GO:0005739
+ERBB4,GO:0005739
 MRPS16,GO:0005739
 NBR1,GO:0005739
 TOMM7,GO:0005739
@@ -168,6 +230,8 @@ USP48,GO:0005739
 PDPR,GO:0005739
 NDFIP2,GO:0005739
 SARS2,GO:0005739
+PITRM1,GO:0005739
+PPP3CC,GO:0005739
 MRPS12,GO:0005739
 COX4I1,GO:0005739
 DCAF8,GO:0005739
@@ -177,8 +241,10 @@ HAX1,GO:0005739
 TMEM177,GO:0005739
 MPC1,GO:0005739
 CDKN2A,GO:0005739
+HGF,GO:0007005
 CDKN2A,GO:0007005
 NDUFS5,GO:0007005
+ERBB4,GO:0007005
 TOMM7,GO:0007005
 MT-ND6,GO:0007005
 MT-ND1,GO:0007005
diff --git a/src/permutation_analysis/04_prioritize_targets.R b/src/permutation_analysis/04_prioritize_targets.R
index 6a3f3dd..6b87e3d 100644
--- a/src/permutation_analysis/04_prioritize_targets.R
+++ b/src/permutation_analysis/04_prioritize_targets.R
@@ -29,7 +29,7 @@ outdir <- args$outdir
 # create output dir if needed
 if (!dir.exists(outdir)) dir.create(outdir, recursive = TRUE)
 # SETBP1 targets
-setbp1_targets_table <- read_csv(paste0(indir, "260303_setbp1_targets.csv"))
+setbp1_targets_table <- read_csv(paste0(indir, "260403_setbp1_targets.csv"))
 setbp1_targets <- unique(setbp1_targets_table$Target)
 gtex_coexpr <- read_csv(paste0(outdir, "gtex_target_coexpression.csv"))
 brainspan_coexpr <- read_csv(
@@ -99,7 +99,10 @@ prioritized_targets <- top_gtex_coexpr %>%
 
 write_csv(prioritized_targets, paste0(outdir, "setbp1_targets_prioritized.csv"))
 cat("\nSaved final prioritized targets to: setbp1_targets_prioritized.csv\n\n")
-cat("\nNumber of top prioritized targets: ", length(unique(prioritized_targets$Target_Gene)))
+cat(
+  "\nNumber of top prioritized targets: ",
+  length(unique(prioritized_targets$Target_Gene))
+)
 cat("\nFrequency of targets by prioritization method:\n")
 
 print(sort(table(prioritized_targets$Target_Gene)))

From dafdedcc66acbb4fe6ad5792fe084cc0906f2787 Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Mon, 6 Apr 2026 14:01:43 -0500
Subject: [PATCH 06/16] updated pathways

---
 .../setbp1_target_pathways.csv                | 360 +++++++++++++++---
 .../setbp1_targets_prioritized.csv            | 360 +++++++++++++++---
 .../04_prioritize_targets.R                   |  24 +-
 3 files changed, 649 insertions(+), 95 deletions(-)

diff --git a/results/permutation_analysis/setbp1_target_pathways.csv b/results/permutation_analysis/setbp1_target_pathways.csv
index 3b963be..7f657b6 100644
--- a/results/permutation_analysis/setbp1_target_pathways.csv
+++ b/results/permutation_analysis/setbp1_target_pathways.csv
@@ -1,49 +1,4 @@
 Method,Target_Gene
-GO:0006325,BRCA1
-GO:0006325,ZMYND11
-GO:0006325,INO80D
-GO:0006325,KMT2A
-GO:0006325,HDAC9
-GO:0006325,SET
-GO:0006325,EPC1
-GO:0006325,BAZ2B
-GO:0006325,EPC2
-GO:0006325,KAT7
-GO:0006325,CHEK1
-GO:0006325,DPY30
-GO:0006325,PBRM1
-GO:0006325,BMI1
-GO:0006325,BPTF
-GO:0006325,JMJD1C
-GO:0006325,PHF8
-GO:0006325,CHD2
-GO:0006325,EED
-GO:0006325,ZZEF1
-GO:0006325,SUPT5H
-GO:0006325,KAT6A
-GO:0006325,MECOM
-GO:0003682,KMT2A
-GO:0003682,SET
-GO:0003682,NCOA5
-GO:0003682,KAT7
-GO:0003682,MEIS1
-GO:0003682,ZEB1
-GO:0003682,PBRM1
-GO:0003682,BMI1
-GO:0003682,JMJD1C
-GO:0003682,PHF8
-GO:0003682,CHD2
-GO:0003682,SUPT5H
-GO:0003682,EED
-GO:0003682,MLLT10
-GO:0003682,KAT6A
-GO:0003682,PAF1
-GO:0007416,EPHA7
-GO:0007416,PTPN13
-GO:0007416,PTEN
-GO:0007416,ERBB4
-GO:0007416,MEF2C
-GO:0007416,RAP2A
 GO:0010467,SARS2
 GO:0010467,RPS16
 GO:0010467,ZMYND11
@@ -167,6 +122,94 @@ GO:0010467,HM13
 GO:0010467,PPP5C
 GO:0010467,NDFIP2
 GO:0010467,BRCA1
+GO:0051254,MED29
+GO:0051254,ABT1
+GO:0051254,CDKN2A
+GO:0051254,ZEB1
+GO:0051254,TAF5
+GO:0051254,ARID5B
+GO:0051254,SFR1
+GO:0051254,CNOT11
+GO:0051254,RUNX1
+GO:0051254,GNL3
+GO:0051254,PITX2
+GO:0051254,LEO1
+GO:0051254,E4F1
+GO:0051254,ZFPM2
+GO:0051254,BPTF
+GO:0051254,PHF8
+GO:0051254,NR2F1
+GO:0051254,ERBB4
+GO:0051254,CSRNP3
+GO:0051254,ALX1
+GO:0051254,TCEA1
+GO:0051254,LIN28B
+GO:0051254,SUPT5H
+GO:0051254,TAF13
+GO:0051254,CEP290
+GO:0051254,BMPR2
+GO:0051254,HOXA10
+GO:0051254,HOXA9
+GO:0051254,PAF1
+GO:0051254,MLLT10
+GO:0051254,MEF2C
+GO:0051254,KAT6A
+GO:0051254,MECOM
+GO:0051254,MZF1
+GO:0051254,BRCA1
+GO:0051254,BMP5
+GO:0051254,HGF
+GO:0051254,INO80D
+GO:0051254,WDR75
+GO:0051254,NFE2L2
+GO:0051254,KMT2A
+GO:0051254,EPC1
+GO:0051254,CDK8
+GO:0051254,EPC2
+GO:0051254,KAT7
+GO:0051254,BMPR1B
+GO:0051254,RIOK2
+GO:0051254,HAX1
+GO:0051254,MEIS1
+GO:0006325,BRCA1
+GO:0006325,ZMYND11
+GO:0006325,INO80D
+GO:0006325,KMT2A
+GO:0006325,HDAC9
+GO:0006325,SET
+GO:0006325,EPC1
+GO:0006325,BAZ2B
+GO:0006325,EPC2
+GO:0006325,KAT7
+GO:0006325,CHEK1
+GO:0006325,DPY30
+GO:0006325,PBRM1
+GO:0006325,BMI1
+GO:0006325,BPTF
+GO:0006325,JMJD1C
+GO:0006325,PHF8
+GO:0006325,CHD2
+GO:0006325,EED
+GO:0006325,ZZEF1
+GO:0006325,SUPT5H
+GO:0006325,KAT6A
+GO:0006325,MECOM
+GO:0003682,KMT2A
+GO:0003682,SET
+GO:0003682,NCOA5
+GO:0003682,KAT7
+GO:0003682,MEIS1
+GO:0003682,ZEB1
+GO:0003682,PBRM1
+GO:0003682,BMI1
+GO:0003682,JMJD1C
+GO:0003682,PHF8
+GO:0003682,CHD2
+GO:0003682,SUPT5H
+GO:0003682,EED
+GO:0003682,MLLT10
+GO:0003682,KAT6A
+GO:0003682,PAF1
 GO:0006412,SARS2
 GO:0006412,RPS16
 GO:0006412,EIF4B
@@ -187,6 +230,233 @@ GO:0006412,MT-TT
 GO:0006412,MCTS1
 GO:0006412,EEF1G
 GO:0006412,EIF3D
+GO:0051896,HAX1
+GO:0051896,PDGFC
+GO:0051896,PTPN13
+GO:0051896,PTEN
+GO:0051896,ERBB4
+GO:0051896,HGF
+GO:0035556,PPP3CC
+GO:0035556,CDKN1A
+GO:0035556,RAP2A
+GO:0035556,TTI2
+GO:0035556,CLEC16A
+GO:0035556,EPHA7
+GO:0035556,KAT7
+GO:0035556,FGF5
+GO:0035556,ANP32A
+GO:0035556,PRKACB
+GO:0035556,HAX1
+GO:0035556,PDGFC
+GO:0035556,GDI2
+GO:0035556,CDKN2A
+GO:0035556,CHEK1
+GO:0035556,PKN2
+GO:0035556,UBR1
+GO:0035556,PTPN13
+GO:0035556,IFT122
+GO:0035556,MYO9A
+GO:0035556,FBXO8
+GO:0035556,BAG5
+GO:0035556,PTEN
+GO:0035556,RALGAPA1
+GO:0035556,NR2F1
+GO:0035556,ERBB4
+GO:0035556,ASB7
+GO:0035556,NBR1
+GO:0035556,PTGS2
+GO:0035556,BMPR2
+GO:0035556,SEMA3A
+GO:0035556,MEF2C
+GO:0035556,PTPRC
+GO:0035556,STK17B
+GO:0035556,KAT6A
+GO:0035556,MECOM
+GO:0035556,CHERP
+GO:0035556,SYDE2
+GO:0035556,NDFIP2
+GO:0035556,PPP5C
+GO:0035556,MAP4K1
+GO:0035556,BRCA1
+GO:0035556,FKTN
+GO:0035556,ACTA2
+GO:0035556,ZMYND11
+GO:0035556,TPD52L1
+GO:0035556,BMP5
+GO:0035556,ARRDC3
+GO:0035556,PDE4D
+GO:0035556,HGF
+GO:0035556,NFE2L2
+GO:0010564,BRCA1
+GO:0010564,CDKN1B
+GO:0010564,CDKN2C
+GO:0010564,CDKN1A
+GO:0010564,TTI2
+GO:0010564,CCNH
+GO:0010564,CDKN2B
+GO:0010564,CDKN2A
+GO:0010564,CHEK1
+GO:0010564,RIOK2
+GO:0010564,PBRM1
+GO:0010564,PKN2
+GO:0010564,E4F1
+GO:0010564,PTEN
+GO:0010564,ANAPC7
+GO:0010564,PAF1
+GO:0044772,BRCA1
+GO:0044772,CDKN1B
+GO:0044772,TPD52L1
+GO:0044772,CDKN2C
+GO:0044772,CDKN1A
+GO:0044772,CCNH
+GO:0044772,CDKN2B
+GO:0044772,CDKN2A
+GO:0044772,CHEK1
+GO:0044772,CACUL1
+GO:0044772,RIOK2
+GO:0044772,PBRM1
+GO:0044772,PTEN
+GO:0044772,PHF8
+GO:0044772,ANAPC7
+GO:0007179,CDKN2B
+GO:0007179,ZEB1
+GO:0007179,RNF111
+GO:0007416,EPHA7
+GO:0007416,PTPN13
+GO:0007416,PTEN
+GO:0007416,ERBB4
+GO:0007416,MEF2C
+GO:0007416,RAP2A
+GO:0043043,NFE2L2
+GO:0043043,AASDH
+GO:0009059,NDFIP2
+GO:0009059,PPP5C
+GO:0009059,BRCA1
+GO:0009059,SARS2
+GO:0009059,RPS16
+GO:0009059,ZNF862
+GO:0009059,FKTN
+GO:0009059,ZMYND11
+GO:0009059,TRDMT1
+GO:0009059,ACTA2
+GO:0009059,PITRM1
+GO:0009059,HGF
+GO:0009059,CDKN1B
+GO:0009059,BMP5
+GO:0009059,PDE4D
+GO:0009059,ST8SIA4
+GO:0009059,INO80D
+GO:0009059,WDR75
+GO:0009059,NFE2L2
+GO:0009059,NDUFAB1
+GO:0009059,ZNHIT6
+GO:0009059,KMT2A
+GO:0009059,SET
+GO:0009059,EPC1
+GO:0009059,BAZ2B
+GO:0009059,NCOA5
+GO:0009059,CDKN1A
+GO:0009059,HDAC9
+GO:0009059,FOXP2
+GO:0009059,MRPS12
+GO:0009059,NSUN5
+GO:0009059,CTNNBL1
+GO:0009059,CDK8
+GO:0009059,ELP3
+GO:0009059,CCNH
+GO:0009059,ZC3H10
+GO:0009059,EPC2
+GO:0009059,KAT7
+GO:0009059,DNAJC1
+GO:0009059,MRPL15
+GO:0009059,RIOK2
+GO:0009059,FGF5
+GO:0009059,BMPR1B
+GO:0009059,TMTC3
+GO:0009059,NAA30
+GO:0009059,EIF4B
+GO:0009059,PRKACB
+GO:0009059,PIGK
+GO:0009059,MED29
+GO:0009059,HAX1
+GO:0009059,MEIS1
+GO:0009059,RBMS3
+GO:0009059,ZMAT2
+GO:0009059,ABT1
+GO:0009059,GOLGA7
+GO:0009059,CDKN2A
+GO:0009059,ZEB1
+GO:0009059,TAF5
+GO:0009059,CHEK1
+GO:0009059,ARID5B
+GO:0009059,ANK3
+GO:0009059,ZC3H15
+GO:0009059,CWF19L2
+GO:0009059,MBNL1
+GO:0009059,HS2ST1
+GO:0009059,TSEN2
+GO:0009059,SFR1
+GO:0009059,UTP14A
+GO:0009059,CNOT11
+GO:0009059,SNF8
+GO:0009059,RUNX1
+GO:0009059,DPY30
+GO:0009059,GNL3
+GO:0009059,PBRM1
+GO:0009059,PITX2
+GO:0009059,NOL6
+GO:0009059,BAG5
+GO:0009059,LEO1
+GO:0009059,E4F1
+GO:0009059,MGAT2
+GO:0009059,BMI1
+GO:0009059,ZFPM2
+GO:0009059,RNF139
+GO:0009059,BPTF
+GO:0009059,PTEN
+GO:0009059,JMJD1C
+GO:0009059,PAF1
+GO:0009059,AFF1
+GO:0009059,PTGS2
+GO:0009059,PHF8
+GO:0009059,CHD2
+GO:0009059,EED
+GO:0009059,NR2F1
+GO:0009059,ERBB4
+GO:0009059,CSRNP3
+GO:0009059,EIF3K
+GO:0009059,ALX1
+GO:0009059,MRPS16
+GO:0009059,RBM33
+GO:0009059,HOXA9
+GO:0009059,MLLT10
+GO:0009059,TCEA1
+GO:0009059,LIN28B
+GO:0009059,SUPT5H
+GO:0009059,MEF2C
+GO:0009059,PTPRC
+GO:0009059,DDI2
+GO:0009059,TAF13
+GO:0009059,CEP290
+GO:0009059,KAT6A
+GO:0009059,MECOM
+GO:0009059,CHERP
+GO:0009059,RBM20
+GO:0009059,BMPR2
+GO:0009059,DNAJC19
+GO:0009059,MT-TL1
+GO:0009059,ZFHX4
+GO:0009059,MT-TF
+GO:0009059,MT-TT
+GO:0009059,DENND1B
+GO:0009059,MCTS1
+GO:0009059,MZF1
+GO:0009059,SNORD13
+GO:0009059,NSUN6
+GO:0009059,HOXA10
+GO:0009059,EEF1G
+GO:0009059,EIF3D
+GO:0009059,HM13
 GO:0005739,DLAT
 GO:0005739,RPIA
 GO:0005739,PDSS2
diff --git a/results/permutation_analysis/setbp1_targets_prioritized.csv b/results/permutation_analysis/setbp1_targets_prioritized.csv
index 5375a7f..83a94f7 100644
--- a/results/permutation_analysis/setbp1_targets_prioritized.csv
+++ b/results/permutation_analysis/setbp1_targets_prioritized.csv
@@ -17,51 +17,6 @@ CWF19L2,GTEx_Coexpr
 ZZEF1,GTEx_Coexpr
 CHERP,GTEx_Coexpr
 NBR1,GTEx_Coexpr
-BRCA1,GO:0006325
-ZMYND11,GO:0006325
-INO80D,GO:0006325
-KMT2A,GO:0006325
-HDAC9,GO:0006325
-SET,GO:0006325
-EPC1,GO:0006325
-BAZ2B,GO:0006325
-EPC2,GO:0006325
-KAT7,GO:0006325
-CHEK1,GO:0006325
-DPY30,GO:0006325
-PBRM1,GO:0006325
-BMI1,GO:0006325
-BPTF,GO:0006325
-JMJD1C,GO:0006325
-PHF8,GO:0006325
-CHD2,GO:0006325
-EED,GO:0006325
-ZZEF1,GO:0006325
-SUPT5H,GO:0006325
-KAT6A,GO:0006325
-MECOM,GO:0006325
-KMT2A,GO:0003682
-SET,GO:0003682
-NCOA5,GO:0003682
-KAT7,GO:0003682
-MEIS1,GO:0003682
-ZEB1,GO:0003682
-PBRM1,GO:0003682
-BMI1,GO:0003682
-JMJD1C,GO:0003682
-PHF8,GO:0003682
-CHD2,GO:0003682
-SUPT5H,GO:0003682
-EED,GO:0003682
-MLLT10,GO:0003682
-KAT6A,GO:0003682
-PAF1,GO:0003682
-EPHA7,GO:0007416
-PTPN13,GO:0007416
-PTEN,GO:0007416
-ERBB4,GO:0007416
-MEF2C,GO:0007416
-RAP2A,GO:0007416
 SARS2,GO:0010467
 RPS16,GO:0010467
 ZMYND11,GO:0010467
@@ -185,6 +140,94 @@ HM13,GO:0010467
 PPP5C,GO:0010467
 NDFIP2,GO:0010467
 BRCA1,GO:0010467
+MED29,GO:0051254
+ABT1,GO:0051254
+CDKN2A,GO:0051254
+ZEB1,GO:0051254
+TAF5,GO:0051254
+ARID5B,GO:0051254
+SFR1,GO:0051254
+CNOT11,GO:0051254
+RUNX1,GO:0051254
+GNL3,GO:0051254
+PITX2,GO:0051254
+LEO1,GO:0051254
+E4F1,GO:0051254
+ZFPM2,GO:0051254
+BPTF,GO:0051254
+PHF8,GO:0051254
+NR2F1,GO:0051254
+ERBB4,GO:0051254
+CSRNP3,GO:0051254
+ALX1,GO:0051254
+TCEA1,GO:0051254
+LIN28B,GO:0051254
+SUPT5H,GO:0051254
+TAF13,GO:0051254
+CEP290,GO:0051254
+BMPR2,GO:0051254
+HOXA10,GO:0051254
+HOXA9,GO:0051254
+PAF1,GO:0051254
+MLLT10,GO:0051254
+MEF2C,GO:0051254
+KAT6A,GO:0051254
+MECOM,GO:0051254
+MZF1,GO:0051254
+BRCA1,GO:0051254
+BMP5,GO:0051254
+HGF,GO:0051254
+INO80D,GO:0051254
+WDR75,GO:0051254
+NFE2L2,GO:0051254
+KMT2A,GO:0051254
+EPC1,GO:0051254
+CDK8,GO:0051254
+EPC2,GO:0051254
+KAT7,GO:0051254
+BMPR1B,GO:0051254
+RIOK2,GO:0051254
+HAX1,GO:0051254
+MEIS1,GO:0051254
+BRCA1,GO:0006325
+ZMYND11,GO:0006325
+INO80D,GO:0006325
+KMT2A,GO:0006325
+HDAC9,GO:0006325
+SET,GO:0006325
+EPC1,GO:0006325
+BAZ2B,GO:0006325
+EPC2,GO:0006325
+KAT7,GO:0006325
+CHEK1,GO:0006325
+DPY30,GO:0006325
+PBRM1,GO:0006325
+BMI1,GO:0006325
+BPTF,GO:0006325
+JMJD1C,GO:0006325
+PHF8,GO:0006325
+CHD2,GO:0006325
+EED,GO:0006325
+ZZEF1,GO:0006325
+SUPT5H,GO:0006325
+KAT6A,GO:0006325
+MECOM,GO:0006325
+KMT2A,GO:0003682
+SET,GO:0003682
+NCOA5,GO:0003682
+KAT7,GO:0003682
+MEIS1,GO:0003682
+ZEB1,GO:0003682
+PBRM1,GO:0003682
+BMI1,GO:0003682
+JMJD1C,GO:0003682
+PHF8,GO:0003682
+CHD2,GO:0003682
+SUPT5H,GO:0003682
+EED,GO:0003682
+MLLT10,GO:0003682
+KAT6A,GO:0003682
+PAF1,GO:0003682
 SARS2,GO:0006412
 RPS16,GO:0006412
 EIF4B,GO:0006412
@@ -205,6 +248,233 @@ MT-TT,GO:0006412
 MCTS1,GO:0006412
 EEF1G,GO:0006412
 EIF3D,GO:0006412
+HAX1,GO:0051896
+PDGFC,GO:0051896
+PTPN13,GO:0051896
+PTEN,GO:0051896
+ERBB4,GO:0051896
+HGF,GO:0051896
+PPP3CC,GO:0035556
+CDKN1A,GO:0035556
+RAP2A,GO:0035556
+TTI2,GO:0035556
+CLEC16A,GO:0035556
+EPHA7,GO:0035556
+KAT7,GO:0035556
+FGF5,GO:0035556
+ANP32A,GO:0035556
+PRKACB,GO:0035556
+HAX1,GO:0035556
+PDGFC,GO:0035556
+GDI2,GO:0035556
+CDKN2A,GO:0035556
+CHEK1,GO:0035556
+PKN2,GO:0035556
+UBR1,GO:0035556
+PTPN13,GO:0035556
+IFT122,GO:0035556
+MYO9A,GO:0035556
+FBXO8,GO:0035556
+BAG5,GO:0035556
+PTEN,GO:0035556
+RALGAPA1,GO:0035556
+NR2F1,GO:0035556
+ERBB4,GO:0035556
+ASB7,GO:0035556
+NBR1,GO:0035556
+PTGS2,GO:0035556
+BMPR2,GO:0035556
+SEMA3A,GO:0035556
+MEF2C,GO:0035556
+PTPRC,GO:0035556
+STK17B,GO:0035556
+KAT6A,GO:0035556
+MECOM,GO:0035556
+CHERP,GO:0035556
+SYDE2,GO:0035556
+NDFIP2,GO:0035556
+PPP5C,GO:0035556
+MAP4K1,GO:0035556
+BRCA1,GO:0035556
+FKTN,GO:0035556
+ACTA2,GO:0035556
+ZMYND11,GO:0035556
+TPD52L1,GO:0035556
+BMP5,GO:0035556
+ARRDC3,GO:0035556
+PDE4D,GO:0035556
+HGF,GO:0035556
+NFE2L2,GO:0035556
+BRCA1,GO:0010564
+CDKN1B,GO:0010564
+CDKN2C,GO:0010564
+CDKN1A,GO:0010564
+TTI2,GO:0010564
+CCNH,GO:0010564
+CDKN2B,GO:0010564
+CDKN2A,GO:0010564
+CHEK1,GO:0010564
+RIOK2,GO:0010564
+PBRM1,GO:0010564
+PKN2,GO:0010564
+E4F1,GO:0010564
+PTEN,GO:0010564
+ANAPC7,GO:0010564
+PAF1,GO:0010564
+BRCA1,GO:0044772
+CDKN1B,GO:0044772
+TPD52L1,GO:0044772
+CDKN2C,GO:0044772
+CDKN1A,GO:0044772
+CCNH,GO:0044772
+CDKN2B,GO:0044772
+CDKN2A,GO:0044772
+CHEK1,GO:0044772
+CACUL1,GO:0044772
+RIOK2,GO:0044772
+PBRM1,GO:0044772
+PTEN,GO:0044772
+PHF8,GO:0044772
+ANAPC7,GO:0044772
+CDKN2B,GO:0007179
+ZEB1,GO:0007179
+RNF111,GO:0007179
+EPHA7,GO:0007416
+PTPN13,GO:0007416
+PTEN,GO:0007416
+ERBB4,GO:0007416
+MEF2C,GO:0007416
+RAP2A,GO:0007416
+NFE2L2,GO:0043043
+AASDH,GO:0043043
+NDFIP2,GO:0009059
+PPP5C,GO:0009059
+BRCA1,GO:0009059
+SARS2,GO:0009059
+RPS16,GO:0009059
+ZNF862,GO:0009059
+FKTN,GO:0009059
+ZMYND11,GO:0009059
+TRDMT1,GO:0009059
+ACTA2,GO:0009059
+PITRM1,GO:0009059
+HGF,GO:0009059
+CDKN1B,GO:0009059
+BMP5,GO:0009059
+PDE4D,GO:0009059
+ST8SIA4,GO:0009059
+INO80D,GO:0009059
+WDR75,GO:0009059
+NFE2L2,GO:0009059
+NDUFAB1,GO:0009059
+ZNHIT6,GO:0009059
+KMT2A,GO:0009059
+SET,GO:0009059
+EPC1,GO:0009059
+BAZ2B,GO:0009059
+NCOA5,GO:0009059
+CDKN1A,GO:0009059
+HDAC9,GO:0009059
+FOXP2,GO:0009059
+MRPS12,GO:0009059
+NSUN5,GO:0009059
+CTNNBL1,GO:0009059
+CDK8,GO:0009059
+ELP3,GO:0009059
+CCNH,GO:0009059
+ZC3H10,GO:0009059
+EPC2,GO:0009059
+KAT7,GO:0009059
+DNAJC1,GO:0009059
+MRPL15,GO:0009059
+RIOK2,GO:0009059
+FGF5,GO:0009059
+BMPR1B,GO:0009059
+TMTC3,GO:0009059
+NAA30,GO:0009059
+EIF4B,GO:0009059
+PRKACB,GO:0009059
+PIGK,GO:0009059
+MED29,GO:0009059
+HAX1,GO:0009059
+MEIS1,GO:0009059
+RBMS3,GO:0009059
+ZMAT2,GO:0009059
+ABT1,GO:0009059
+GOLGA7,GO:0009059
+CDKN2A,GO:0009059
+ZEB1,GO:0009059
+TAF5,GO:0009059
+CHEK1,GO:0009059
+ARID5B,GO:0009059
+ANK3,GO:0009059
+ZC3H15,GO:0009059
+CWF19L2,GO:0009059
+MBNL1,GO:0009059
+HS2ST1,GO:0009059
+TSEN2,GO:0009059
+SFR1,GO:0009059
+UTP14A,GO:0009059
+CNOT11,GO:0009059
+SNF8,GO:0009059
+RUNX1,GO:0009059
+DPY30,GO:0009059
+GNL3,GO:0009059
+PBRM1,GO:0009059
+PITX2,GO:0009059
+NOL6,GO:0009059
+BAG5,GO:0009059
+LEO1,GO:0009059
+E4F1,GO:0009059
+MGAT2,GO:0009059
+BMI1,GO:0009059
+ZFPM2,GO:0009059
+RNF139,GO:0009059
+BPTF,GO:0009059
+PTEN,GO:0009059
+JMJD1C,GO:0009059
+PAF1,GO:0009059
+AFF1,GO:0009059
+PTGS2,GO:0009059
+PHF8,GO:0009059
+CHD2,GO:0009059
+EED,GO:0009059
+NR2F1,GO:0009059
+ERBB4,GO:0009059
+CSRNP3,GO:0009059
+EIF3K,GO:0009059
+ALX1,GO:0009059
+MRPS16,GO:0009059
+RBM33,GO:0009059
+HOXA9,GO:0009059
+MLLT10,GO:0009059
+TCEA1,GO:0009059
+LIN28B,GO:0009059
+SUPT5H,GO:0009059
+MEF2C,GO:0009059
+PTPRC,GO:0009059
+DDI2,GO:0009059
+TAF13,GO:0009059
+CEP290,GO:0009059
+KAT6A,GO:0009059
+MECOM,GO:0009059
+CHERP,GO:0009059
+RBM20,GO:0009059
+BMPR2,GO:0009059
+DNAJC19,GO:0009059
+MT-TL1,GO:0009059
+ZFHX4,GO:0009059
+MT-TF,GO:0009059
+MT-TT,GO:0009059
+DENND1B,GO:0009059
+MCTS1,GO:0009059
+MZF1,GO:0009059
+SNORD13,GO:0009059
+NSUN6,GO:0009059
+HOXA10,GO:0009059
+EEF1G,GO:0009059
+EIF3D,GO:0009059
+HM13,GO:0009059
 DLAT,GO:0005739
 RPIA,GO:0005739
 PDSS2,GO:0005739
diff --git a/src/permutation_analysis/04_prioritize_targets.R b/src/permutation_analysis/04_prioritize_targets.R
index 6b87e3d..3445f32 100644
--- a/src/permutation_analysis/04_prioritize_targets.R
+++ b/src/permutation_analysis/04_prioritize_targets.R
@@ -45,14 +45,14 @@ top_gtex_coexpr <- gtex_coexpr %>%
   slice_max(abs(Spearman_Rho), prop = 0.10) %>%
   mutate(Method = "GTEx_Coexpr")
 cat("\nTop quartile significantly coexpressed targets across tissues/ages:\n")
-print(top_gtex_coexpr)
+print(head(top_gtex_coexpr))
 
 top_brainspan_coexpr <- brainspan_coexpr %>%
   filter(FDR < 0.05) %>%
   slice_max(abs(Spearman_Rho), prop = 0.10) %>%
   mutate(Method = "Brainspan_Coexpr")
 cat("\nTop quartile significantly coexpressed targets across tissues/ages:\n")
-print(top_brainspan_coexpr)
+print(head(top_brainspan_coexpr))
 
 write_csv(
   rbind(top_gtex_coexpr, top_brainspan_coexpr),
@@ -61,13 +61,27 @@ write_csv(
 
 ### gene functional pathway annotations ###
 pathway_map <- list(
+  # Transcriptional and epigenetic regulation
+  "Gene_expression" = "GO:0010467",
+  "Positive_regulation_RNA_metabolic_process" = "GO:0051254",
   "Chromatin_organization" = "GO:0006325",
   "Chromatin_binding" = "GO:0003682",
-  "Prostaglandin_receptor_activity" = "GO:0004955",
-  "Synapse_assembly" = "GO:0007416",
-  "Gene_expression" = "GO:0010467",
   "Translation" = "GO:0006412",
   "Translation_regulator_activity" = "GO:0045182",
+  # Cell proliferation and survival
+  "Negative regulation of protein phosphatase activity" = "GO:0010923",
+  "Regulation of protein kinase B signaling" = "GO:0051896",
+  "Intracellular signal transduction" = "GO:0035556",
+  "Regulation of cell cycle process" = "GO:0010564",
+  "Mitotic cell cycle phase transition" = "GO:0044772",
+  "Transforming growth factor beta receptor signaling pathway" = "GO:0007179",
+  # Neurodevelopment and circuitry
+  "Regulation of neural precursor cell proliferation" = "GO:2000177",
+  "Synapse_assembly" = "GO:0007416",
+  "Prostaglandin_receptor_activity" = "GO:0004955",  
+  # Metabolism and bioenergetics
+  "Peptide_biosynthetic_process" = "GO:0043043",
+  "Macromolecule_biosynthetic_process" =  "GO:0009059",
   "Mitochondrion" = "GO:0005739",
   "Mitochondrion_organization" = "GO:0007005"
 )

From 4995bbd5c232b3c25cecd7e7a6294bc02dc8f216 Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Tue, 7 Apr 2026 11:18:11 -0500
Subject: [PATCH 07/16] update with PHAROS annotations

---
 data/260403_setbp1_targets.csv | 725 +++++++++++++++++----------------
 1 file changed, 363 insertions(+), 362 deletions(-)

diff --git a/data/260403_setbp1_targets.csv b/data/260403_setbp1_targets.csv
index 7425f22..058b1fb 100644
--- a/data/260403_setbp1_targets.csv
+++ b/data/260403_setbp1_targets.csv
@@ -1,386 +1,387 @@
-Target,Aliases,Organism,Interactions,Regulation_Effect,Databases,Publications,Other_Resources,Additional_Notes,SETBP1_Associated_Annotations,Biologic_Annotations
+Target,Aliases,Organism,Interactions,Regulation_Effect,Databases,Publications,Other_Resources,Additional_Notes,SETBP1_Associated_Annotations,Biologic_Annotations,UniProt,Name,Target Development Level,IDG Family,Novelty
 342666,,Human,,,,"IM-23318
-25416956",,,Interaction Type: physical association; confidence value: 0.56,
-AASDH,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ABT1,,Human,"RNA coexpression shows inverse correlation between SETBP1 gene and ABP1; Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Downregulation (coexpression-inferred),GTRD; SigCom LINCS,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100; SigCom LINCS: Down Gene",,
-AC007731.1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-AC009403.2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-AC026954.6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-AC093323.3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ACTA2,ENSG00000107796,Human,SETBP1 binding in promoter and DEG,Repression/Downregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-AFF1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-AKT,,Human,"SETBP1 inhibits PP2A, incresing AKT phosphorylation; not a direct target of SETBP1",Increased phosphorylation,,https://doi.org/10.1093/hmg/ddaf003,,,Activation/Increased Phospho-AKT in GoF; Decreased in extreme LoF,
-ALX1,ENSG00000180318,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-ANAPC7,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ANK3,ENSG00000151150,Human,SETBP1 binding in promoter and DEG,Maintenance; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-ANP32A,,,Protein interaction,,,https://doi.org/10.1093/hmg/ddaf003,,,,
-APOPT1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ARID5B,ENSG00000150347,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-ARL5B,ENSG00000165997,Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); SETBP1 binding in promoter and DEG",Activation/Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; https://www.nature.com/articles/s41467-018-04462-8,,"GTRD Binding Parameter: -1000, +100","Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-ARRDC3,ENSG00000113369,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-ASB7,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ATP6V1G3,ENSG00000151418,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-ATP9B,ENSG00000166377,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-BAG5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-BAZ2B,ENSG00000123636,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-BET1L,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Downregulation (coexpression-inferred),GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; PMID: 27924024,,"GTRD Binding Parameter: -1000, +100; SigCom LINCS: Down Gene; Detection method: chromatin",,
-BMI1,ENSG00000168283,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-BMP5,ENSG00000112175,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-BMPR1B,ENSG00000138696,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-BMPR2,ENSG00000204217,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-BPTF,ENSG00000171634,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-BRCA1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-C12orf40,ENSG00000180116,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-C16orf70,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-C1orf123 (CZIB),,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-C4orf36,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-C4orf46,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CACNB2,ENSG00000165995,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-CACUL1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CASC1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CCDC174,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CCDC184,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CCDC50,ENSG00000152492,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-CCNH,ENSG00000134480,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-CDK8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CDKN1A,,Human,,Upregulated,,https://doi.org/10.1093/hmg/ddaf003,,,"""We observed that CDKN1A levels were reduced in response to PFT treatment confirming that CDKN1A is an output marker of p53 in NPC cells (Fig. 5D). We then evaluated the levels of CDKN1A in SGS, SHD and KO cells to determine if CDKN1A levels reflect SETBP1 dosage changes. We reasoned that if CDKN1A levels show reciprocal changes in SHD and SGS, this might suggest that β-Catenin, FOXO3A, and LMNA/C may be regulated via p53. We found no differences in CDKN1A levels in SHD cells but found a strong increase in CDKN1A levels in SGS cells and KO2 cells (Fig. 5E, Fig. S19A and B). This might suggest that increased levels of SETBP1 in SGS are having an effect on CDKN1A independent of p53 action. This could be occurring through the reported direct action of SET binding to CDKN1A [73].""",
-CDKN1B,ENSG00000111276,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-CDKN2A,ENSG00000147889,Human; Human,SETBP1 binding in promoter and DEG,Upregulation; Activation/Upregulation,CollecTRI,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-CDKN2B,ENSG00000147883,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-CDKN2C,ENSG00000123080,Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); SETBP1 binding in promoter and DEG",Activation/Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; https://www.nature.com/articles/s41467-018-04462-8,,"GTRD Binding Parameter: -1000, +100","Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-CENPBD1P1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CEP192,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CEP290,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CEP44,ENSG00000164118,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-CEPT1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CHD2,ENSG00000173575,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
+25416956",,,Interaction Type: physical association; confidence value: 0.56,,NA,NA,NA,NA,NA
+AASDH,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q4L235,Beta-alanine-activating enzyme,Tbio,Enzyme,0.17181708
+ABT1,,Human,"RNA coexpression shows inverse correlation between SETBP1 gene and ABP1; Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Downregulation (coexpression-inferred),GTRD; SigCom LINCS,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100; SigCom LINCS: Down Gene",,,Q9ULW3,Activator of basal transcription 1,Tbio,Other,0.05236553
+AC007731.1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+AC009403.2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+AC026954.6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+AC093323.3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+ACTA2,ENSG00000107796; ENSG00000107796,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Repression/Downregulation; Repression/Downregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P62736,"Actin, aortic smooth muscle",Tbio,Other,0.00199354
+AFF1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P51825,AF4/FMR2 family member 1,Tbio,Transcription Factor,9.4358e-4
+AKT,,Human,"SETBP1 inhibits PP2A, incresing AKT phosphorylation; not a direct target of SETBP1",Increased phosphorylation,,https://doi.org/10.1093/hmg/ddaf003,,,Activation/Increased Phospho-AKT in GoF; Decreased in extreme LoF,,NA,NA,NA,NA,NA
+ALX1,ENSG00000180318; ENSG00000180318,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q15699,ALX homeobox protein 1,Tbio,Transcription Factor,0.01880208
+ANAPC7,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9UJX3,Anaphase-promoting complex subunit 7,Tbio,Enzyme,0.17956785
+ANK3,ENSG00000151150; ENSG00000151150,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Maintenance; Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q12955,Ankyrin-3,Tbio,Other,0.00429246
+ANP32A,,,Protein interaction,,,https://doi.org/10.1093/hmg/ddaf003,,,,,P39687,Acidic leucine-rich nuclear phosphoprotein 32 family member A,Tbio,Other,0.00567095
+APOPT1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q96IL0,"Apoptogenic protein 1, mitochondrial",Tdark,Other,0.05090202
+ARID5B,ENSG00000150347; ENSG00000150347,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q14865,AT-rich interactive domain-containing protein 5B,Tbio,Transcription Factor,0.01201607
+ARL5B,ENSG00000165997; ENSG00000165997,Human; Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG",Activation/Upregulation; Activation/Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,"GTRD Binding Parameter: -1000, +100","Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q96KC2,ADP-ribosylation factor-like protein 5B,Tbio,Enzyme,0.03703395
+ARRDC3,ENSG00000113369; ENSG00000113369,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q96B67,Arrestin domain-containing protein 3,Tbio,Other,0.04840692
+ASB7,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9H672,Ankyrin repeat and SOCS box protein 7,Tbio,Other,0.21883348
+ATP6V1G3,ENSG00000151418; ENSG00000151418,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q96LB4,V-type proton ATPase subunit G 3,Tbio,Enzyme,0.1203764
+ATP9B,ENSG00000166377; ENSG00000166377,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,O43861,Probable phospholipid-transporting ATPase IIB,Tdark,Transporter,0.18986483
+BAG5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9UL15,BAG family molecular chaperone regulator 5,Tbio,Other,0.0318404
+BAZ2B,ENSG00000123636; ENSG00000123636,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9UIF8,Bromodomain adjacent to zinc finger domain protein 2B,Tchem,TF-Epigenetic,0.00518472
+BET1L,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Downregulation (coexpression-inferred),GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; PMID: 27924024,,"GTRD Binding Parameter: -1000, +100; SigCom LINCS: Down Gene; Detection method: chromatin",,,Q9NYM9,BET1-like protein,Tbio,Other,0.25170424
+BMI1,ENSG00000168283; ENSG00000168283,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P35226,Polycomb complex protein BMI-1,Tbio,Other,0.00158043
+BMP5,ENSG00000112175; ENSG00000112175,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P22003,Bone morphogenetic protein 5,Tbio,Other,0.00866987
+BMPR1B,ENSG00000138696; ENSG00000138696,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,O00238,Bone morphogenetic protein receptor type-1B,Tchem,Kinase,0.00698763
+BMPR2,ENSG00000204217; ENSG00000204217,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q13873,Bone morphogenetic protein receptor type-2,Tchem,Kinase,0.00155912
+BPTF,ENSG00000171634; ENSG00000171634,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q12830,Nucleosome-remodeling factor subunit BPTF,Tchem,Epigenetic,0.00826037
+BRCA1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P38398,Breast cancer type 1 susceptibility protein,Tchem,Other,1.1146e-4
+C12orf40,ENSG00000180116; ENSG00000180116,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q86WS4,Uncharacterized protein C12orf40,Tdark,Other,11.25
+C16orf70,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9BSU1,UPF0183 protein C16orf70,Tdark,Other,2.12573065
+C1orf123 (CZIB),,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+C4orf36,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q96KX1,Uncharacterized protein C4orf36,Tdark,Other,18
+C4orf46,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q504U0,Renal cancer differentiation gene 1 protein,Tdark,Other,0.77486427
+CACNB2,ENSG00000165995; ENSG00000165995,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q08289,Voltage-dependent L-type calcium channel subunit beta-2,Tbio,Ion Channel,0.01745218
+CACUL1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q86Y37,CDK2-associated and cullin domain-containing protein 1,Tbio,Other,0.17361884
+CASC1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q6TDU7,Protein CASC1,Tdark,Other,0.07508229
+CCDC174,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q6PII3,Coiled-coil domain-containing protein 174,Tdark,Other,0.37189828
+CCDC184,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q52MB2,Coiled-coil domain-containing protein 184,Tdark,Other,5.36558454
+CCDC50,ENSG00000152492; ENSG00000152492,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q8IVM0,Coiled-coil domain-containing protein 50,Tbio,Other,0.05903068
+CCNH,ENSG00000134480; ENSG00000134480,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P51946,Cyclin-H,Tbio,Other,0.00693072
+CDK8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P49336,Cyclin-dependent kinase 8,Tchem,Kinase,0.00508026
+CDKN1A,,Human,,Upregulated,,https://doi.org/10.1093/hmg/ddaf003,,,"""We observed that CDKN1A levels were reduced in response to PFT treatment confirming that CDKN1A is an output marker of p53 in NPC cells (Fig. 5D). We then evaluated the levels of CDKN1A in SGS, SHD and KO cells to determine if CDKN1A levels reflect SETBP1 dosage changes. We reasoned that if CDKN1A levels show reciprocal changes in SHD and SGS, this might suggest that β-Catenin, FOXO3A, and LMNA/C may be regulated via p53. We found no differences in CDKN1A levels in SHD cells but found a strong increase in CDKN1A levels in SGS cells and KO2 cells (Fig. 5E, Fig. S19A and B). This might suggest that increased levels of SETBP1 in SGS are having an effect on CDKN1A independent of p53 action. This could be occurring through the reported direct action of SET binding to CDKN1A [73].""",,P38936,Cyclin-dependent kinase inhibitor 1,Tchem,Enzyme,3.3009e-4
+CDKN1B,ENSG00000111276; ENSG00000111276,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P46527,Cyclin-dependent kinase inhibitor 1B,Tbio,Enzyme,6.9449e-4
+CDKN2A,ENSG00000147889; ENSG00000147889,Human; Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Upregulation; Activation/Upregulation; Activation/Upregulation,CollecTRI,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P42771,Cyclin-dependent kinase inhibitor 2A,Tbio,Enzyme,1.4147e-4
+CDKN2A,ENSG00000147889; ENSG00000147889,Human; Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Upregulation; Activation/Upregulation; Activation/Upregulation,CollecTRI,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q8N726,Tumor suppressor ARF,Tbio,Other,1.4147e-4
+CDKN2B,ENSG00000147883; ENSG00000147883,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P42772,Cyclin-dependent kinase 4 inhibitor B,Tbio,Enzyme,0.00166614
+CDKN2C,ENSG00000123080; ENSG00000123080,Human; Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG",Activation/Upregulation; Activation/Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,"GTRD Binding Parameter: -1000, +100","Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P42773,Cyclin-dependent kinase 4 inhibitor C,Tbio,Enzyme,0.00806886
+CENPBD1P1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+CEP192,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8TEP8,Centrosomal protein of 192 kDa,Tbio,Other,0.05738998
+CEP290,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O15078,Centrosomal protein of 290 kDa,Tbio,Other,0.00526375
+CEP44,ENSG00000164118; ENSG00000164118,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9C0F1,Centrosomal protein of 44 kDa,Tdark,Other,1.20621472
+CEPT1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9Y6K0,Choline/ethanolaminephosphotransferase 1,Tchem,Enzyme,0.01816476
+CHD2,ENSG00000173575; ENSG00000173575,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,O14647,Chromodomain-helicase-DNA-binding protein 2,Tbio,Epigenetic,0.09602647
 CHEBI:6092,,Human,Protein interaction,,,"20375348
-IM-26494",,,Interaction Type: direct interaction; confidence value: 0.44,
-CHEK1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CHERP,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CLEC16A,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CNIH2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CNOT11,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-COBLL1,ENSG00000082438,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-COL5A2,ENSG00000204262,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-COMMD3,ENSG00000148444,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-COX4I1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CRLS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CSRNP3,ENSG00000178662,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-CTD-3222D19.12,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CTNNBL1,,Human,"RNA coexpression shows inverse correlation between SETBP1 gene and ABP1; Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CWF19L2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-CXorf57,ENSG00000147231,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-CYB5D2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-DCAF8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-DDI2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-DENND1B,ENSG00000213047,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-DGCR6L,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-DIEXF,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-DLAT,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-DNAJC1,ENSG00000136770,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-DNAJC12,ENSG00000108176,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-DNAJC19,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-DNAJC9-AS1,,Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD; GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100; GTRD Binding Parameter: -1000, +100",,
-DPH5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-DPY30,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-DRAM2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-DST,ENSG00000151914,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-E4F1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-EDIL3,ENSG00000164176,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-EED,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-EEF1G,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-EIF3D,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-EIF3K,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-EIF4B,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ELP3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-EMC8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Downregulation?,GTRD; SigCom LINCS,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100; SigCom LINCS: Down Gene",,
-EPC1,ENSG00000120616,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-EPC2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-EPHA7,ENSG00000135333,Human,SETBP1 binding in promoter and DEG,Upregulation; Activation/Upregulation,,10.1016/j.ymthe.2026.01.034; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-EPRS,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ERBB4,ENSG00000178568,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-ESYT1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ETFDH,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-FAAP100,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-FAF1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-FAM129A,ENSG00000135842,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-FAM174B,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-FAM188A,ENSG00000148481,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-FAM229B,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-FBRS,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-FBXL17,ENSG00000145743,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-FBXO8,ENSG00000164117,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-FGF5,ENSG00000138675,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-FKBP15,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-FKTN,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-FOXP2,,Human,LOF variants cause reduced transcription action,Upregulated,,https://www.nature.com/articles/s41467-025-64074-x#Sec12,,,Transcriptionally activated by SETBP1 at two different sites (via luciferase reporter assay,
-FRZB,ENSG00000162998,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
+IM-26494",,,Interaction Type: direct interaction; confidence value: 0.44,,NA,NA,NA,NA,NA
+CHEK1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O14757,Serine/threonine-protein kinase Chk1,Tchem,Kinase,6.6843e-4
+CHERP,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8IWX8,Calcium homeostasis endoplasmic reticulum protein,Tbio,Other,0.06955626
+CLEC16A,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q2KHT3,Protein CLEC16A,Tbio,Other,0.0212098
+CNIH2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q6PI25,Protein cornichon homolog 2,Tbio,Other,0.08676822
+CNOT11,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9UKZ1,CCR4-NOT transcription complex subunit 11,Tbio,Other,0.01687183
+COBLL1,ENSG00000082438; ENSG00000082438,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q53SF7,Cordon-bleu protein-like 1,Tbio,Other,0.09264701
+COL5A2,ENSG00000204262; ENSG00000204262,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P05997,Collagen alpha-2(V) chain,Tbio,Other,0.01352973
+COMMD3,ENSG00000148444; ENSG00000148444,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9UBI1,COMM domain-containing protein 3,Tbio,Other,0.07399068
+COX4I1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P13073,"Cytochrome c oxidase subunit 4 isoform 1, mitochondrial",Tbio,Enzyme,0.00208873
+CRLS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9UJA2,Cardiolipin synthase (CMP-forming),Tbio,Enzyme,0.08214782
+CSRNP3,ENSG00000178662; ENSG00000178662,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q8WYN3,Cysteine/serine-rich nuclear protein 3,Tdark,Other,0.49305974
+CTD-3222D19.12,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+CTNNBL1,,Human,"RNA coexpression shows inverse correlation between SETBP1 gene and ABP1; Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8WYA6,Beta-catenin-like protein 1,Tbio,Other,0.0189038
+CWF19L2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q2TBE0,CWF19-like protein 2,Tdark,Other,0.80210985
+CXorf57,ENSG00000147231; ENSG00000147231,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,NA,NA,NA,NA,NA
+CYB5D2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8WUJ1,Neuferricin,Tbio,Other,0.23122479
+DCAF8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q5TAQ9,DDB1- and CUL4-associated factor 8,Tbio,Other,0.12456534
+DDI2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q5TDH0,Protein DDI1 homolog 2,Tbio,Other,0.09288646
+DENND1B,ENSG00000213047; ENSG00000213047,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q6P3S1,DENN domain-containing protein 1B,Tbio,Other,0.07206972
+DGCR6L,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9BY27,Protein DGCR6L,Tbio,Other,0.11554203
+DIEXF,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q68CQ4,Digestive organ expansion factor homolog,Tbio,Other,0.05892659
+DLAT,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P10515,"Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial",Tbio,Enzyme,0.00311191
+DNAJC1,ENSG00000136770; ENSG00000136770,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q96KC8,DnaJ homolog subfamily C member 1,Tbio,Transcription Factor,0.07277849
+DNAJC12,ENSG00000108176; ENSG00000108176,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9UKB3,DnaJ homolog subfamily C member 12,Tbio,Other,0.05214775
+DNAJC19,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q96DA6,Mitochondrial import inner membrane translocase subunit TIM14,Tbio,Enzyme,0.02938164
+DNAJC9-AS1,,Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD; GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100; GTRD Binding Parameter: -1000, +100",,,A6NH13,Putative uncharacterized protein DNAJC9-AS1,Tdark,Other,NA
+DPH5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9H2P9,Diphthine methyl ester synthase,Tbio,Enzyme,0.09745698
+DPY30,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9C005,Protein dpy-30 homolog,Tbio,Other,0.03098629
+DRAM2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q6UX65,DNA damage-regulated autophagy modulator protein 2,Tbio,Other,0.07642816
+DST,ENSG00000151914; ENSG00000151914,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q03001,Dystonin,Tbio,Other,0.00238839
+E4F1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q66K89,Transcription factor E4F1,Tbio,Transcription Factor,0.02192338
+EDIL3,ENSG00000164176; ENSG00000164176,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,O43854,EGF-like repeat and discoidin I-like domain-containing protein 3,Tbio,Other,0.00848858
+EED,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O75530,Polycomb protein EED,Tchem,Other,0.00615758
+EEF1G,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P26641,Elongation factor 1-gamma,Tbio,Other,0.01473013
+EIF3D,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O15371,Eukaryotic translation initiation factor 3 subunit D,Tbio,Other,0.0360717
+EIF3K,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9UBQ5,Eukaryotic translation initiation factor 3 subunit K,Tbio,Other,0.04938688
+EIF4B,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P23588,Eukaryotic translation initiation factor 4B,Tbio,Other,0.00665561
+ELP3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9H9T3,Elongator complex protein 3,Tbio,Epigenetic,0.0166061
+EMC8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Downregulation?,GTRD; SigCom LINCS,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100; SigCom LINCS: Down Gene",,,O43402,ER membrane protein complex subunit 8,Tbio,Other,0.2452967
+EPC1,ENSG00000120616; ENSG00000120616,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9H2F5,Enhancer of polycomb homolog 1,Tbio,Other,0.03216371
+EPC2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q52LR7,Enhancer of polycomb homolog 2,Tbio,Other,0.02760809
+EPHA7,ENSG00000135333; ENSG00000135333,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Upregulation; Activation/Upregulation; Activation/Upregulation,,10.1016/j.ymthe.2026.01.034; https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q15375,Ephrin type-A receptor 7,Tchem,Kinase,0.01065563
+EPRS,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P07814,Bifunctional glutamate/proline--tRNA ligase,Tchem,Enzyme,8.4896e-4
+ERBB4,ENSG00000178568; ENSG00000178568,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q15303,Receptor tyrosine-protein kinase erbB-4,Tclin,Kinase,0.00112919
+ESYT1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9BSJ8,Extended synaptotagmin-1,Tbio,Other,0.03069611
+ETFDH,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q16134,"Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial",Tbio,Enzyme,0.00970137
+FAAP100,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q0VG06,Fanconi anemia core complex-associated protein 100,Tdark,Other,0.1698504
+FAF1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9UNN5,FAS-associated factor 1,Tbio,Other,0.01526275
+FAM129A,ENSG00000135842; ENSG00000135842,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9BZQ8,Protein Niban,Tbio,Other,0.05298391
+FAM174B,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q3ZCQ3,Membrane protein FAM174B,Tdark,Other,0.54823112
+FAM188A,ENSG00000148481; ENSG00000148481,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,NA,NA,NA,NA,NA
+FAM229B,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q4G0N7,Protein FAM229B,Tdark,Other,6.66666667
+FBRS,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9HAH7,Probable fibrosin-1,Tbio,Other,0.13646817
+FBXL17,ENSG00000145743; ENSG00000145743,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9UF56,F-box/LRR-repeat protein 17,Tbio,Other,0.16122137
+FBXO8,ENSG00000164117; ENSG00000164117,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9NRD0,F-box only protein 8,Tbio,Other,0.00682751
+FGF5,ENSG00000138675; ENSG00000138675,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P12034,Fibroblast growth factor 5,Tbio,Other,0.00575584
+FKBP15,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q5T1M5,FK506-binding protein 15,Tbio,Other,0.0570695
+FKTN,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O75072,Fukutin,Tbio,Other,0.00981221
+FOXP2,,Human,LOF variants cause reduced transcription action,Upregulated,,https://www.nature.com/articles/s41467-025-64074-x#Sec12,,,Transcriptionally activated by SETBP1 at two different sites (via luciferase reporter assay,,O15409,Forkhead box protein P2,Tbio,Transcription Factor,0.00190504
+FRZB,ENSG00000162998; ENSG00000162998,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q92765,Secreted frizzled-related protein 3,Tbio,Other,0.00201307
 G2XKQ0,,Human,Protein interaction,,,"IM-23318
-25416956",,,Interaction Type: physical association; confidence value: 0.56,
-GDI2,ENSG00000057608,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-GGCX,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-GNL3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-GOLGA7,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-HAX1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-HCF1,,Human,"By recruiting a multiprotein epigenetic complex, it activates a network of genes that are key to controlling visceral organ development and brain morphogenesis.",Complex recruitment,,PMID: 29875417,,,"""Here we show that SETBP1 binds to gDNA in AT-rich promoter regions, causing activation of gene expression through recruitment of a HCF1/KMT2A/PHF8 epigenetic complex. Deletion of two AT-hooks abrogates the binding of SETBP1 to gDNA and impairs target gene upregulation. "" https://pubmed.ncbi.nlm.nih.gov/29875417/","""SETBP1 revealed direct interaction of both WT and mutated SETBP1 with HCF1, a core protein of the SET1/KMT2A complex, responsible for H3K4 mono- and di-methylation."""
-HDAC9,ENSG00000048052,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-HGF,ENSG00000019991,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-HM13,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-HMGCLL1,ENSG00000146151,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-HOXA10,,Human,Protein upregulates quantity by expression indirectly activating transcriptional regulation of target,Upregulation,SIGNOR; CollecTRI,PMID: 22566606,,SignorScore: 0.350; Cell Line: leukemia cell,Upregulation - https://academic.oup.com/hmg/advance-article/doi/10.1093/hmg/ddaf003/7959539 https://pmc.ncbi.nlm.nih.gov/articles/PMC4703539/ https://ashpublications.org/blood/article/119/25/6099/30053/Setbp1-promotes-the-self-renewal-of-murine-myeloid,
-HOXA9,,Human,Protein upregulates quantity by expression indirectly activating transcriptional regulation of target,Upregulation,SIGNOR; CollecTRI,PMID: 22566606,,SignorScore: 0.429; Cell_Line: leukemia cell,Upregulation - https://academic.oup.com/hmg/advance-article/doi/10.1093/hmg/ddaf003/7959539 https://pmc.ncbi.nlm.nih.gov/articles/PMC4703539/ https://ashpublications.org/blood/article/119/25/6099/30053/Setbp1-promotes-the-self-renewal-of-murine-myeloid,
-HS2ST1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-Hoxa10,,Mouse,Protein upregulates quantity by expression indirectly activating transcriptional regulation of target,Unknown,TRRUST; SIGNOR,PMID: 22566606,,,,
-Hoxa9,,Mouse,Protein upregulates quantity by expression indirectly activating transcriptional regulation of target,Upregulation,SIGNOR,PMID: 22566607,,SignorScore: 0.351; Cell_Line: leukemia cell,,
-IFT122,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-INO80D,ENSG00000114933,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-IPO8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ITFG1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-JMJD1C,ENSG00000171988,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-KAT6A,MOZ,,Protein interaction with MYST acetyltransferases (KAT6A and KAT7A); oncogenic mutant leads to upregulation that increases expression of MEIS1,Complex recruitment,,https://doi.org/10.64898/2026.01.08.697228,,,,
-KAT7,HBO1,,Protein interaction with MYST acetyltransferases (KAT6A and KAT7A); oncogenic mutant leads to upregulation that increases expression of MEIS1,Complex recruitment,,https://doi.org/10.64898/2026.01.08.697228,,,,
-KIAA2013,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; PMID: 27924024,,"GTRD Binding Parameter: -1000, +100",,
-KIF1BP,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-KLHDC9,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-KLHL1,ENSG00000150361,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-KLHL14,ENSG00000197705,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-KLRC2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-KMT2A,,Human,"By recruiting a multiprotein epigenetic complex, it activates a network of genes that are key to controlling visceral organ development and brain morphogenesis.",Complex recruitment,,PMID: 29875417,,,"""Here we show that SETBP1 binds to gDNA in AT-rich promoter regions, causing activation of gene expression through recruitment of a HCF1/KMT2A/PHF8 epigenetic complex. Deletion of two AT-hooks abrogates the binding of SETBP1 to gDNA and impairs target gene upregulation. "" https://pubmed.ncbi.nlm.nih.gov/29875417/",
-LAMA2,ENSG00000196569,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-LEO1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-LIN28B,ENSG00000187772,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-LINS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-LIPK,ENSG00000204021,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-LRRCC1,ENSG00000133739,Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); SETBP1 binding in promoter and DEG",Repression/Downregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; https://www.nature.com/articles/s41467-018-04462-8,,"GTRD Binding Parameter: -1000, +100","Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-LRRIQ1,ENSG00000133640,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-LSM 4.00,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-LYRM5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MAP4K1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MBD4,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MBNL1,ENSG00000152601,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-MCM8-AS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MCTS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MCTS2P,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MECOM,ENSG00000085276,Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); SETBP1 binding in promoter and DEG",Upregulation; Activation/Upregulation,GTRD,"https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html , PMID: 29875417; https://www.nature.com/articles/s41467-018-04462-8",,"GTRD Binding Parameter: -1000, +100",""" Genes controlled by SETBP1 such as MECOM are significantly upregulated in leukemias containing SETBP1 mutations"" https://pubmed.ncbi.nlm.nih.gov/29875417/; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-MED29,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MEF2C,ENSG00000081189,Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); SETBP1 binding in promoter and DEG",Activation/Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; https://www.nature.com/articles/s41467-018-04462-8,,"GTRD Binding Parameter: -1000, +100","Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-MEIS1,,,Oncogenic mutants in KAT6A and KAT7A)lead to upregulation that increases the expression of MEIS1,Activation,,https://doi.org/10.64898/2026.01.08.697228,,,,
-METAP1D,ENSG00000172878,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-MGAT2,ENSG00000168282,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-MIR4461,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MKS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MLLT10,ENSG00000078403,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-MPC1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MRFAP1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MRFAP1L1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MRPL15,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MRPS12,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MRPS16,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MT-ND1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MT-ND6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MT-RNR1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Downregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Downregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,
-MT-TE,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MT-TF,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Downregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Downregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,
-MT-TL1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MT-TP,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MT-TT,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MTCO3P12,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MTND5P11,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MYO9A,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-MZF1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-Myb,,Mouse,,Activation,,PMID: 27863435,,,"""We further identify Myb as a critical mediator of Setbp1-induced self-renewal as its knockdown caused efficient differentiation of myeloid progenitors immortalized by wild-type Setbp1 and Setbp1 missense mutants. Interestingly, Myb is also a direct transcriptional target of Setbp1 and Setbp1 missense mutants as they directly bind to the Myb locus in immortalized cells and dramatically activate a critical enhancer/promoter region of Myb in luciferase reporter assays. Furthermore, Myb knockdown in Setbp1 and Setbp1 missense mutations-induced AML cells also efficiently induced their differentiation in culture and significantly prolonged the survival of their secondary recipient mice, suggesting that targeting MYB pathway could be a promising strategy for treating human myeloid neoplasms with SETBP1 activation.""","""Setbp1 missense mutants as they directly bind to the Myb locus in immortalized cells and dramatically activate a critical enhancer/promoter region of Myb in luciferase reporter assays."""
-NAA30,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-NAALADL2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-NARFL,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-NBR1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-NBR2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-NCOA5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-NDFIP2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-NDFIP2-AS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-NDUFAB1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; PMID: 27924024,,"GTRD Binding Parameter: -1000, +100",,
-NDUFS5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-NEBL,ENSG00000078114,Human,SETBP1 binding in promoter and DEG,Repression/Downregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-NEURL4,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-NFE2L2,ENSG00000116044,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-NOL6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-NR2F1,ENSG00000175745,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-NSUN5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-NSUN6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-NUDT9,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
+25416956",,,Interaction Type: physical association; confidence value: 0.56,,NA,NA,NA,NA,NA
+GDI2,ENSG00000057608; ENSG00000057608,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P50395,Rab GDP dissociation inhibitor beta,Tbio,Other,0.02861013
+GGCX,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P38435,Vitamin K-dependent gamma-carboxylase,Tclin,Enzyme,0.00819484
+GNL3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9BVP2,Guanine nucleotide-binding protein-like 3,Tbio,Other,0.00886703
+GOLGA7,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q7Z5G4,Golgin subfamily A member 7,Tbio,Other,0.17108842
+HAX1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O00165,HCLS1-associated protein X-1,Tbio,Other,0.00749205
+HCF1,,Human,"By recruiting a multiprotein epigenetic complex, it activates a network of genes that are key to controlling visceral organ development and brain morphogenesis.",Complex recruitment,,PMID: 29875417,,,"""Here we show that SETBP1 binds to gDNA in AT-rich promoter regions, causing activation of gene expression through recruitment of a HCF1/KMT2A/PHF8 epigenetic complex. Deletion of two AT-hooks abrogates the binding of SETBP1 to gDNA and impairs target gene upregulation. "" https://pubmed.ncbi.nlm.nih.gov/29875417/","""SETBP1 revealed direct interaction of both WT and mutated SETBP1 with HCF1, a core protein of the SET1/KMT2A complex, responsible for H3K4 mono- and di-methylation.""",NA,NA,NA,NA,NA
+HDAC9,ENSG00000048052; ENSG00000048052,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9UKV0,Histone deacetylase 9,Tclin,Epigenetic,0.00382278
+HGF,ENSG00000019991; ENSG00000019991,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P14210,Hepatocyte growth factor,Tchem,Enzyme,3.5574e-4
+HM13,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8TCT9,Minor histocompatibility antigen H13,Tbio,Enzyme,0.0051333
+HMGCLL1,ENSG00000146151; ENSG00000146151,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q8TB92,"3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic",Tbio,Enzyme,0.13131046
+HOXA10,,Human,Protein upregulates quantity by expression indirectly activating transcriptional regulation of target,Upregulation,SIGNOR; CollecTRI,PMID: 22566606,,SignorScore: 0.350; Cell Line: leukemia cell,Upregulation - https://academic.oup.com/hmg/advance-article/doi/10.1093/hmg/ddaf003/7959539 https://pmc.ncbi.nlm.nih.gov/articles/PMC4703539/ https://ashpublications.org/blood/article/119/25/6099/30053/Setbp1-promotes-the-self-renewal-of-murine-myeloid,,P31260,Homeobox protein Hox-A10,Tbio,Transcription Factor,0.00324357
+HOXA9,,Human,Protein upregulates quantity by expression indirectly activating transcriptional regulation of target,Upregulation,SIGNOR; CollecTRI,PMID: 22566606,,SignorScore: 0.429; Cell_Line: leukemia cell,Upregulation - https://academic.oup.com/hmg/advance-article/doi/10.1093/hmg/ddaf003/7959539 https://pmc.ncbi.nlm.nih.gov/articles/PMC4703539/ https://ashpublications.org/blood/article/119/25/6099/30053/Setbp1-promotes-the-self-renewal-of-murine-myeloid,,P31269,Homeobox protein Hox-A9,Tbio,Transcription Factor,0.00249963
+HS2ST1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q7LGA3,Heparan sulfate 2-O-sulfotransferase 1,Tbio,Enzyme,0.04520207
+Hoxa10,,Mouse,Protein upregulates quantity by expression indirectly activating transcriptional regulation of target,Unknown,TRRUST; SIGNOR,PMID: 22566606,,,,,NA,NA,NA,NA,NA
+Hoxa9,,Mouse,Protein upregulates quantity by expression indirectly activating transcriptional regulation of target,Upregulation,SIGNOR,PMID: 22566607,,SignorScore: 0.351; Cell_Line: leukemia cell,,,NA,NA,NA,NA,NA
+IFT122,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9HBG6,Intraflagellar transport protein 122 homolog,Tbio,Other,0.02235986
+INO80D,ENSG00000114933; ENSG00000114933,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q53TQ3,INO80 complex subunit D,Tdark,Other,0.33070971
+IPO8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O15397,Importin-8,Tbio,Other,0.00934966
+ITFG1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8TB96,T-cell immunomodulatory protein,Tbio,Other,0.01886566
+JMJD1C,ENSG00000171988; ENSG00000171988,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q15652,Probable JmjC domain-containing histone demethylation protein 2C,Tbio,Epigenetic,0.02919389
+KAT6A,MOZ,,Protein interaction with MYST acetyltransferases (KAT6A and KAT7A); oncogenic mutant leads to upregulation that increases expression of MEIS1,Complex recruitment,,https://doi.org/10.64898/2026.01.08.697228,,,,,Q92794,Histone acetyltransferase KAT6A,Tchem,Epigenetic,0.00478771
+KAT7,HBO1,,Protein interaction with MYST acetyltransferases (KAT6A and KAT7A); oncogenic mutant leads to upregulation that increases expression of MEIS1,Complex recruitment,,https://doi.org/10.64898/2026.01.08.697228,,,,,O95251,Histone acetyltransferase KAT7,Tbio,TF-Epigenetic,0.01783137
+KIAA2013,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; PMID: 27924024,,"GTRD Binding Parameter: -1000, +100",,,Q8IYS2,Uncharacterized protein KIAA2013,Tdark,Other,0.4705158
+KIF1BP,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q96EK5,KIF1-binding protein,Tbio,Other,0.03932922
+KLHDC9,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8NEP7,Kelch domain-containing protein 9,Tbio,Other,1.56875574
+KLHL1,ENSG00000150361; ENSG00000150361,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9NR64,Kelch-like protein 1,Tbio,Other,0.05206893
+KLHL14,ENSG00000197705; ENSG00000197705,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9P2G3,Kelch-like protein 14,Tbio,Other,0.1214402
+KLRC2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P26717,NKG2-C type II integral membrane protein,Tbio,Other,0.00912237
+KMT2A,,Human,"By recruiting a multiprotein epigenetic complex, it activates a network of genes that are key to controlling visceral organ development and brain morphogenesis.",Complex recruitment,,PMID: 29875417,,,"""Here we show that SETBP1 binds to gDNA in AT-rich promoter regions, causing activation of gene expression through recruitment of a HCF1/KMT2A/PHF8 epigenetic complex. Deletion of two AT-hooks abrogates the binding of SETBP1 to gDNA and impairs target gene upregulation. "" https://pubmed.ncbi.nlm.nih.gov/29875417/",,Q03164,Histone-lysine N-methyltransferase 2A,Tchem,Epigenetic,0.00192554
+LAMA2,ENSG00000196569; ENSG00000196569,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P24043,Laminin subunit alpha-2,Tbio,Other,0.00210486
+LEO1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8WVC0,RNA polymerase-associated protein LEO1,Tbio,Enzyme,0.00851903
+LIN28B,ENSG00000187772; ENSG00000187772,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q6ZN17,Protein lin-28 homolog B,Tbio,Transcription Factor,0.00564546
+LINS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8NG48,Protein Lines homolog 1,Tbio,Other,0.00317377
+LIPK,ENSG00000204021; ENSG00000204021,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q5VXJ0,Lipase member K,Tbio,Enzyme,0.11313187
+LRRCC1,ENSG00000133739; ENSG00000133739,Human; Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG",Repression/Downregulation; Repression/Downregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,"GTRD Binding Parameter: -1000, +100","Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9C099,Leucine-rich repeat and coiled-coil domain-containing protein 1,Tdark,Other,0.14730953
+LRRIQ1,ENSG00000133640; ENSG00000133640,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q96JM4,Leucine-rich repeat and IQ domain-containing protein 1,Tdark,Other,1.8251367
+LSM 4.00,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+LYRM5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+MAP4K1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q92918,Mitogen-activated protein kinase kinase kinase kinase 1,Tchem,Kinase,0.02861969
+MBD4,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O95243,Methyl-CpG-binding domain protein 4,Tbio,Transcription Factor,0.00876432
+MBNL1,ENSG00000152601; ENSG00000152601,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9NR56,Muscleblind-like protein 1,Tbio,Other,0.00441241
+MCM8-AS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+MCTS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9ULC4,Malignant T-cell-amplified sequence 1,Tbio,Other,0.07039427
+MCTS2P,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+MECOM,ENSG00000085276; ENSG00000085276,Human; Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG",Upregulation; Activation/Upregulation; Activation/Upregulation,GTRD,"https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html , PMID: 29875417; https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8",,"GTRD Binding Parameter: -1000, +100",""" Genes controlled by SETBP1 such as MECOM are significantly upregulated in leukemias containing SETBP1 mutations"" https://pubmed.ncbi.nlm.nih.gov/29875417/; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q03112,MDS1 and EVI1 complex locus protein,Tbio,TF-Epigenetic,0.00500501
+MED29,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9NX70,Mediator of RNA polymerase II transcription subunit 29,Tbio,Enzyme,0.01740647
+MEF2C,ENSG00000081189; ENSG00000081189,Human; Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG",Activation/Upregulation; Activation/Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,"GTRD Binding Parameter: -1000, +100","Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q06413,Myocyte-specific enhancer factor 2C,Tbio,Transcription Factor,0.00232724
+MEIS1,,,Oncogenic mutants in KAT6A and KAT7A)lead to upregulation that increases the expression of MEIS1,Activation,,https://doi.org/10.64898/2026.01.08.697228,,,,,O00470,Homeobox protein Meis1,Tbio,Transcription Factor,0.00480433
+METAP1D,ENSG00000172878; ENSG00000172878,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q6UB28,"Methionine aminopeptidase 1D, mitochondrial",Tbio,Enzyme,0.17714714
+MGAT2,ENSG00000168282; ENSG00000168282,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q10469,"Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase",Tchem,Enzyme,0.02440696
+MIR4461,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+MKS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9NXB0,Meckel syndrome type 1 protein,Tbio,Other,0.02463305
+MLLT10,ENSG00000078403; ENSG00000078403,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P55197,Protein AF-10,Tbio,Epigenetic,0.00590548
+MPC1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9Y5U8,Mitochondrial pyruvate carrier 1,Tbio,Other,0.01315849
+MRFAP1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9Y605,MORF4 family-associated protein 1,Tbio,Other,0.11341713
+MRFAP1L1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q96HT8,MORF4 family-associated protein 1-like 1,Tdark,Other,0.87470289
+MRPL15,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9P015,"39S ribosomal protein L15, mitochondrial",Tdark,Other,4.6875335400000004
+MRPS12,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O15235,"28S ribosomal protein S12, mitochondrial",Tbio,Other,0.15394123
+MRPS16,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9Y3D3,"28S ribosomal protein S16, mitochondrial",Tbio,Other,0.24108603
+MT-ND1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P03886,NADH-ubiquinone oxidoreductase chain 1,Tclin,Enzyme,9.0183e-4
+MT-ND6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P03923,NADH-ubiquinone oxidoreductase chain 6,Tclin,Enzyme,0.00104547
+MT-RNR1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Downregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Downregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,,A0A0C5B5G6,Mitochondrial-derived peptide MOTS-c,Tbio,Other,NA
+MT-TE,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+MT-TF,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Downregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Downregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,,NA,NA,NA,NA,NA
+MT-TL1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+MT-TP,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+MT-TT,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+MTCO3P12,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+MTND5P11,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+MYO9A,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,B2RTY4,Unconventional myosin-IXa,Tbio,Other,0.09467086
+MZF1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P28698,Myeloid zinc finger 1,Tbio,Transcription Factor,0.01193919
+Myb,,Mouse,,Activation,,PMID: 27863435,,,"""We further identify Myb as a critical mediator of Setbp1-induced self-renewal as its knockdown caused efficient differentiation of myeloid progenitors immortalized by wild-type Setbp1 and Setbp1 missense mutants. Interestingly, Myb is also a direct transcriptional target of Setbp1 and Setbp1 missense mutants as they directly bind to the Myb locus in immortalized cells and dramatically activate a critical enhancer/promoter region of Myb in luciferase reporter assays. Furthermore, Myb knockdown in Setbp1 and Setbp1 missense mutations-induced AML cells also efficiently induced their differentiation in culture and significantly prolonged the survival of their secondary recipient mice, suggesting that targeting MYB pathway could be a promising strategy for treating human myeloid neoplasms with SETBP1 activation.""","""Setbp1 missense mutants as they directly bind to the Myb locus in immortalized cells and dramatically activate a critical enhancer/promoter region of Myb in luciferase reporter assays.""",NA,NA,NA,NA,NA
+NAA30,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q147X3,N-alpha-acetyltransferase 30,Tbio,Enzyme,0.04701961
+NAALADL2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q58DX5,Inactive N-acetylated-alpha-linked acidic dipeptidase-like protein 2,Tbio,Enzyme,0.17299124
+NARFL,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+NBR1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q14596,Next to BRCA1 gene 1 protein,Tbio,Other,0.00893066
+NBR2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+NCOA5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9HCD5,Nuclear receptor coactivator 5,Tbio,Other,0.09053523
+NDFIP2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9NV92,NEDD4 family-interacting protein 2,Tbio,Other,0.13102829
+NDFIP2-AS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+NDUFAB1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; PMID: 27924024,,"GTRD Binding Parameter: -1000, +100",,,O14561,"Acyl carrier protein, mitochondrial",Tclin,Other,0.00190242
+NDUFS5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O43920,NADH dehydrogenase [ubiquinone] iron-sulfur protein 5,Tclin,Enzyme,0.13274675
+NEBL,ENSG00000078114; ENSG00000078114,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Repression/Downregulation; Repression/Downregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,O76041,Nebulette,Tbio,Other,0.02155964
+NEURL4,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q96JN8,Neuralized-like protein 4,Tbio,Other,0.20430708
+NFE2L2,ENSG00000116044; ENSG00000116044,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q16236,Nuclear factor erythroid 2-related factor 2,Tchem,Transcription Factor,4.3828e-4
+NOL6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9H6R4,Nucleolar protein 6,Tbio,Other,0.10002413
+NR2F1,ENSG00000175745; ENSG00000175745,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P10589,COUP transcription factor 1,Tbio,Nuclear Receptor,0.00588095
+NSUN5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q96P11,Probable 28S rRNA (cytosine-C(5))-methyltransferase,Tbio,Enzyme,0.05373996
+NSUN6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8TEA1,Putative methyltransferase NSUN6,Tbio,Enzyme,0.14260431
+NUDT9,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9BW91,"ADP-ribose pyrophosphatase, mitochondrial",Tbio,Enzyme,0.0482661
 O35381,,Mouse,Protein interaction,,,"17557114
 IM-9565
-mint:MINT-5225803",,,,
+mint:MINT-5225803",,,,,NA,NA,NA,NA,NA
 P06821,,Human,Protein interaction,,,"IM-13585
-20064372",,,Interaction Type: physical association; confidence value: 0.37,
+20064372",,,Interaction Type: physical association; confidence value: 0.37,,NA,NA,NA,NA,NA
 P0DOF2,,Human,Protein interaction,,,"IM-27674
-33208464",,,Interaction Type: physical association; confidence value: 0.35,
+33208464",,,Interaction Type: physical association; confidence value: 0.35,,NA,NA,NA,NA,NA
 P0DOF5,,Human,Protein interaction,,,"IM-13585
-20064372",,,Interaction Type: physical association; confidence value: 0.37,
+20064372",,,Interaction Type: physical association; confidence value: 0.37,,NA,NA,NA,NA,NA
 P51957-1,,Human,Protein interaction,,,"IM-26491
-25798074",,,Interaction Type: association; confidence value: 0.35,
-P53,,Human,,Inhibits,,PMID: 34193871,,,"""Mechanistically, we demonstrate that high SETBP1 levels inhibit P53 function through the stabilization of SET, which in turn hinders P53 acetylation."" https://pubmed.ncbi.nlm.nih.gov/34193871/",
-PAF1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-PARG,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-PARGP1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-PBRM1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Upregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,
-PCDH7,ENSG00000169851,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-PCDH9,ENSG00000184226,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-PCNX4,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-PDE4D,ENSG00000113448,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-PDGFC,ENSG00000145431,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-PDPR,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-PDSS2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-PHF8,,Human,"By recruiting a multiprotein epigenetic complex, it activates a network of genes that are key to controlling visceral organ development and brain morphogenesis.",Complex recruitment,,PMID: 29875417,,,"""Here we show that SETBP1 binds to gDNA in AT-rich promoter regions, causing activation of gene expression through recruitment of a HCF1/KMT2A/PHF8 epigenetic complex. Deletion of two AT-hooks abrogates the binding of SETBP1 to gDNA and impairs target gene upregulation. "" https://pubmed.ncbi.nlm.nih.gov/29875417/",
-PHKB,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-PIGK,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-PITRM1,ENSG00000107959,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-PITX2,ENSG00000164093,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-PKN2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-PP2A,,,Protein interaction,Repression,,"https://doi.org/10.1093/hmg/ddaf003 , PMID: 11231286 , https://doi.org/10.1182/blood-2009-06-227363",,,"SETBP1 inhibits PP2A activity in non-CNS cancer cells; PP2A is involved in the AKT cascade, which is known to drive cell proliferation. PP2A targets FOXO3A and B-Catenin",
-PPP3CC,ENSG00000120910,Human,SETBP1 binding in promoter and DEG,Repression/Downregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-PPP5C,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-PRKACB,ENSG00000142875,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-PRR15,ENSG00000176532,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-PSMB6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-PSMD8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-PTEGER2,,Human,,Repression,TRRUST; CollecTRI,PMID: 18419541; PMID: 29087512,,"PMID: 18419541 is about Staphylococcus aureus enterotoxin B (SEB) -- likely confused with previous gene alias ""SEB"" for SETBP1 (other PMID is for TRRUST, which only cites the first as evidence)",Named target - https://edgar.biocomp.unibo.it/cgi-bin/gene_disease_db/gene.py?gene=SETBP1; Detection method: inferred by curator,
-PTEN,ENSG00000171862,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-PTER,ENSG00000165983,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-PTGS2,,Human,,RepressionUpregulation,TRRUST; CollecTRI,PMID: 18419541,,"PMID: 18419541 is about Staphylococcus aureus enterotoxin B (SEB) -- likely confused with previous gene alias ""SEB"" for SETBP1","In https://doi.org/10.18632/oncotarget.17231 -- increased PTGS2 expression in SETBP1 GoF functional studies, due to inhibition of PP2a; Named target - https://edgar.biocomp.unibo.it/cgi-bin/gene_disease_db/gene.py?gene=SETBP2; Detection method: inferred by curator",PTGS2 is indirectly upregulated by SETBP1 via the PP2A pathway.
-PTPA,,Human; Human,,Repression; Repression,TRRUST; CollecTRI; TRRUST; CollecTRI,PMID: 21233840; PMID: 21233840,,Uniprod ID: P35354; Detection method: inferred by curator; Uniprod ID: P35354; Detection method: inferred by curator,Named target - https://edgar.biocomp.unibo.it/cgi-bin/gene_disease_db/gene.py?gene=SETBP1; Detection method: inferred by curator,
-PTPN13,ENSG00000163629,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-PTPRA,,Human,,,,PMID: 29087512; PMID: 21233840,,Uniprot ID: P18433; NCBI Gene: 5786: Detection Method: inferred by curator,,
-PTPRC,ENSG00000081237,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
+25798074",,,Interaction Type: association; confidence value: 0.35,,NA,NA,NA,NA,NA
+P53,,Human,,Inhibits,,PMID: 34193871,,,"""Mechanistically, we demonstrate that high SETBP1 levels inhibit P53 function through the stabilization of SET, which in turn hinders P53 acetylation."" https://pubmed.ncbi.nlm.nih.gov/34193871/",,NA,NA,NA,NA,NA
+PAF1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8N7H5,RNA polymerase II-associated factor 1 homolog,Tbio,Enzyme,0.00200047
+PARG,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q86W56,Poly(ADP-ribose) glycohydrolase,Tchem,Enzyme,0.00424731
+PARGP1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+PBRM1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Upregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,,Q86U86,Protein polybromo-1,Tchem,TF-Epigenetic,0.00608093
+PCDH7,ENSG00000169851; ENSG00000169851,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,O60245,Protocadherin-7,Tbio,Other,0.04017185
+PCDH9,ENSG00000184226; ENSG00000184226,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9HC56,Protocadherin-9,Tbio,Other,0.03928208
+PCNX4,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q63HM2,Pecanex-like protein 4,Tdark,Other,8.76521739
+PDE4D,ENSG00000113448; ENSG00000113448,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q08499,"cAMP-specific 3',5'-cyclic phosphodiesterase 4D",Tclin,Enzyme,0.0033948200000000002
+PDGFC,ENSG00000145431; ENSG00000145431,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9NRA1,Platelet-derived growth factor C,Tbio,Other,0.00642236
+PDPR,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8NCN5,"Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial",Tbio,Enzyme,0.04223174
+PDSS2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q86YH6,Decaprenyl-diphosphate synthase subunit 2,Tbio,Enzyme,0.02716477
+PHF8,,Human,"By recruiting a multiprotein epigenetic complex, it activates a network of genes that are key to controlling visceral organ development and brain morphogenesis.",Complex recruitment,,PMID: 29875417,,,"""Here we show that SETBP1 binds to gDNA in AT-rich promoter regions, causing activation of gene expression through recruitment of a HCF1/KMT2A/PHF8 epigenetic complex. Deletion of two AT-hooks abrogates the binding of SETBP1 to gDNA and impairs target gene upregulation. "" https://pubmed.ncbi.nlm.nih.gov/29875417/",,Q9UPP1,Histone lysine demethylase PHF8,Tchem,Epigenetic,0.01946151
+PHKB,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q93100,Phosphorylase b kinase regulatory subunit beta,Tbio,Enzyme,0.05506418
+PIGK,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q92643,GPI-anchor transamidase,Tbio,Enzyme,0.02333499
+PITRM1,ENSG00000107959; ENSG00000107959,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q5JRX3,"Presequence protease, mitochondrial",Tchem,Enzyme,0.08067518
+PITX2,ENSG00000164093; ENSG00000164093,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q99697,Pituitary homeobox 2,Tbio,Transcription Factor,0.00216568
+PKN2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q16513,Serine/threonine-protein kinase N2,Tchem,Kinase,0.0088412
+PP2A,,,Protein interaction,Repression,,"https://doi.org/10.1093/hmg/ddaf003 , PMID: 11231286 , https://doi.org/10.1182/blood-2009-06-227363",,,"SETBP1 inhibits PP2A activity in non-CNS cancer cells; PP2A is involved in the AKT cascade, which is known to drive cell proliferation. PP2A targets FOXO3A and B-Catenin",,NA,NA,NA,NA,NA
+PPP3CC,ENSG00000120910; ENSG00000120910,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Repression/Downregulation; Repression/Downregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P48454,Serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform,Tbio,Enzyme,0.02633046
+PPP5C,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P53041,Serine/threonine-protein phosphatase 5,Tbio,Enzyme,0.01990823
+PRKACB,ENSG00000142875; ENSG00000142875,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P22694,cAMP-dependent protein kinase catalytic subunit beta,Tchem,Kinase,0.01962222
+PRR15,ENSG00000176532; ENSG00000176532,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q8IV56,Proline-rich protein 15,Tbio,Other,0.19831311
+PSMB6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P28072,Proteasome subunit beta type-6,Tbio,Enzyme,0.04738037
+PSMD8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P48556,26S proteasome non-ATPase regulatory subunit 8,Tbio,Enzyme,0.03053455
+PTEGER2,,Human,,Repression,TRRUST; CollecTRI,PMID: 18419541; PMID: 29087512,,"PMID: 18419541 is about Staphylococcus aureus enterotoxin B (SEB) -- likely confused with previous gene alias ""SEB"" for SETBP1 (other PMID is for TRRUST, which only cites the first as evidence)",Named target - https://edgar.biocomp.unibo.it/cgi-bin/gene_disease_db/gene.py?gene=SETBP1; Detection method: inferred by curator,,NA,NA,NA,NA,NA
+PTEN,ENSG00000171862; ENSG00000171862,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P60484,"Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN",Tbio,Enzyme,1.3818e-4
+PTER,ENSG00000165983; ENSG00000165983,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q96BW5,Phosphotriesterase-related protein,Tbio,Enzyme,0.01347498
+PTGS2,,Human,,RepressionUpregulation,TRRUST; CollecTRI,PMID: 18419541,,"PMID: 18419541 is about Staphylococcus aureus enterotoxin B (SEB) -- likely confused with previous gene alias ""SEB"" for SETBP1","In https://doi.org/10.18632/oncotarget.17231 -- increased PTGS2 expression in SETBP1 GoF functional studies, due to inhibition of PP2a; Named target - https://edgar.biocomp.unibo.it/cgi-bin/gene_disease_db/gene.py?gene=SETBP2; Detection method: inferred by curator",PTGS2 is indirectly upregulated by SETBP1 via the PP2A pathway.,P35354,Prostaglandin G/H synthase 2,Tclin,Enzyme,7.089e-5
+PTPA,,Human; Human,,Repression; Repression,TRRUST; CollecTRI; TRRUST; CollecTRI,PMID: 21233840; PMID: 21233840,,Uniprod ID: P35354; Detection method: inferred by curator; Uniprod ID: P35354; Detection method: inferred by curator,Named target - https://edgar.biocomp.unibo.it/cgi-bin/gene_disease_db/gene.py?gene=SETBP1; Detection method: inferred by curator,,Q15257,Serine/threonine-protein phosphatase 2A activator,Tchem,Enzyme,4.8652e-4
+PTPN13,ENSG00000163629; ENSG00000163629,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q12923,Tyrosine-protein phosphatase non-receptor type 13,Tchem,Enzyme,0.00434963
+PTPRA,,Human,,,,PMID: 29087512; PMID: 21233840,,Uniprot ID: P18433; NCBI Gene: 5786: Detection Method: inferred by curator,,,P18433,Receptor-type tyrosine-protein phosphatase alpha,Tchem,Enzyme,0.01392344
+PTPRC,ENSG00000081237; ENSG00000081237,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P08575,Receptor-type tyrosine-protein phosphatase C,Tchem,Enzyme,1.2027e-4
 Q15326,,Human,Protein interaction,,,"IM-29361
-35044719",,,Interaction Type: direct interaction; confidence value: 0.44,
+35044719",,,Interaction Type: direct interaction; confidence value: 0.44,,NA,NA,NA,NA,NA
 Q7KZS0,,Human; Human,Protein interaction; Protein interaction,,,"IM-23318
 25416956; 32296183
-IM-25472",,,"Interaction Type: physical association; confidence value: 0.56; Interaction Type: physical association; confidence value: author score=0.67, intact-miscore=0.56",
+IM-25472",,,"Interaction Type: physical association; confidence value: 0.56; Interaction Type: physical association; confidence value: author score=0.67, intact-miscore=0.56",,NA,NA,NA,NA,NA
 Q8IY57,,Human,Protein interaction,,,"IM-23318
-25416956",,,Interaction Type: physical association; confidence value: 0.37,
+25416956",,,Interaction Type: physical association; confidence value: 0.37,,NA,NA,NA,NA,NA
 Q93079,,Human,Protein interaction,,,"30021884
 IM-26653
-doi:10.1074/mcp.ra118.000924",,,Interaction Type: physical association; confidence value: 0.40,
+doi:10.1074/mcp.ra118.000924",,,Interaction Type: physical association; confidence value: 0.40,,NA,NA,NA,NA,NA
 Q9BXN6,,Human; Human,Protein interaction; Protein interaction,,,"IM-23318
 25416956; 32296183
-IM-25472",,,"Interaction Type: physical association; confidence value: 0.38; Interaction Type: physical association; confidence value: author score=0.867, intact-miscore:0.56",
+IM-25472",,,"Interaction Type: physical association; confidence value: 0.38; Interaction Type: physical association; confidence value: author score=0.867, intact-miscore:0.56",,NA,NA,NA,NA,NA
 Q9H8W4,,Human; Human,Protein interaction; Protein interaction,,,"IM-23318
 25416956; 32296183
-IM-25472",,,"Interaction Type: physical association; confidence value: 0.56; Interaction Type: physical association; confidence value: author score=0.888, intact-miscore: 0.56",
+IM-25472",,,"Interaction Type: physical association; confidence value: 0.56; Interaction Type: physical association; confidence value: author score=0.888, intact-miscore: 0.56",,NA,NA,NA,NA,NA
 Q9HD64,,Human,Protein interaction,,,"IM-23318
-25416956",,,Interaction Type: physical association; confidence value: 0.56,
+25416956",,,Interaction Type: physical association; confidence value: 0.56,,NA,NA,NA,NA,NA
 Q9NS26,,Human; Human,Protein interaction; Protein interaction,,,"IM-23318
 25416956; 32296183
-IM-25472",,,"Interaction Type: physical association; confidence value: 0.56; Interaction Type: physical association; confidenced value: author score=0.8669, intact-miscore=0.56",
+IM-25472",,,"Interaction Type: physical association; confidence value: 0.56; Interaction Type: physical association; confidenced value: author score=0.8669, intact-miscore=0.56",,NA,NA,NA,NA,NA
 Q9NY87,,Human,Protein interaction,,,"IM-23318
-25416956",,,Interaction Type: physical association; confidence value: 0.56,
+25416956",,,Interaction Type: physical association; confidence value: 0.56,,NA,NA,NA,NA,NA
 Q9P1C9,,Human,Protein interaction,,,"IM-23318
-25416956",,,Interaction Type: physical association; confidence value: 0.56,
-RAD52,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Upregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,
-RALGAPA1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Upregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,
-RAP2A,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RBM20,ENSG00000203867,Human,SETBP1 binding in promoter and DEG,Repression/Downregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-RBM33,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RBMS3,ENSG00000144642,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-REEP3,ENSG00000165476,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-RHOBTB3,ENSG00000164292,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-RIC8A,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RIOK2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RNF111,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RNF139,,Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD; GTRD,PMID: 27924024; https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Detection method: chromatin,
-RNF139-AS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RNF217,ENSG00000146373,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-RP1-168L15.5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP11-16B13.1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP11-235C23.5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP11-242D8.1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP11-242D8.3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP11-252A24.2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP11-277P12.6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP11-421L21.3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP11-472I20.4,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP11-539L10.3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP11-646I6.5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP11-680H20.2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP11-73M18.2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP11-773H22.4,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP5-1024G6.7,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP5-1103G7.10,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP5-857K21.4,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RP5-912I13.2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RPIA,ENSG00000153574,Human,SETBP1 binding in promoter and DEG,Repression/Downregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-RPS16,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-RPS6KL1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",?Potential relation to phosphorylating rpS6; Increase in RpS6 phosphorylation with in increased SETBP1 dose https://academic.oup.com/hmg/advance-article/doi/10.1093/hmg/ddaf003/7959539,
-RUNX1,,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 '...in our human 293 FLP-In model we found a similar downregulation (Supp Fig 11a). ChIP experiments, however, demonstrated only a very weak binding of SETBP1 to the human RUNX1 promoter (Supp Fig 11b), likely due to the expression of SETBP1 being much lower in our model than in traditional high-titer retroviral transduction systems or to differences in species specificity. To test this hypothesis, we repeated ChIP experiments using a transient transfection model, achieving a 4.2- and 6.9-fold increase in SETBP1-WT and G870S expression, respectively, when compared with FLP-In (Supp Fig 11c). Indeed, ChIP experiments performed using transient SETBP1 transfectants showed a significant increase in the binding to RUNX1 promoter (Supp Fig 11d). This, however, was accompanied by an increase in RUNX1 expression (Supp Fig 11e), confirming that SETBP1 promotes upregulation of gene expression and suggesting that RUNX1 downmodulation is not a direct effect of SETBP1.'",
-Runx1,,Mouse,,Repression,,PMID: 26205084; https://www.nature.com/articles/leu2015200,,,"""Figure 3 Setbp1 directly represses Runx1 transcription.""https://pubmed.ncbi.nlm.nih.gov/26205084/","""Runx1 repression is induced by Setbp1-mediated recruitment of a nucleosome remodeling deacetylase (NuRD) complex to Runx1 promoters and can be reversed by treatment with histone deacetylase (HDAC) inhibitors Entinostat and Vorinostat."""
-SARS2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-SEMA3A,ENSG00000075213,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-SEMA3D,ENSG00000153993,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-SENP8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-SEP15,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-SET,,Human,Protein pregulates activating binding of target,Upregulation,SIGNOR,PMID: 22566606,,SignorScore: 0.492,,
-SFR1,,Human,"RNA coexpression shows inverse correlation between SETBP1 gene and SFR1; Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Downregulation (coexpression-inferred),GTRD; SigCom LINCS,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100; SigCom LINCS: Down Gene",,
-SLC31A1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-SLC38A11,ENSG00000169507,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-SNF8,ENSG00000159210,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-SNORD13,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-SOX2-OT,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-SPAG6,ENSG00000077327,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-ST8SIA4,ENSG00000113532,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-STK17B,ENSG00000081320,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-SUGT1P,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-SUPT5H,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-SYDE2,ENSG00000097096,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-Set,,Mouse,Protein upregulates activating binding of target,Upregulation,SIGNOR,PMID: 22566608,,SignorScore: 0.492,,
-Smad1,,Mouse,"When ASXL1 and SETBP1 mutations are present, this gene is repressed; not a direct target of SETBP1",Repressed via histone acetylation,,PMID: 30367089,,,,
-Smad3,,Mouse,"When ASXL1 and SETBP1 mutations are present, this gene is repressed; not a direct target of SETBP1",Repressed via histone acetylation,,PMID: 30367089,,,,
-Smad4,,Mouse,"When ASXL1 and SETBP1 mutations are present, this gene is repressed; not a direct target of SETBP1",Repressed via histone acetylation,,PMID: 30367089,,,,
-TAF13,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TAF5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TANC1,ENSG00000115183,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-TAZ,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TBC1D23,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TBC1D8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TCEA1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TFPI,ENSG00000003436,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-TGDS,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TIMM23,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TIMM23B,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TMEM177,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TMTC3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TOMM7,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TPD52L1,ENSG00000111907,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-TRAPPC5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TRDMT1,ENSG00000107614,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-TRDN,ENSG00000186439,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-TSEN2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TTC23,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Upregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,
-TTI2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TUBE1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-TXNL1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-Tgfbr1,,Mouse,"When ASXL1 and SETBP1 mutations are present, this gene is repressed; not a direct target of SETBP1",Repressed via histone acetylation,,PMID: 30367089,,,"""Histone acetylation is associated with active transcription, and it was recently shown that SETBP1 represses Runx1 expression through histone deacetylation20. We therefore examined levels of histone acetylation around the promoter regions of TGFβ pathway genes in c-Kit+ cSAM cells and normal c-Kit+ bone marrow progenitor cells. Consistent with our previous report19, multiple TGFβ pathway genes (Tgfbr1, Tgfbr2, Tgfbr3, Smad1, Smad3, and Smad4) were downregulated, whereas Hox genes (Hoxa9 and Hoxa10) were upregulated in cSAM cells compared with control cells (Fig. 2a,b). "" https://pmc.ncbi.nlm.nih.gov/articles/PMC6203835/",
-Tgfbr2,,Mouse,"When ASXL1 and SETBP1 mutations are present, this gene is repressed; not a direct target of SETBP1",Repressed via histone acetylation,,PMID: 30367089,,,,
-Tgfbr3,,Mouse,"When ASXL1 and SETBP1 mutations are present, this gene is repressed; not a direct target of SETBP1",Repressed via histone acetylation,,PMID: 30367089,,,,
-UBR1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-USP48,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-UTP14A,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-VAMP8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-VMP1,ENSG00000062716,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-WDR7,ENSG00000091157,Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); SETBP1 binding in promoter and DEG",Activation/Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; https://www.nature.com/articles/s41467-018-04462-8,,"GTRD Binding Parameter: -1000, +100","Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-WDR75,ENSG00000115368,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-XXbac-B444P24.14,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ZC3H10,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ZC3H15,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ZEB1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Upregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,
-ZEB1-AS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ZFHX4,ENSG00000091656,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-ZFPM2,ENSG00000169946,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-ZFYVE16,ENSG00000039319,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-ZMAT2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ZMYND11,ENSG00000015171,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-ZNF330,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ZNF862,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
-ZNHIT6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; PMID: 27924024,,"GTRD Binding Parameter: -1000, +100",,
-ZSWIM2,ENSG00000163012,Human,SETBP1 binding in promoter and DEG,Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",
-ZZEF1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,
+25416956",,,Interaction Type: physical association; confidence value: 0.56,,NA,NA,NA,NA,NA
+RAD52,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Upregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,,P43351,DNA repair protein RAD52 homolog,Tchem,Other,0.00125282
+RALGAPA1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Upregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,,Q6GYQ0,Ral GTPase-activating protein subunit alpha-1,Tbio,Enzyme,0.11591036
+RAP2A,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P10114,Ras-related protein Rap-2a,Tbio,Enzyme,0.00541101
+RBM20,ENSG00000203867; ENSG00000203867,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Repression/Downregulation; Repression/Downregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q5T481,RNA-binding protein 20,Tbio,Other,0.02126441
+RBM33,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q96EV2,RNA-binding protein 33,Tdark,Other,0.1482404
+RBMS3,ENSG00000144642; ENSG00000144642,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q6XE24,"RNA-binding motif, single-stranded-interacting protein 3",Tbio,Other,0.07024309
+REEP3,ENSG00000165476; ENSG00000165476,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q6NUK4,Receptor expression-enhancing protein 3,Tbio,Other,0.19673119
+RHOBTB3,ENSG00000164292; ENSG00000164292,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,O94955,Rho-related BTB domain-containing protein 3,Tbio,Other,0.09149494
+RIC8A,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9NPQ8,Synembryn-A,Tbio,Other,0.01846696
+RIOK2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9BVS4,Serine/threonine-protein kinase RIO2,Tbio,Kinase,0.02940435
+RNF111,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q6ZNA4,E3 ubiquitin-protein ligase Arkadia,Tbio,Enzyme,0.03059486
+RNF139,,Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD; GTRD,PMID: 27924024; https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Detection method: chromatin,,Q8WU17,E3 ubiquitin-protein ligase RNF139,Tbio,Enzyme,0.05828557
+RNF139-AS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RNF217,ENSG00000146373; ENSG00000146373,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q8TC41,Probable E3 ubiquitin-protein ligase RNF217,Tbio,Enzyme,0.37676903
+RP1-168L15.5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP11-16B13.1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP11-235C23.5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP11-242D8.1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP11-242D8.3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP11-252A24.2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP11-277P12.6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP11-421L21.3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP11-472I20.4,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP11-539L10.3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP11-646I6.5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP11-680H20.2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP11-73M18.2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP11-773H22.4,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP5-1024G6.7,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP5-1103G7.10,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP5-857K21.4,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RP5-912I13.2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+RPIA,ENSG00000153574; ENSG00000153574,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Repression/Downregulation; Repression/Downregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P49247,Ribose-5-phosphate isomerase,Tbio,Enzyme,0.0096870499999999991
+RPS16,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P62249,40S ribosomal protein S16,Tbio,Other,0.00261983
+RPS6KL1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",?Potential relation to phosphorylating rpS6; Increase in RpS6 phosphorylation with in increased SETBP1 dose https://academic.oup.com/hmg/advance-article/doi/10.1093/hmg/ddaf003/7959539,,Q9Y6S9,Ribosomal protein S6 kinase-like 1,Tdark,Kinase,1.17416149
+RUNX1,,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 '...in our human 293 FLP-In model we found a similar downregulation (Supp Fig 11a). ChIP experiments, however, demonstrated only a very weak binding of SETBP1 to the human RUNX1 promoter (Supp Fig 11b), likely due to the expression of SETBP1 being much lower in our model than in traditional high-titer retroviral transduction systems or to differences in species specificity. To test this hypothesis, we repeated ChIP experiments using a transient transfection model, achieving a 4.2- and 6.9-fold increase in SETBP1-WT and G870S expression, respectively, when compared with FLP-In (Supp Fig 11c). Indeed, ChIP experiments performed using transient SETBP1 transfectants showed a significant increase in the binding to RUNX1 promoter (Supp Fig 11d). This, however, was accompanied by an increase in RUNX1 expression (Supp Fig 11e), confirming that SETBP1 promotes upregulation of gene expression and suggesting that RUNX1 downmodulation is not a direct effect of SETBP1.'; Piazza et al. 2018 '...in our human 293 FLP-In model we found a similar downregulation (Supp Fig 11a). ChIP experiments, however, demonstrated only a very weak binding of SETBP1 to the human RUNX1 promoter (Supp Fig 11b), likely due to the expression of SETBP1 being much lower in our model than in traditional high-titer retroviral transduction systems or to differences in species specificity. To test this hypothesis, we repeated ChIP experiments using a transient transfection model, achieving a 4.2- and 6.9-fold increase in SETBP1-WT and G870S expression, respectively, when compared with FLP-In (Supp Fig 11c). Indeed, ChIP experiments performed using transient SETBP1 transfectants showed a significant increase in the binding to RUNX1 promoter (Supp Fig 11d). This, however, was accompanied by an increase in RUNX1 expression (Supp Fig 11e), confirming that SETBP1 promotes upregulation of gene expression and suggesting that RUNX1 downmodulation is not a direct effect of SETBP1.'",,Q01196,Runt-related transcription factor 1,Tbio,Transcription Factor,0.0085181
+Runx1,,Mouse,,Repression,,PMID: 26205084; https://www.nature.com/articles/leu2015200,,,"""Figure 3 Setbp1 directly represses Runx1 transcription.""https://pubmed.ncbi.nlm.nih.gov/26205084/","""Runx1 repression is induced by Setbp1-mediated recruitment of a nucleosome remodeling deacetylase (NuRD) complex to Runx1 promoters and can be reversed by treatment with histone deacetylase (HDAC) inhibitors Entinostat and Vorinostat.""",NA,NA,NA,NA,NA
+SARS2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9NP81,"Serine--tRNA ligase, mitochondrial",Tbio,Enzyme,0.00772323
+SEMA3A,ENSG00000075213; ENSG00000075213,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q14563,Semaphorin-3A,Tbio,Other,0.00167362
+SEMA3D,ENSG00000153993; ENSG00000153993,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,O95025,Semaphorin-3D,Tbio,Other,0.00821843
+SENP8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q96LD8,Sentrin-specific protease 8,Tchem,Enzyme,0.00774396
+SEP15,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+SET,,Human,Protein pregulates activating binding of target,Upregulation,SIGNOR,PMID: 22566606,,SignorScore: 0.492,,,Q01105,Protein SET,Tbio,Other,0.01012327
+SFR1,,Human,"RNA coexpression shows inverse correlation between SETBP1 gene and SFR1; Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Downregulation (coexpression-inferred),GTRD; SigCom LINCS,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100; SigCom LINCS: Down Gene",,,Q86XK3,Swi5-dependent recombination DNA repair protein 1 homolog,Tbio,Other,0.03522725
+SLC31A1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O15431,High affinity copper uptake protein 1,Tbio,Transporter,0.00658529
+SLC38A11,ENSG00000169507; ENSG00000169507,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q08AI6,Putative sodium-coupled neutral amino acid transporter 11,Tdark,Transporter,0.31184686
+SNF8,ENSG00000159210; ENSG00000159210,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q96H20,Vacuolar-sorting protein SNF8,Tbio,Other,0.04841708
+SNORD13,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+SOX2-OT,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+SPAG6,ENSG00000077327; ENSG00000077327,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,O75602,Sperm-associated antigen 6,Tbio,Other,0.01327217
+ST8SIA4,ENSG00000113532; ENSG00000113532,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q92187,"CMP-N-acetylneuraminate-poly-alpha-2,8-sialyltransferase",Tbio,Enzyme,0.00338436
+STK17B,ENSG00000081320; ENSG00000081320,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,O94768,Serine/threonine-protein kinase 17B,Tchem,Kinase,0.0420158
+SUGT1P,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+SUPT5H,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O00267,Transcription elongation factor SPT5,Tbio,Other,0.00775042
+SYDE2,ENSG00000097096; ENSG00000097096,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q5VT97,Rho GTPase-activating protein SYDE2,Tdark,Enzyme,1.77288781
+Set,,Mouse,Protein upregulates activating binding of target,Upregulation,SIGNOR,PMID: 22566608,,SignorScore: 0.492,,,NA,NA,NA,NA,NA
+Smad1,,Mouse,"When ASXL1 and SETBP1 mutations are present, this gene is repressed; not a direct target of SETBP1",Repressed via histone acetylation,,PMID: 30367089,,,,,NA,NA,NA,NA,NA
+Smad3,,Mouse,"When ASXL1 and SETBP1 mutations are present, this gene is repressed; not a direct target of SETBP1",Repressed via histone acetylation,,PMID: 30367089,,,,,NA,NA,NA,NA,NA
+Smad4,,Mouse,"When ASXL1 and SETBP1 mutations are present, this gene is repressed; not a direct target of SETBP1",Repressed via histone acetylation,,PMID: 30367089,,,,,NA,NA,NA,NA,NA
+TAF13,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q15543,Transcription initiation factor TFIID subunit 13,Tbio,Other,0.08566117
+TAF5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q15542,Transcription initiation factor TFIID subunit 5,Tbio,Other,0.05443551
+TANC1,ENSG00000115183; ENSG00000115183,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9C0D5,Protein TANC1,Tdark,Other,0.09147304
+TAZ,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q16635,Tafazzin,Tbio,Other,0.00372301
+TBC1D23,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9NUY8,TBC1 domain family member 23,Tbio,Other,0.18566729
+TBC1D8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O95759,TBC1 domain family member 8,Tdark,Other,0.40162575
+TCEA1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,P23193,Transcription elongation factor A protein 1,Tbio,Other,0.00547888
+TFPI,ENSG00000003436; ENSG00000003436,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,P10646,Tissue factor pathway inhibitor,Tchem,Other,6.0355e-4
+TGDS,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O95455,"dTDP-D-glucose 4,6-dehydratase",Tbio,Enzyme,0.01813871
+TIMM23,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O14925,Mitochondrial import inner membrane translocase subunit Tim23,Tbio,Enzyme,0.06463808
+TIMM23B,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q5SRD1,Putative mitochondrial import inner membrane translocase subunit Tim23B,Tdark,Enzyme,0.20164487
+TMEM177,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q53S58,Transmembrane protein 177,Tdark,Other,2.94456186
+TMTC3,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q6ZXV5,Transmembrane and TPR repeat-containing protein 3,Tbio,Other,0.17411457
+TOMM7,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9P0U1,Mitochondrial import receptor subunit TOM7 homolog,Tbio,Other,0.03885154
+TPD52L1,ENSG00000111907; ENSG00000111907,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q16890,Tumor protein D53,Tbio,Other,0.04828057
+TRAPPC5,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8IUR0,Trafficking protein particle complex subunit 5,Tdark,Other,0.22558077
+TRDMT1,ENSG00000107614; ENSG00000107614,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,O14717,tRNA (cytosine(38)-C(5))-methyltransferase,Tbio,Enzyme,0.00712649
+TRDN,ENSG00000186439; ENSG00000186439,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q13061,Triadin,Tbio,Other,0.00501554
+TSEN2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8NCE0,tRNA-splicing endonuclease subunit Sen2,Tbio,Enzyme,0.04151213
+TTC23,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Upregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,,Q5W5X9,Tetratricopeptide repeat protein 23,Tdark,Other,0.88342635
+TTI2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q6NXR4,TELO2-interacting protein 2,Tdark,Other,0.18394695
+TUBE1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9UJT0,Tubulin epsilon chain,Tbio,Other,0.03897856
+TXNL1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O43396,Thioredoxin-like protein 1,Tbio,Other,0.01151931
+Tgfbr1,,Mouse,"When ASXL1 and SETBP1 mutations are present, this gene is repressed; not a direct target of SETBP1",Repressed via histone acetylation,,PMID: 30367089,,,"""Histone acetylation is associated with active transcription, and it was recently shown that SETBP1 represses Runx1 expression through histone deacetylation20. We therefore examined levels of histone acetylation around the promoter regions of TGFβ pathway genes in c-Kit+ cSAM cells and normal c-Kit+ bone marrow progenitor cells. Consistent with our previous report19, multiple TGFβ pathway genes (Tgfbr1, Tgfbr2, Tgfbr3, Smad1, Smad3, and Smad4) were downregulated, whereas Hox genes (Hoxa9 and Hoxa10) were upregulated in cSAM cells compared with control cells (Fig. 2a,b). "" https://pmc.ncbi.nlm.nih.gov/articles/PMC6203835/",,NA,NA,NA,NA,NA
+Tgfbr2,,Mouse,"When ASXL1 and SETBP1 mutations are present, this gene is repressed; not a direct target of SETBP1",Repressed via histone acetylation,,PMID: 30367089,,,,,NA,NA,NA,NA,NA
+Tgfbr3,,Mouse,"When ASXL1 and SETBP1 mutations are present, this gene is repressed; not a direct target of SETBP1",Repressed via histone acetylation,,PMID: 30367089,,,,,NA,NA,NA,NA,NA
+UBR1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8IWV7,E3 ubiquitin-protein ligase UBR1,Tbio,Enzyme,0.00998888
+USP48,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q86UV5,Ubiquitin carboxyl-terminal hydrolase 48,Tbio,Enzyme,0.10103618
+UTP14A,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9BVJ6,U3 small nucleolar RNA-associated protein 14 homolog A,Tbio,Other,0.06076507
+VAMP8,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9BV40,Vesicle-associated membrane protein 8,Tbio,Other,0.01083228
+VMP1,ENSG00000062716; ENSG00000062716,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q96GC9,Vacuole membrane protein 1,Tbio,Other,0.00997613
+WDR7,ENSG00000091157; ENSG00000091157,Human; Human; Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp); SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG",Activation/Upregulation; Activation/Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,"GTRD Binding Parameter: -1000, +100","Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q9Y4E6,WD repeat-containing protein 7,Tdark,Other,0.00602015
+WDR75,ENSG00000115368; ENSG00000115368,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q8IWA0,WD repeat-containing protein 75,Tbio,Other,0.09443914
+XXbac-B444P24.14,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+ZC3H10,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q96K80,Zinc finger CCCH domain-containing protein 10,Tbio,Other,0.22647282
+ZC3H15,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q8WU90,Zinc finger CCCH domain-containing protein 15,Tbio,Other,0.15630592
+ZEB1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",Upregulation,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",Upregulation - Whitlock paper https://pmc.ncbi.nlm.nih.gov/articles/PMC10760659/,,P37275,Zinc finger E-box-binding homeobox 1,Tbio,Transcription Factor,8.5257e-4
+ZEB1-AS1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,NA,NA,NA,NA,NA
+ZFHX4,ENSG00000091656; ENSG00000091656,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q86UP3,Zinc finger homeobox protein 4,Tbio,Transcription Factor,0.06538087
+ZFPM2,ENSG00000169946; ENSG00000169946,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q8WW38,Zinc finger protein ZFPM2,Tbio,Transcription Factor,0.01019523
+ZFYVE16,ENSG00000039319; ENSG00000039319,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q7Z3T8,Zinc finger FYVE domain-containing protein 16,Tbio,Other,0.10765234
+ZMAT2,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q96NC0,Zinc finger matrin-type protein 2,Tbio,Other,0.16771752
+ZMYND11,ENSG00000015171; ENSG00000015171,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q15326,Zinc finger MYND domain-containing protein 11,Tbio,Epigenetic,0.02485283
+ZNF330,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,Q9Y3S2,Zinc finger protein 330,Tdark,Other,0.32566699
+ZNF862,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O60290,Zinc finger protein 862,Tdark,Other,2.22047603
+ZNHIT6,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html; PMID: 27924024,,"GTRD Binding Parameter: -1000, +100",,,Q9NWK9,Box C/D snoRNA protein 1,Tbio,Other,1.1021845
+ZSWIM2,ENSG00000163012; ENSG00000163012,Human; Human,SETBP1 binding in promoter and DEG; SETBP1 binding in promoter and DEG,Activation/Upregulation; Activation/Upregulation,,https://www.nature.com/articles/s41467-018-04462-8; https://www.nature.com/articles/s41467-018-04462-8,,,"Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'; Piazza et al. 2018 'The intersection between genes bound by SETBP1 in promoter regions and DEGs (FDR<0.001) revealed 105 co-occurring genes (Fig. 2c, Supplementary Data 4).'",,Q8NEG5,E3 ubiquitin-protein ligase ZSWIM2,Tbio,Enzyme,0.02135835
+ZZEF1,,Human,"Genes containing one or more binding sites for UniProt:Q9Y6X0 (SETBP1) in their promoter regions (TSS -1000,+100 bp)",,GTRD,https://www.gsea-msigdb.org/gsea/msigdb/cards/SETBP1_TARGET_GENES.html,,"GTRD Binding Parameter: -1000, +100",,,O43149,Zinc finger ZZ-type and EF-hand domain-containing protein 1,Tdark,Other,0.33216648

From 05d5e2a4ac77199d0f84f09579e15d34259ed3ee Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Tue, 7 Apr 2026 11:19:30 -0500
Subject: [PATCH 08/16] update SETBP1 relevant pathways

---
 .../setbp1_target_pathways.csv                |  35 -----
 .../top_target_coexpression.csv               | 128 +++++++++++++++---
 2 files changed, 112 insertions(+), 51 deletions(-)

diff --git a/results/permutation_analysis/setbp1_target_pathways.csv b/results/permutation_analysis/setbp1_target_pathways.csv
index 7f657b6..71b0dfb 100644
--- a/results/permutation_analysis/setbp1_target_pathways.csv
+++ b/results/permutation_analysis/setbp1_target_pathways.csv
@@ -210,26 +210,6 @@ GO:0003682,EED
 GO:0003682,MLLT10
 GO:0003682,KAT6A
 GO:0003682,PAF1
-GO:0006412,SARS2
-GO:0006412,RPS16
-GO:0006412,EIF4B
-GO:0006412,MRPS12
-GO:0006412,NSUN5
-GO:0006412,ZC3H15
-GO:0006412,ELP3
-GO:0006412,DNAJC1
-GO:0006412,MRPL15
-GO:0006412,CNOT11
-GO:0006412,RNF139
-GO:0006412,EIF3K
-GO:0006412,MRPS16
-GO:0006412,TCEA1
-GO:0006412,MT-TL1
-GO:0006412,MT-TF
-GO:0006412,MT-TT
-GO:0006412,MCTS1
-GO:0006412,EEF1G
-GO:0006412,EIF3D
 GO:0051896,HAX1
 GO:0051896,PDGFC
 GO:0051896,PTPN13
@@ -303,21 +283,6 @@ GO:0010564,E4F1
 GO:0010564,PTEN
 GO:0010564,ANAPC7
 GO:0010564,PAF1
-GO:0044772,BRCA1
-GO:0044772,CDKN1B
-GO:0044772,TPD52L1
-GO:0044772,CDKN2C
-GO:0044772,CDKN1A
-GO:0044772,CCNH
-GO:0044772,CDKN2B
-GO:0044772,CDKN2A
-GO:0044772,CHEK1
-GO:0044772,CACUL1
-GO:0044772,RIOK2
-GO:0044772,PBRM1
-GO:0044772,PTEN
-GO:0044772,PHF8
-GO:0044772,ANAPC7
 GO:0007179,CDKN2B
 GO:0007179,ZEB1
 GO:0007179,RNF111
diff --git a/results/permutation_analysis/top_target_coexpression.csv b/results/permutation_analysis/top_target_coexpression.csv
index 8b00193..acaff22 100644
--- a/results/permutation_analysis/top_target_coexpression.csv
+++ b/results/permutation_analysis/top_target_coexpression.csv
@@ -1,35 +1,131 @@
 Target_Gene,Spearman_Rho,P_Value,FDR,Method
+RNF217,0.840891425714916,0,0,GTEx_Coexpr
 MYO9A,0.8390821820084338,0,0,GTEx_Coexpr
 UBR1,0.8236870308086461,0,0,GTEx_Coexpr
+MLLT10,0.8230857009832709,0,0,GTEx_Coexpr
 EPC2,0.816869184030563,0,0,GTEx_Coexpr
 RALGAPA1,0.8104387281195069,0,0,GTEx_Coexpr
 DCAF8,0.8012994667679644,0,0,GTEx_Coexpr
+PITRM1,0.8009589013448437,0,0,GTEx_Coexpr
 PBRM1,0.7847282679214185,0,0,GTEx_Coexpr
 IPO8,0.7796582882643719,0,0,GTEx_Coexpr
+ATP9B,0.7726039181088198,0,0,GTEx_Coexpr
+ZFPM2,0.7724182273098258,0,0,GTEx_Coexpr
 TBC1D23,0.7715737178414818,0,0,GTEx_Coexpr
 ESYT1,0.7715601969412416,0,0,GTEx_Coexpr
+EPC1,0.7693798677668975,0,0,GTEx_Coexpr
+CCDC50,0.7688489620428584,0,0,GTEx_Coexpr
 KAT7,0.7687530389441259,0,0,GTEx_Coexpr
 KMT2A,0.7670202217905395,0,0,GTEx_Coexpr
 ZEB1,0.7619917916837197,0,0,GTEx_Coexpr
+INO80D,0.7593816752528586,0,0,GTEx_Coexpr
 GGCX,0.756490182916181,0,0,GTEx_Coexpr
 TTC23,0.7507166573294056,0,0,GTEx_Coexpr
+BMPR2,0.7474918810945999,0,0,GTEx_Coexpr
 CWF19L2,0.7391402818207754,0,0,GTEx_Coexpr
+BMI1,0.7379064473392568,0,0,GTEx_Coexpr
 ZZEF1,0.7379008632291393,0,0,GTEx_Coexpr
 CHERP,0.7344391458096833,0,0,GTEx_Coexpr
+REEP3,0.7286550009563179,0,0,GTEx_Coexpr
+COL5A2,0.7284376040921356,0,0,GTEx_Coexpr
 NBR1,0.7245617593047815,0,0,GTEx_Coexpr
-PBRM1,0.8996528291815317,5.193292567810596e-190,9.659524176127708e-188,Brainspan_Coexpr
-EPC2,0.8762826658548637,1.1355972204798998e-167,1.0561054150463067e-165,Brainspan_Coexpr
-KAT6A,0.8672590603243179,3.1127564134570265e-160,1.9299089763433566e-158,Brainspan_Coexpr
-EPHA7,0.8350026342237999,1.554269060737794e-137,7.227351132430745e-136,Brainspan_Coexpr
-CHERP,0.8332364869232324,1.9505681581718096e-136,7.256113548399131e-135,Brainspan_Coexpr
-LEO1,0.8284393994049094,1.6228175973952227e-133,5.030734551925189e-132,Brainspan_Coexpr
-NCOA5,0.8238664195116253,8.140169847519039e-131,2.162959416626488e-129,Brainspan_Coexpr
-EPRS,0.8214159148107448,2.1167805269964606e-129,4.921514725266771e-128,Brainspan_Coexpr
-TAF5,0.807397303118699,1.0549756973773712e-121,2.1802831079132336e-120,Brainspan_Coexpr
-COX4I1,-0.7988146566553582,2.6920388850845556e-117,5.0071923262572733e-116,Brainspan_Coexpr
-DIEXF,0.795646457085308,1.0071212605623211e-115,1.7029504951326522e-114,Brainspan_Coexpr
-RP11-277P12.6,-0.7931057016452419,1.756225695962438e-114,2.7221498287417787e-113,Brainspan_Coexpr
-ETFDH,-0.7918503891857853,7.104770329187421e-114,1.0165286778683539e-112,Brainspan_Coexpr
-EIF4B,0.7879218750977395,5.300302652475869e-112,7.041830666860798e-111,Brainspan_Coexpr
-ANP32A,0.7743391348044478,8.017808306260882e-106,9.942082299763495e-105,Brainspan_Coexpr
-KLHDC9,-0.7738174402772361,1.357569109536665e-105,1.578174089836373e-104,Brainspan_Coexpr
+TMTC3,0.7226914832831698,0,0,GTEx_Coexpr
+RBMS3,0.720715773126173,0,0,GTEx_Coexpr
+ZMYND11,0.7199296437460875,0,0,GTEx_Coexpr
+TIMM23B,0.7181462446481214,0,0,GTEx_Coexpr
+ZC3H10,0.7180324747959462,0,0,GTEx_Coexpr
+CDK8,0.7159809072200963,0,0,GTEx_Coexpr
+ARID5B,0.7138676651009463,0,0,GTEx_Coexpr
+RAD52,0.7136436441109464,0,0,GTEx_Coexpr
+BPTF,0.7115373235084295,0,0,GTEx_Coexpr
+ACTA2,0.71144787918701,0,0,GTEx_Coexpr
+NUDT9,0.7083930145296485,0,0,GTEx_Coexpr
+NAALADL2,0.7049563171171831,0,0,GTEx_Coexpr
+BAG5,0.7049074964618852,0,0,GTEx_Coexpr
+PDPR,0.7021572429222492,0,0,GTEx_Coexpr
+FAF1,0.697608819191427,0,0,GTEx_Coexpr
+RIOK2,0.6971399082050161,0,0,GTEx_Coexpr
+TANC1,0.6970615667419872,0,0,GTEx_Coexpr
+MBNL1,0.6954854270496389,0,0,GTEx_Coexpr
+CEP44,0.6942782495488128,0,0,GTEx_Coexpr
+JMJD1C,0.6920506583096422,0,0,GTEx_Coexpr
+PPP3CC,0.6910649104120933,0,0,GTEx_Coexpr
+PARG,0.6898706050987761,0,0,GTEx_Coexpr
+WDR75,0.6845241005777399,0,0,GTEx_Coexpr
+BET1L,0.6841960228971125,0,0,GTEx_Coexpr
+FRZB,0.6836835073553298,0,0,GTEx_Coexpr
+SUPT5H,0.6834033866980204,0,0,GTEx_Coexpr
+PKN2,0.6827336547886925,0,0,GTEx_Coexpr
+E4F1,0.6802659037190822,0,0,GTEx_Coexpr
+FBXO8,0.6779230817658755,0,0,GTEx_Coexpr
+CHD2,0.6747043484877061,0,0,GTEx_Coexpr
+UTP14A,0.6716843489426706,0,0,GTEx_Coexpr
+RNF139,0.6707941030803772,0,0,GTEx_Coexpr
+TFPI,0.6707791054807377,0,0,GTEx_Coexpr
+EIF4B,0.670426056616079,0,0,GTEx_Coexpr
+NAA30,0.6684199360192891,0,0,GTEx_Coexpr
+USP48,0.6664224211523371,0,0,GTEx_Coexpr
+AFF1,0.6650660374207301,0,0,GTEx_Coexpr
+PHF8,0.6645806548466711,0,0,GTEx_Coexpr
+PBRM1,0.8996528291815317,5.193292567810596e-190,1.4697017966903987e-187,Brainspan_Coexpr
+EPC2,0.8762826658548637,1.1355972204798998e-167,1.606870066979058e-165,Brainspan_Coexpr
+EPC1,0.87202904141237,4.2832205362191945e-164,4.0405047058334403e-162,Brainspan_Coexpr
+KAT6A,0.8672590603243179,3.1127564134570265e-160,2.2022751625208465e-158,Brainspan_Coexpr
+EPHA7,0.8350026342237999,1.554269060737794e-137,8.797162883775917e-136,Brainspan_Coexpr
+CHERP,0.8332364869232324,1.9505681581718096e-136,9.200179812710367e-135,Brainspan_Coexpr
+JMJD1C,0.829780708979109,2.529303147305518e-134,1.0225611295535167e-132,Brainspan_Coexpr
+LEO1,0.8284393994049094,1.6228175973952227e-133,5.740717250785599e-132,Brainspan_Coexpr
+NCOA5,0.8238664195116253,8.140169847519039e-131,2.559631185386542e-129,Brainspan_Coexpr
+EPRS,0.8214159148107448,2.1167805269964606e-129,5.990488891399984e-128,Brainspan_Coexpr
+SEMA3A,0.8106506754849587,1.9693470866781127e-123,5.066592959362779e-122,Brainspan_Coexpr
+BPTF,0.8101252108567508,3.76554009118376e-123,8.880398715041698e-122,Brainspan_Coexpr
+TAF5,0.807397303118699,1.0549756973773712e-121,2.296600941213816e-120,Brainspan_Coexpr
+COX4I1,-0.7988146566553582,2.6920388850845556e-117,5.441764317706638e-116,Brainspan_Coexpr
+DIEXF,0.795646457085308,1.0071212605623211e-115,1.9001021115942462e-114,Brainspan_Coexpr
+RP11-277P12.6,-0.7931057016452419,1.756225695962438e-114,3.1063241997335616e-113,Brainspan_Coexpr
+ETFDH,-0.7918503891857853,7.104770329187421e-114,1.1827352959764944e-112,Brainspan_Coexpr
+INO80D,0.79156456230413,9.75366087700904e-114,1.5334922378853102e-112,Brainspan_Coexpr
+MLLT10,0.7882284696752022,3.7982391608918364e-112,5.657377276486262e-111,Brainspan_Coexpr
+EIF4B,0.7879218750977395,5.300302652475869e-112,7.499928253253356e-111,Brainspan_Coexpr
+ANP32A,0.7743391348044478,8.017808306260882e-106,1.080495119367538e-104,Brainspan_Coexpr
+KLHDC9,-0.7738174402772361,1.357569109536665e-105,1.7463275363585282e-104,Brainspan_Coexpr
+TPD52L1,-0.7610120031654475,3.639392048656096e-100,4.478034564215978e-99,Brainspan_Coexpr
+C4orf46,0.7566507294757406,2.1494242026551718e-98,2.5345293722975565e-97,Brainspan_Coexpr
+MTND5P11,-0.7551099905913948,8.894982566998288e-98,1.0069120265842063e-96,Brainspan_Coexpr
+ARRDC3,0.75204705676295,1.4515814087778164e-96,1.5799905334004696e-95,Brainspan_Coexpr
+RPIA,0.7517068502119513,1.9744314367952134e-96,2.0694966541223903e-95,Brainspan_Coexpr
+CCDC50,0.7499507705524081,9.58571355793698e-96,9.688417631772018e-95,Brainspan_Coexpr
+ARL5B,0.7492345769624533,1.819002104942758e-95,1.7750951575820706e-94,Brainspan_Coexpr
+PDE4D,0.7469482121224126,1.3857857781923623e-94,1.3072579174281282e-93,Brainspan_Coexpr
+UTP14A,0.7407309978711025,3.107612509634212e-92,2.836949484601555e-91,Brainspan_Coexpr
+C4orf36,-0.7385191702621436,2.0534979010351325e-91,1.8160622062279454e-90,Brainspan_Coexpr
+KLHL1,0.7282073266595911,1.067768227684585e-87,9.15692146771932e-87,Brainspan_Coexpr
+FAF1,0.7270254028953836,2.776396577490415e-87,2.3109418571464344e-86,Brainspan_Coexpr
+MED29,-0.7267797769349299,3.384179617567856e-87,2.7134059890128766e-86,Brainspan_Coexpr
+CDK8,0.7267552560410849,3.451682530193058e-87,2.7134059890128766e-86,Brainspan_Coexpr
+MGAT2,0.724337445865331,2.3945140996815147e-86,1.8314797032699149e-85,Brainspan_Coexpr
+NSUN6,0.7221188053987667,1.390728602196525e-85,1.0357268274253071e-84,Brainspan_Coexpr
+NEBL,-0.7212387221611747,2.781341420442779e-85,2.0182554409879655e-84,Brainspan_Coexpr
+CHD2,0.7199546280059466,7.609774448730088e-85,5.383915422476537e-84,Brainspan_Coexpr
+SET,0.7193114966711217,1.2571274056587338e-84,8.677245263449308e-84,Brainspan_Coexpr
+ASB7,0.7172030334180581,6.454081713678158e-84,4.3488217261212345e-83,Brainspan_Coexpr
+TAF13,-0.7166272928391065,1.0062464156349854e-83,6.622505479644205e-83,Brainspan_Coexpr
+EIF3D,0.7060276777504164,2.94843652392418e-80,1.8963807642512335e-79,Brainspan_Coexpr
+ST8SIA4,0.7024050639483449,4.1604938794666977e-79,2.6164883730868347e-78,Brainspan_Coexpr
+CTNNBL1,0.6997359833691623,2.8511815086808275e-78,1.7540964499058134e-77,Brainspan_Coexpr
+RNF111,0.6964448457122839,2.9718333970820386e-77,1.7894230880302487e-76,Brainspan_Coexpr
+ZC3H10,0.6950595820188451,7.895542075076033e-77,4.655080015096911e-76,Brainspan_Coexpr
+CDKN2B,-0.6943851114360652,1.2680092026490292e-76,7.323400088768884e-76,Brainspan_Coexpr
+CSRNP3,0.6921310032923886,6.117808962340094e-76,3.462679872684494e-75,Brainspan_Coexpr
+SOX2-OT,-0.6899719135680192,2.7250559448783583e-75,1.5121388870599516e-74,Brainspan_Coexpr
+ACTA2,-0.6871438371445668,1.8905956255154546e-74,1.0289203115786032e-73,Brainspan_Coexpr
+MIR4461,-0.6854989312355636,5.77388982814577e-74,3.083039285594817e-73,Brainspan_Coexpr
+DNAJC19,-0.6838761361243224,1.7245614069128133e-73,9.037979225117153e-73,Brainspan_Coexpr
+WDR75,0.6793497792911042,3.514937285352324e-72,1.8085950031903776e-71,Brainspan_Coexpr
+GNL3,0.6793224226476309,3.5789750460865523e-72,1.8086606036473113e-71,Brainspan_Coexpr
+DNAJC12,-0.6772208819598365,1.4241936218958036e-71,7.070996403447585e-71,Brainspan_Coexpr
+ZZEF1,0.6641655910974141,5.895870184580735e-68,2.8767780383385313e-67,Brainspan_Coexpr
+VAMP8,-0.6637569095333314,7.600243107522766e-68,3.645540338015157e-67,Brainspan_Coexpr
+SLC38A11,-0.6628154127749565,1.3621381232645518e-67,6.424751481397803e-67,Brainspan_Coexpr
+KLRC2,-0.6598509159233871,8.435331365720325e-67,3.9134406172112334e-66,Brainspan_Coexpr
+TRDMT1,0.6567367331066833,5.601661177386085e-66,2.556887279355261e-65,Brainspan_Coexpr

From 00c91e933ba420a47a08f90a91435decf717a91a Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Tue, 7 Apr 2026 11:20:47 -0500
Subject: [PATCH 09/16] filter prioritized targets by PHAROS druggability level
 and updated SETBP1 pathways

---
 .../setbp1_targets_prioritized.csv            | 560 ++----------------
 .../04_prioritize_targets.R                   |  45 +-
 2 files changed, 72 insertions(+), 533 deletions(-)

diff --git a/results/permutation_analysis/setbp1_targets_prioritized.csv b/results/permutation_analysis/setbp1_targets_prioritized.csv
index 83a94f7..f581a27 100644
--- a/results/permutation_analysis/setbp1_targets_prioritized.csv
+++ b/results/permutation_analysis/setbp1_targets_prioritized.csv
@@ -1,522 +1,38 @@
-Target_Gene,Method
-MYO9A,GTEx_Coexpr
-UBR1,GTEx_Coexpr
-EPC2,GTEx_Coexpr
-RALGAPA1,GTEx_Coexpr
-DCAF8,GTEx_Coexpr
-PBRM1,GTEx_Coexpr
-IPO8,GTEx_Coexpr
-TBC1D23,GTEx_Coexpr
-ESYT1,GTEx_Coexpr
-KAT7,GTEx_Coexpr
-KMT2A,GTEx_Coexpr
-ZEB1,GTEx_Coexpr
-GGCX,GTEx_Coexpr
-TTC23,GTEx_Coexpr
-CWF19L2,GTEx_Coexpr
-ZZEF1,GTEx_Coexpr
-CHERP,GTEx_Coexpr
-NBR1,GTEx_Coexpr
-SARS2,GO:0010467
-RPS16,GO:0010467
-ZMYND11,GO:0010467
-ZNF862,GO:0010467
-TRDMT1,GO:0010467
-ACTA2,GO:0010467
-PITRM1,GO:0010467
-HGF,GO:0010467
-CDKN1B,GO:0010467
-BMP5,GO:0010467
-PDE4D,GO:0010467
-INO80D,GO:0010467
-NDUFAB1,GO:0010467
-WDR75,GO:0010467
-NFE2L2,GO:0010467
-ZNHIT6,GO:0010467
-KMT2A,GO:0010467
-SET,GO:0010467
-EPC1,GO:0010467
-BAZ2B,GO:0010467
-NCOA5,GO:0010467
-CDKN1A,GO:0010467
-HDAC9,GO:0010467
-FOXP2,GO:0010467
-MRPS12,GO:0010467
-NSUN5,GO:0010467
-CTNNBL1,GO:0010467
-CDK8,GO:0010467
-ELP3,GO:0010467
-CCNH,GO:0010467
-ZC3H10,GO:0010467
-EPC2,GO:0010467
-KAT7,GO:0010467
-DNAJC1,GO:0010467
-RIOK2,GO:0010467
-MRPL15,GO:0010467
-FGF5,GO:0010467
-BMPR1B,GO:0010467
-NAA30,GO:0010467
-EIF4B,GO:0010467
-MED29,GO:0010467
-PRKACB,GO:0010467
-PIGK,GO:0010467
-HAX1,GO:0010467
-MEIS1,GO:0010467
-RBMS3,GO:0010467
-ZMAT2,GO:0010467
-ABT1,GO:0010467
-CDKN2A,GO:0010467
-ZEB1,GO:0010467
-TAF5,GO:0010467
-CHEK1,GO:0010467
-ARID5B,GO:0010467
-ZC3H15,GO:0010467
-ANK3,GO:0010467
-CWF19L2,GO:0010467
-MBNL1,GO:0010467
-HS2ST1,GO:0010467
-TSEN2,GO:0010467
-SFR1,GO:0010467
-UTP14A,GO:0010467
-CNOT11,GO:0010467
-SNF8,GO:0010467
-RUNX1,GO:0010467
-DPY30,GO:0010467
-GNL3,GO:0010467
-PBRM1,GO:0010467
-PITX2,GO:0010467
-NOL6,GO:0010467
-BAG5,GO:0010467
-LEO1,GO:0010467
-E4F1,GO:0010467
-BMI1,GO:0010467
-ZFPM2,GO:0010467
-RNF139,GO:0010467
-BPTF,GO:0010467
-PTEN,GO:0010467
-JMJD1C,GO:0010467
-AFF1,GO:0010467
-PAF1,GO:0010467
-PHF8,GO:0010467
-PTGS2,GO:0010467
-CHD2,GO:0010467
-EED,GO:0010467
-NR2F1,GO:0010467
-ERBB4,GO:0010467
-CSRNP3,GO:0010467
-EIF3K,GO:0010467
-ALX1,GO:0010467
-MRPS16,GO:0010467
-RBM33,GO:0010467
-HOXA9,GO:0010467
-MLLT10,GO:0010467
-TCEA1,GO:0010467
-LIN28B,GO:0010467
-SUPT5H,GO:0010467
-MEF2C,GO:0010467
-DDI2,GO:0010467
-PTPRC,GO:0010467
-TAF13,GO:0010467
-CEP290,GO:0010467
-KAT6A,GO:0010467
-MECOM,GO:0010467
-CHERP,GO:0010467
-RBM20,GO:0010467
-BMPR2,GO:0010467
-DNAJC19,GO:0010467
-ZFHX4,GO:0010467
-MT-TL1,GO:0010467
-MT-TF,GO:0010467
-MT-TT,GO:0010467
-DENND1B,GO:0010467
-MCTS1,GO:0010467
-MZF1,GO:0010467
-SNORD13,GO:0010467
-NSUN6,GO:0010467
-HOXA10,GO:0010467
-EEF1G,GO:0010467
-EIF3D,GO:0010467
-HM13,GO:0010467
-PPP5C,GO:0010467
-NDFIP2,GO:0010467
-BRCA1,GO:0010467
-MED29,GO:0051254
-ABT1,GO:0051254
-CDKN2A,GO:0051254
-ZEB1,GO:0051254
-TAF5,GO:0051254
-ARID5B,GO:0051254
-SFR1,GO:0051254
-CNOT11,GO:0051254
-RUNX1,GO:0051254
-GNL3,GO:0051254
-PITX2,GO:0051254
-LEO1,GO:0051254
-E4F1,GO:0051254
-ZFPM2,GO:0051254
-BPTF,GO:0051254
-PHF8,GO:0051254
-NR2F1,GO:0051254
-ERBB4,GO:0051254
-CSRNP3,GO:0051254
-ALX1,GO:0051254
-TCEA1,GO:0051254
-LIN28B,GO:0051254
-SUPT5H,GO:0051254
-TAF13,GO:0051254
-CEP290,GO:0051254
-BMPR2,GO:0051254
-HOXA10,GO:0051254
-HOXA9,GO:0051254
-PAF1,GO:0051254
-MLLT10,GO:0051254
-MEF2C,GO:0051254
-KAT6A,GO:0051254
-MECOM,GO:0051254
-MZF1,GO:0051254
-BRCA1,GO:0051254
-BMP5,GO:0051254
-HGF,GO:0051254
-INO80D,GO:0051254
-WDR75,GO:0051254
-NFE2L2,GO:0051254
-KMT2A,GO:0051254
-EPC1,GO:0051254
-CDK8,GO:0051254
-EPC2,GO:0051254
-KAT7,GO:0051254
-BMPR1B,GO:0051254
-RIOK2,GO:0051254
-HAX1,GO:0051254
-MEIS1,GO:0051254
-BRCA1,GO:0006325
-ZMYND11,GO:0006325
-INO80D,GO:0006325
-KMT2A,GO:0006325
-HDAC9,GO:0006325
-SET,GO:0006325
-EPC1,GO:0006325
-BAZ2B,GO:0006325
-EPC2,GO:0006325
-KAT7,GO:0006325
-CHEK1,GO:0006325
-DPY30,GO:0006325
-PBRM1,GO:0006325
-BMI1,GO:0006325
-BPTF,GO:0006325
-JMJD1C,GO:0006325
-PHF8,GO:0006325
-CHD2,GO:0006325
-EED,GO:0006325
-ZZEF1,GO:0006325
-SUPT5H,GO:0006325
-KAT6A,GO:0006325
-MECOM,GO:0006325
-KMT2A,GO:0003682
-SET,GO:0003682
-NCOA5,GO:0003682
-KAT7,GO:0003682
-MEIS1,GO:0003682
-ZEB1,GO:0003682
-PBRM1,GO:0003682
-BMI1,GO:0003682
-JMJD1C,GO:0003682
-PHF8,GO:0003682
-CHD2,GO:0003682
-SUPT5H,GO:0003682
-EED,GO:0003682
-MLLT10,GO:0003682
-KAT6A,GO:0003682
-PAF1,GO:0003682
-SARS2,GO:0006412
-RPS16,GO:0006412
-EIF4B,GO:0006412
-MRPS12,GO:0006412
-NSUN5,GO:0006412
-ZC3H15,GO:0006412
-ELP3,GO:0006412
-DNAJC1,GO:0006412
-MRPL15,GO:0006412
-CNOT11,GO:0006412
-RNF139,GO:0006412
-EIF3K,GO:0006412
-MRPS16,GO:0006412
-TCEA1,GO:0006412
-MT-TL1,GO:0006412
-MT-TF,GO:0006412
-MT-TT,GO:0006412
-MCTS1,GO:0006412
-EEF1G,GO:0006412
-EIF3D,GO:0006412
-HAX1,GO:0051896
-PDGFC,GO:0051896
-PTPN13,GO:0051896
-PTEN,GO:0051896
-ERBB4,GO:0051896
-HGF,GO:0051896
-PPP3CC,GO:0035556
-CDKN1A,GO:0035556
-RAP2A,GO:0035556
-TTI2,GO:0035556
-CLEC16A,GO:0035556
-EPHA7,GO:0035556
-KAT7,GO:0035556
-FGF5,GO:0035556
-ANP32A,GO:0035556
-PRKACB,GO:0035556
-HAX1,GO:0035556
-PDGFC,GO:0035556
-GDI2,GO:0035556
-CDKN2A,GO:0035556
-CHEK1,GO:0035556
-PKN2,GO:0035556
-UBR1,GO:0035556
-PTPN13,GO:0035556
-IFT122,GO:0035556
-MYO9A,GO:0035556
-FBXO8,GO:0035556
-BAG5,GO:0035556
-PTEN,GO:0035556
-RALGAPA1,GO:0035556
-NR2F1,GO:0035556
-ERBB4,GO:0035556
-ASB7,GO:0035556
-NBR1,GO:0035556
-PTGS2,GO:0035556
-BMPR2,GO:0035556
-SEMA3A,GO:0035556
-MEF2C,GO:0035556
-PTPRC,GO:0035556
-STK17B,GO:0035556
-KAT6A,GO:0035556
-MECOM,GO:0035556
-CHERP,GO:0035556
-SYDE2,GO:0035556
-NDFIP2,GO:0035556
-PPP5C,GO:0035556
-MAP4K1,GO:0035556
-BRCA1,GO:0035556
-FKTN,GO:0035556
-ACTA2,GO:0035556
-ZMYND11,GO:0035556
-TPD52L1,GO:0035556
-BMP5,GO:0035556
-ARRDC3,GO:0035556
-PDE4D,GO:0035556
-HGF,GO:0035556
-NFE2L2,GO:0035556
-BRCA1,GO:0010564
-CDKN1B,GO:0010564
-CDKN2C,GO:0010564
-CDKN1A,GO:0010564
-TTI2,GO:0010564
-CCNH,GO:0010564
-CDKN2B,GO:0010564
-CDKN2A,GO:0010564
-CHEK1,GO:0010564
-RIOK2,GO:0010564
-PBRM1,GO:0010564
-PKN2,GO:0010564
-E4F1,GO:0010564
-PTEN,GO:0010564
-ANAPC7,GO:0010564
-PAF1,GO:0010564
-BRCA1,GO:0044772
-CDKN1B,GO:0044772
-TPD52L1,GO:0044772
-CDKN2C,GO:0044772
-CDKN1A,GO:0044772
-CCNH,GO:0044772
-CDKN2B,GO:0044772
-CDKN2A,GO:0044772
-CHEK1,GO:0044772
-CACUL1,GO:0044772
-RIOK2,GO:0044772
-PBRM1,GO:0044772
-PTEN,GO:0044772
-PHF8,GO:0044772
-ANAPC7,GO:0044772
-CDKN2B,GO:0007179
-ZEB1,GO:0007179
-RNF111,GO:0007179
-EPHA7,GO:0007416
-PTPN13,GO:0007416
-PTEN,GO:0007416
-ERBB4,GO:0007416
-MEF2C,GO:0007416
-RAP2A,GO:0007416
-NFE2L2,GO:0043043
-AASDH,GO:0043043
-NDFIP2,GO:0009059
-PPP5C,GO:0009059
-BRCA1,GO:0009059
-SARS2,GO:0009059
-RPS16,GO:0009059
-ZNF862,GO:0009059
-FKTN,GO:0009059
-ZMYND11,GO:0009059
-TRDMT1,GO:0009059
-ACTA2,GO:0009059
-PITRM1,GO:0009059
-HGF,GO:0009059
-CDKN1B,GO:0009059
-BMP5,GO:0009059
-PDE4D,GO:0009059
-ST8SIA4,GO:0009059
-INO80D,GO:0009059
-WDR75,GO:0009059
-NFE2L2,GO:0009059
-NDUFAB1,GO:0009059
-ZNHIT6,GO:0009059
-KMT2A,GO:0009059
-SET,GO:0009059
-EPC1,GO:0009059
-BAZ2B,GO:0009059
-NCOA5,GO:0009059
-CDKN1A,GO:0009059
-HDAC9,GO:0009059
-FOXP2,GO:0009059
-MRPS12,GO:0009059
-NSUN5,GO:0009059
-CTNNBL1,GO:0009059
-CDK8,GO:0009059
-ELP3,GO:0009059
-CCNH,GO:0009059
-ZC3H10,GO:0009059
-EPC2,GO:0009059
-KAT7,GO:0009059
-DNAJC1,GO:0009059
-MRPL15,GO:0009059
-RIOK2,GO:0009059
-FGF5,GO:0009059
-BMPR1B,GO:0009059
-TMTC3,GO:0009059
-NAA30,GO:0009059
-EIF4B,GO:0009059
-PRKACB,GO:0009059
-PIGK,GO:0009059
-MED29,GO:0009059
-HAX1,GO:0009059
-MEIS1,GO:0009059
-RBMS3,GO:0009059
-ZMAT2,GO:0009059
-ABT1,GO:0009059
-GOLGA7,GO:0009059
-CDKN2A,GO:0009059
-ZEB1,GO:0009059
-TAF5,GO:0009059
-CHEK1,GO:0009059
-ARID5B,GO:0009059
-ANK3,GO:0009059
-ZC3H15,GO:0009059
-CWF19L2,GO:0009059
-MBNL1,GO:0009059
-HS2ST1,GO:0009059
-TSEN2,GO:0009059
-SFR1,GO:0009059
-UTP14A,GO:0009059
-CNOT11,GO:0009059
-SNF8,GO:0009059
-RUNX1,GO:0009059
-DPY30,GO:0009059
-GNL3,GO:0009059
-PBRM1,GO:0009059
-PITX2,GO:0009059
-NOL6,GO:0009059
-BAG5,GO:0009059
-LEO1,GO:0009059
-E4F1,GO:0009059
-MGAT2,GO:0009059
-BMI1,GO:0009059
-ZFPM2,GO:0009059
-RNF139,GO:0009059
-BPTF,GO:0009059
-PTEN,GO:0009059
-JMJD1C,GO:0009059
-PAF1,GO:0009059
-AFF1,GO:0009059
-PTGS2,GO:0009059
-PHF8,GO:0009059
-CHD2,GO:0009059
-EED,GO:0009059
-NR2F1,GO:0009059
-ERBB4,GO:0009059
-CSRNP3,GO:0009059
-EIF3K,GO:0009059
-ALX1,GO:0009059
-MRPS16,GO:0009059
-RBM33,GO:0009059
-HOXA9,GO:0009059
-MLLT10,GO:0009059
-TCEA1,GO:0009059
-LIN28B,GO:0009059
-SUPT5H,GO:0009059
-MEF2C,GO:0009059
-PTPRC,GO:0009059
-DDI2,GO:0009059
-TAF13,GO:0009059
-CEP290,GO:0009059
-KAT6A,GO:0009059
-MECOM,GO:0009059
-CHERP,GO:0009059
-RBM20,GO:0009059
-BMPR2,GO:0009059
-DNAJC19,GO:0009059
-MT-TL1,GO:0009059
-ZFHX4,GO:0009059
-MT-TF,GO:0009059
-MT-TT,GO:0009059
-DENND1B,GO:0009059
-MCTS1,GO:0009059
-MZF1,GO:0009059
-SNORD13,GO:0009059
-NSUN6,GO:0009059
-HOXA10,GO:0009059
-EEF1G,GO:0009059
-EIF3D,GO:0009059
-HM13,GO:0009059
-DLAT,GO:0005739
-RPIA,GO:0005739
-PDSS2,GO:0005739
-NDUFAB1,GO:0005739
-NOL6,GO:0005739
-BAG5,GO:0005739
-NDUFS5,GO:0005739
-NUDT9,GO:0005739
-ETFDH,GO:0005739
-METAP1D,GO:0005739
-ERBB4,GO:0005739
-MRPS16,GO:0005739
-NBR1,GO:0005739
-TOMM7,GO:0005739
-MT-ND6,GO:0005739
-MT-ND1,GO:0005739
-TIMM23B,GO:0005739
-DNAJC19,GO:0005739
-PARG,GO:0005739
-TIMM23,GO:0005739
-CRLS1,GO:0005739
-USP48,GO:0005739
-PDPR,GO:0005739
-NDFIP2,GO:0005739
-SARS2,GO:0005739
-PITRM1,GO:0005739
-PPP3CC,GO:0005739
-MRPS12,GO:0005739
-COX4I1,GO:0005739
-DCAF8,GO:0005739
-MRPL15,GO:0005739
-PSMB6,GO:0005739
-HAX1,GO:0005739
-TMEM177,GO:0005739
-MPC1,GO:0005739
-CDKN2A,GO:0005739
-HGF,GO:0007005
-CDKN2A,GO:0007005
-NDUFS5,GO:0007005
-ERBB4,GO:0007005
-TOMM7,GO:0007005
-MT-ND6,GO:0007005
-MT-ND1,GO:0007005
-NEURL4,GO:0007005
-NDUFAB1,GO:0007005
+Target_Gene,Method,Spearman_Rho,GO_Term
+BAZ2B,GO:0010467; GO:0006325; GO:0009059,,Gene_expression; Chromatin_organization; Macromolecule_biosynthetic_process
+BMPR1B,GO:0010467; GO:0051254; GO:0009059,,Gene_expression; Positive_regulation_RNA_metabolic_process; Macromolecule_biosynthetic_process
+BMPR2,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0035556; GO:0009059,0.7474918810946,Gene_expression; Positive_regulation_RNA_metabolic_process; Intracellular signal transduction; Macromolecule_biosynthetic_process
+BPTF,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0009059,0.711537323508429; 0.810125210856751,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Macromolecule_biosynthetic_process
+BRCA1,GO:0010467; GO:0051254; GO:0006325; GO:0035556; GO:0010564; GO:0009059,,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Intracellular signal transduction; Regulation of cell cycle process; Macromolecule_biosynthetic_process
+CDK8,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0051254; GO:0009059,0.715980907220096; 0.726755256041085,Gene_expression; Positive_regulation_RNA_metabolic_process; Macromolecule_biosynthetic_process
+CDKN1A,GO:0010467; GO:0035556; GO:0010564; GO:0009059,,Gene_expression; Intracellular signal transduction; Regulation of cell cycle process; Macromolecule_biosynthetic_process
+CHEK1,GO:0010467; GO:0006325; GO:0035556; GO:0010564; GO:0009059,,Gene_expression; Chromatin_organization; Intracellular signal transduction; Regulation of cell cycle process; Macromolecule_biosynthetic_process
+EED,GO:0010467; GO:0006325; GO:0003682; GO:0009059,,Gene_expression; Chromatin_organization; Chromatin_binding; Macromolecule_biosynthetic_process
+EPHA7,Brainspan_Coexpr; GO:0035556; GO:0007416,0.8350026342238,Intracellular signal transduction; Synapse_assembly
+EPRS,Brainspan_Coexpr,0.821415914810745,
+ERBB4,GO:0010467; GO:0051254; GO:0051896; GO:0035556; GO:0007416; GO:0009059; GO:0005739; GO:0007005,,Gene_expression; Positive_regulation_RNA_metabolic_process; Regulation of protein kinase B signaling; Intracellular signal transduction; Synapse_assembly; Macromolecule_biosynthetic_process; Mitochondrion; Mitochondrion_organization
+GGCX,GTEx_Coexpr,0.756490182916181,
+HDAC9,GO:0010467; GO:0006325; GO:0009059,,Gene_expression; Chromatin_organization; Macromolecule_biosynthetic_process
+HGF,GO:0010467; GO:0051254; GO:0051896; GO:0035556; GO:0009059; GO:0007005,,Gene_expression; Positive_regulation_RNA_metabolic_process; Regulation of protein kinase B signaling; Intracellular signal transduction; Macromolecule_biosynthetic_process; Mitochondrion_organization
+KAT6A,Brainspan_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682; GO:0035556; GO:0009059,0.867259060324318,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Chromatin_binding; Intracellular signal transduction; Macromolecule_biosynthetic_process
+KMT2A,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682; GO:0009059,0.76702022179054,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Chromatin_binding; Macromolecule_biosynthetic_process
+MAP4K1,GO:0035556,,Intracellular signal transduction
+MGAT2,Brainspan_Coexpr; GO:0009059,0.724337445865331,Macromolecule_biosynthetic_process
+MT-ND1,GO:0005739; GO:0007005,,Mitochondrion; Mitochondrion_organization
+MT-ND6,GO:0005739; GO:0007005,,Mitochondrion; Mitochondrion_organization
+NDUFAB1,GO:0010467; GO:0009059; GO:0005739; GO:0007005,,Gene_expression; Macromolecule_biosynthetic_process; Mitochondrion; Mitochondrion_organization
+NDUFS5,GO:0005739; GO:0007005,,Mitochondrion; Mitochondrion_organization
+NFE2L2,GO:0010467; GO:0051254; GO:0035556; GO:0043043; GO:0009059,,Gene_expression; Positive_regulation_RNA_metabolic_process; Intracellular signal transduction; Peptide_biosynthetic_process; Macromolecule_biosynthetic_process
+PARG,GTEx_Coexpr; GO:0005739,0.689870605098776,Mitochondrion
+PBRM1,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0006325; GO:0003682; GO:0010564; GO:0009059,0.784728267921418; 0.899652829181532,Gene_expression; Chromatin_organization; Chromatin_binding; Regulation of cell cycle process; Macromolecule_biosynthetic_process
+PDE4D,Brainspan_Coexpr; GO:0010467; GO:0035556; GO:0009059,0.746948212122413,Gene_expression; Intracellular signal transduction; Macromolecule_biosynthetic_process
+PHF8,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682; GO:0009059,0.664580654846671,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Chromatin_binding; Macromolecule_biosynthetic_process
+PITRM1,GTEx_Coexpr; GO:0010467; GO:0009059; GO:0005739,0.800958901344844,Gene_expression; Macromolecule_biosynthetic_process; Mitochondrion
+PKN2,GTEx_Coexpr; GO:0035556; GO:0010564,0.682733654788693,Intracellular signal transduction; Regulation of cell cycle process
+PRKACB,GO:0010467; GO:0035556; GO:0009059,,Gene_expression; Intracellular signal transduction; Macromolecule_biosynthetic_process
+PTGS2,GO:0010467; GO:0035556; GO:0009059,,Gene_expression; Intracellular signal transduction; Macromolecule_biosynthetic_process
+PTPN13,GO:0051896; GO:0035556; GO:0007416,,Regulation of protein kinase B signaling; Intracellular signal transduction; Synapse_assembly
+PTPRC,GO:0010467; GO:0035556; GO:0009059,,Gene_expression; Intracellular signal transduction; Macromolecule_biosynthetic_process
+RAD52,GTEx_Coexpr,0.713643644110946,
+STK17B,GO:0035556,,Intracellular signal transduction
+TFPI,GTEx_Coexpr,0.670779105480738,
diff --git a/src/permutation_analysis/04_prioritize_targets.R b/src/permutation_analysis/04_prioritize_targets.R
index 3445f32..57ad367 100644
--- a/src/permutation_analysis/04_prioritize_targets.R
+++ b/src/permutation_analysis/04_prioritize_targets.R
@@ -42,21 +42,22 @@ cat("\nTotal number of unique SETBP1 targets: ", length(setbp1_targets))
 ### TOP COEXPRESSED TARGETS ###
 top_gtex_coexpr <- gtex_coexpr %>%
   filter(FDR < 0.05) %>%
-  slice_max(abs(Spearman_Rho), prop = 0.10) %>%
+  slice_max(abs(Spearman_Rho), prop = 0.25) %>%
   mutate(Method = "GTEx_Coexpr")
 cat("\nTop quartile significantly coexpressed targets across tissues/ages:\n")
 print(head(top_gtex_coexpr))
 
 top_brainspan_coexpr <- brainspan_coexpr %>%
   filter(FDR < 0.05) %>%
-  slice_max(abs(Spearman_Rho), prop = 0.10) %>%
+  slice_max(abs(Spearman_Rho), prop = 0.25) %>%
   mutate(Method = "Brainspan_Coexpr")
 cat("\nTop quartile significantly coexpressed targets across tissues/ages:\n")
 print(head(top_brainspan_coexpr))
 
+top_coexpr <- rbind(top_gtex_coexpr, top_brainspan_coexpr)
+
 write_csv(
-  rbind(top_gtex_coexpr, top_brainspan_coexpr),
-  paste0(outdir, "top_target_coexpression.csv")
+  top_coexpr, paste0(outdir, "top_target_coexpression.csv")
 )
 
 ### gene functional pathway annotations ###
@@ -66,14 +67,12 @@ pathway_map <- list(
   "Positive_regulation_RNA_metabolic_process" = "GO:0051254",
   "Chromatin_organization" = "GO:0006325",
   "Chromatin_binding" = "GO:0003682",
-  "Translation" = "GO:0006412",
   "Translation_regulator_activity" = "GO:0045182",
   # Cell proliferation and survival
   "Negative regulation of protein phosphatase activity" = "GO:0010923",
   "Regulation of protein kinase B signaling" = "GO:0051896",
   "Intracellular signal transduction" = "GO:0035556",
   "Regulation of cell cycle process" = "GO:0010564",
-  "Mitotic cell cycle phase transition" = "GO:0044772",
   "Transforming growth factor beta receptor signaling pathway" = "GO:0007179",
   # Neurodevelopment and circuitry
   "Regulation of neural precursor cell proliferation" = "GO:2000177",
@@ -107,9 +106,24 @@ setbp1_pathways <- pathway_df %>%
 write_csv(setbp1_pathways, paste0(outdir, "setbp1_target_pathways.csv"))
 
 ### COMBINED TARGET PRIORITIZATION ###
-prioritized_targets <- top_gtex_coexpr %>%
-  select(Target_Gene, Method) %>%
-  bind_rows(setbp1_pathways)
+# Targets filtered by PHAROS development leve
+pharos_druggable <- setbp1_targets_table %>%
+filter(`Target Development Level` %in% c("Tchem", "Tclin"))
+
+# Convert pathway map to df
+pathway_map_df <- data.frame(
+"Method" = target_pathway_ids,
+"GO_Term" = names(pathway_map) 
+)
+str(pathway_map_df)
+
+prioritized_targets <- top_coexpr %>%
+  select(Target_Gene, Method, Spearman_Rho) %>%
+  bind_rows(setbp1_pathways) %>%
+  left_join(pathway_map_df, by = c("Method")) %>%
+  group_by(Target_Gene) %>%
+  summarize(across(everything(), ~ paste(na.omit(.), collapse = "; ")), .groups = "drop") %>%
+  filter(Target_Gene %in% pharos_druggable$Target)
 
 write_csv(prioritized_targets, paste0(outdir, "setbp1_targets_prioritized.csv"))
 cat("\nSaved final prioritized targets to: setbp1_targets_prioritized.csv\n\n")
@@ -117,6 +131,15 @@ cat(
   "\nNumber of top prioritized targets: ",
   length(unique(prioritized_targets$Target_Gene))
 )
-cat("\nFrequency of targets by prioritization method:\n")
+cat("\nStructure of saved table:\n")
+print(str(prioritized_targets))
+
+#### END ####
+
+# end timer
+fptm <- proc.time()
+cat("\n\nTotal runtime:  ", (fptm[3] / 60), "\n")
 
-print(sort(table(prioritized_targets$Target_Gene)))
+#  session info
+cat("\n\nSession Info:\n")
+print(sessionInfo())

From 17a117b88fb2004f2f050033934a7b1d9e3c6377 Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Tue, 7 Apr 2026 12:02:10 -0500
Subject: [PATCH 10/16] rename output files

---
 ...ized.csv => prioritized_setbp1_targets.csv} |  0
 ...csv => prioritized_target_coexpression.csv} |  0
 ...ays.csv => prioritized_target_pathways.csv} |  0
 .../04_prioritize_targets.R                    | 18 +++++++++---------
 4 files changed, 9 insertions(+), 9 deletions(-)
 rename results/permutation_analysis/{setbp1_targets_prioritized.csv => prioritized_setbp1_targets.csv} (100%)
 rename results/permutation_analysis/{top_target_coexpression.csv => prioritized_target_coexpression.csv} (100%)
 rename results/permutation_analysis/{setbp1_target_pathways.csv => prioritized_target_pathways.csv} (100%)

diff --git a/results/permutation_analysis/setbp1_targets_prioritized.csv b/results/permutation_analysis/prioritized_setbp1_targets.csv
similarity index 100%
rename from results/permutation_analysis/setbp1_targets_prioritized.csv
rename to results/permutation_analysis/prioritized_setbp1_targets.csv
diff --git a/results/permutation_analysis/top_target_coexpression.csv b/results/permutation_analysis/prioritized_target_coexpression.csv
similarity index 100%
rename from results/permutation_analysis/top_target_coexpression.csv
rename to results/permutation_analysis/prioritized_target_coexpression.csv
diff --git a/results/permutation_analysis/setbp1_target_pathways.csv b/results/permutation_analysis/prioritized_target_pathways.csv
similarity index 100%
rename from results/permutation_analysis/setbp1_target_pathways.csv
rename to results/permutation_analysis/prioritized_target_pathways.csv
diff --git a/src/permutation_analysis/04_prioritize_targets.R b/src/permutation_analysis/04_prioritize_targets.R
index 57ad367..2145473 100644
--- a/src/permutation_analysis/04_prioritize_targets.R
+++ b/src/permutation_analysis/04_prioritize_targets.R
@@ -57,7 +57,7 @@ print(head(top_brainspan_coexpr))
 top_coexpr <- rbind(top_gtex_coexpr, top_brainspan_coexpr)
 
 write_csv(
-  top_coexpr, paste0(outdir, "top_target_coexpression.csv")
+  top_coexpr, paste0(outdir, "prioritized_target_coexpression.csv")
 )
 
 ### gene functional pathway annotations ###
@@ -77,10 +77,10 @@ pathway_map <- list(
   # Neurodevelopment and circuitry
   "Regulation of neural precursor cell proliferation" = "GO:2000177",
   "Synapse_assembly" = "GO:0007416",
-  "Prostaglandin_receptor_activity" = "GO:0004955",  
+  "Prostaglandin_receptor_activity" = "GO:0004955",
   # Metabolism and bioenergetics
   "Peptide_biosynthetic_process" = "GO:0043043",
-  "Macromolecule_biosynthetic_process" =  "GO:0009059",
+  "Macromolecule_biosynthetic_process" = "GO:0009059",
   "Mitochondrion" = "GO:0005739",
   "Mitochondrion_organization" = "GO:0007005"
 )
@@ -103,17 +103,17 @@ setbp1_pathways <- pathway_df %>%
   filter(!is.na(Target_Gene)) %>%
   filter(Target_Gene %in% setbp1_targets)
 
-write_csv(setbp1_pathways, paste0(outdir, "setbp1_target_pathways.csv"))
+write_csv(setbp1_pathways, paste0(outdir, "prioritized_target_pathways.csv"))
 
 ### COMBINED TARGET PRIORITIZATION ###
 # Targets filtered by PHAROS development leve
 pharos_druggable <- setbp1_targets_table %>%
-filter(`Target Development Level` %in% c("Tchem", "Tclin"))
+  filter(`Target Development Level` %in% c("Tchem", "Tclin"))
 
 # Convert pathway map to df
 pathway_map_df <- data.frame(
-"Method" = target_pathway_ids,
-"GO_Term" = names(pathway_map) 
+  "Method" = target_pathway_ids,
+  "GO_Term" = names(pathway_map)
 )
 str(pathway_map_df)
 
@@ -125,8 +125,8 @@ prioritized_targets <- top_coexpr %>%
   summarize(across(everything(), ~ paste(na.omit(.), collapse = "; ")), .groups = "drop") %>%
   filter(Target_Gene %in% pharos_druggable$Target)
 
-write_csv(prioritized_targets, paste0(outdir, "setbp1_targets_prioritized.csv"))
-cat("\nSaved final prioritized targets to: setbp1_targets_prioritized.csv\n\n")
+write_csv(prioritized_targets, paste0(outdir, "prioritized_setbp1_targets.csv"))
+cat("\nSaved final prioritized targets to: prioritized_setbp1_targets.csv\n\n")
 cat(
   "\nNumber of top prioritized targets: ",
   length(unique(prioritized_targets$Target_Gene))

From 4b16167f4dd6beafc69f06613e99f4a54f577ea0 Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Tue, 7 Apr 2026 12:04:55 -0500
Subject: [PATCH 11/16] lint, style, and verify

---
 src/permutation_analysis/04_prioritize_targets.R | 7 ++++++-
 verifications/permutations_prioritize.out        | 3 +++
 verifications/permutations_prioritize.sh         | 3 +++
 3 files changed, 12 insertions(+), 1 deletion(-)
 create mode 100644 verifications/permutations_prioritize.out
 create mode 100644 verifications/permutations_prioritize.sh

diff --git a/src/permutation_analysis/04_prioritize_targets.R b/src/permutation_analysis/04_prioritize_targets.R
index 2145473..e2a3a71 100644
--- a/src/permutation_analysis/04_prioritize_targets.R
+++ b/src/permutation_analysis/04_prioritize_targets.R
@@ -122,7 +122,12 @@ prioritized_targets <- top_coexpr %>%
   bind_rows(setbp1_pathways) %>%
   left_join(pathway_map_df, by = c("Method")) %>%
   group_by(Target_Gene) %>%
-  summarize(across(everything(), ~ paste(na.omit(.), collapse = "; ")), .groups = "drop") %>%
+  summarize(
+    across(
+      everything(), ~ paste(na.omit(.), collapse = "; ")
+    ),
+    .groups = "drop"
+  ) %>%
   filter(Target_Gene %in% pharos_druggable$Target)
 
 write_csv(prioritized_targets, paste0(outdir, "prioritized_setbp1_targets.csv"))
diff --git a/verifications/permutations_prioritize.out b/verifications/permutations_prioritize.out
new file mode 100644
index 0000000..a677973
--- /dev/null
+++ b/verifications/permutations_prioritize.out
@@ -0,0 +1,3 @@
+f8da1713d0477c4362a2fffe798af60c  results/permutation_analysis/prioritized_setbp1_targets.csv
+78f4b96de1889ad86651415c78abf5e1  results/permutation_analysis/prioritized_target_coexpression.csv
+7948a1fafc5fb54f1c3db0eaac857252  results/permutation_analysis/prioritized_target_pathways.csv
diff --git a/verifications/permutations_prioritize.sh b/verifications/permutations_prioritize.sh
new file mode 100644
index 0000000..a21c848
--- /dev/null
+++ b/verifications/permutations_prioritize.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+cap_verify_md5 "results/permutation_analysis/prioritized_*"

From e9b5fd04984b66ac16edea2fc596a9a7c1aa608a Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Tue, 7 Apr 2026 12:58:52 -0500
Subject: [PATCH 12/16] update slurm resources requested

---
 src/permutation_analysis/04_job_prioritize.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/permutation_analysis/04_job_prioritize.sh b/src/permutation_analysis/04_job_prioritize.sh
index dcebf2b..edfcb4d 100644
--- a/src/permutation_analysis/04_job_prioritize.sh
+++ b/src/permutation_analysis/04_job_prioritize.sh
@@ -1,8 +1,9 @@
 #!/bin/bash
 
 #SBATCH --ntasks=1
-#SBATCH --mem-per-cpu=64G
+#SBATCH --mem-per-cpu=16G
 #SBATCH --partition=short
+#SBATCH --time=00:30:00
 
 #### DATASETS ####
 

From 2bba18c6195dc490b5f14403d3abb2f1682ce5d4 Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Tue, 7 Apr 2026 13:39:29 -0500
Subject: [PATCH 13/16] prioritize by 3 core pathway modules with most direct
 evidence (mitochondrial/bioenergetic pathway evidence too limited)

---
 .../prioritized_setbp1_targets.csv            |  53 +++---
 .../prioritized_target_pathways.csv           | 175 ------------------
 .../04_prioritize_targets.R                   |   7 +-
 verifications/permutations_prioritize.out     |   4 +-
 4 files changed, 28 insertions(+), 211 deletions(-)

diff --git a/results/permutation_analysis/prioritized_setbp1_targets.csv b/results/permutation_analysis/prioritized_setbp1_targets.csv
index f581a27..5b48f51 100644
--- a/results/permutation_analysis/prioritized_setbp1_targets.csv
+++ b/results/permutation_analysis/prioritized_setbp1_targets.csv
@@ -1,38 +1,35 @@
 Target_Gene,Method,Spearman_Rho,GO_Term
-BAZ2B,GO:0010467; GO:0006325; GO:0009059,,Gene_expression; Chromatin_organization; Macromolecule_biosynthetic_process
-BMPR1B,GO:0010467; GO:0051254; GO:0009059,,Gene_expression; Positive_regulation_RNA_metabolic_process; Macromolecule_biosynthetic_process
-BMPR2,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0035556; GO:0009059,0.7474918810946,Gene_expression; Positive_regulation_RNA_metabolic_process; Intracellular signal transduction; Macromolecule_biosynthetic_process
-BPTF,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0009059,0.711537323508429; 0.810125210856751,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Macromolecule_biosynthetic_process
-BRCA1,GO:0010467; GO:0051254; GO:0006325; GO:0035556; GO:0010564; GO:0009059,,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Intracellular signal transduction; Regulation of cell cycle process; Macromolecule_biosynthetic_process
-CDK8,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0051254; GO:0009059,0.715980907220096; 0.726755256041085,Gene_expression; Positive_regulation_RNA_metabolic_process; Macromolecule_biosynthetic_process
-CDKN1A,GO:0010467; GO:0035556; GO:0010564; GO:0009059,,Gene_expression; Intracellular signal transduction; Regulation of cell cycle process; Macromolecule_biosynthetic_process
-CHEK1,GO:0010467; GO:0006325; GO:0035556; GO:0010564; GO:0009059,,Gene_expression; Chromatin_organization; Intracellular signal transduction; Regulation of cell cycle process; Macromolecule_biosynthetic_process
-EED,GO:0010467; GO:0006325; GO:0003682; GO:0009059,,Gene_expression; Chromatin_organization; Chromatin_binding; Macromolecule_biosynthetic_process
+BAZ2B,GO:0010467; GO:0006325,,Gene_expression; Chromatin_organization
+BMPR1B,GO:0010467; GO:0051254,,Gene_expression; Positive_regulation_RNA_metabolic_process
+BMPR2,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0035556,0.7474918810946,Gene_expression; Positive_regulation_RNA_metabolic_process; Intracellular signal transduction
+BPTF,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0051254; GO:0006325,0.711537323508429; 0.810125210856751,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization
+BRCA1,GO:0010467; GO:0051254; GO:0006325; GO:0035556; GO:0010564,,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Intracellular signal transduction; Regulation of cell cycle process
+CDK8,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0051254,0.715980907220096; 0.726755256041085,Gene_expression; Positive_regulation_RNA_metabolic_process
+CDKN1A,GO:0010467; GO:0035556; GO:0010564,,Gene_expression; Intracellular signal transduction; Regulation of cell cycle process
+CHEK1,GO:0010467; GO:0006325; GO:0035556; GO:0010564,,Gene_expression; Chromatin_organization; Intracellular signal transduction; Regulation of cell cycle process
+EED,GO:0010467; GO:0006325; GO:0003682,,Gene_expression; Chromatin_organization; Chromatin_binding
 EPHA7,Brainspan_Coexpr; GO:0035556; GO:0007416,0.8350026342238,Intracellular signal transduction; Synapse_assembly
 EPRS,Brainspan_Coexpr,0.821415914810745,
-ERBB4,GO:0010467; GO:0051254; GO:0051896; GO:0035556; GO:0007416; GO:0009059; GO:0005739; GO:0007005,,Gene_expression; Positive_regulation_RNA_metabolic_process; Regulation of protein kinase B signaling; Intracellular signal transduction; Synapse_assembly; Macromolecule_biosynthetic_process; Mitochondrion; Mitochondrion_organization
+ERBB4,GO:0010467; GO:0051254; GO:0051896; GO:0035556; GO:0007416,,Gene_expression; Positive_regulation_RNA_metabolic_process; Regulation of protein kinase B signaling; Intracellular signal transduction; Synapse_assembly
 GGCX,GTEx_Coexpr,0.756490182916181,
-HDAC9,GO:0010467; GO:0006325; GO:0009059,,Gene_expression; Chromatin_organization; Macromolecule_biosynthetic_process
-HGF,GO:0010467; GO:0051254; GO:0051896; GO:0035556; GO:0009059; GO:0007005,,Gene_expression; Positive_regulation_RNA_metabolic_process; Regulation of protein kinase B signaling; Intracellular signal transduction; Macromolecule_biosynthetic_process; Mitochondrion_organization
-KAT6A,Brainspan_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682; GO:0035556; GO:0009059,0.867259060324318,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Chromatin_binding; Intracellular signal transduction; Macromolecule_biosynthetic_process
-KMT2A,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682; GO:0009059,0.76702022179054,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Chromatin_binding; Macromolecule_biosynthetic_process
+HDAC9,GO:0010467; GO:0006325,,Gene_expression; Chromatin_organization
+HGF,GO:0010467; GO:0051254; GO:0051896; GO:0035556,,Gene_expression; Positive_regulation_RNA_metabolic_process; Regulation of protein kinase B signaling; Intracellular signal transduction
+KAT6A,Brainspan_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682; GO:0035556,0.867259060324318,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Chromatin_binding; Intracellular signal transduction
+KMT2A,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682,0.76702022179054,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Chromatin_binding
 MAP4K1,GO:0035556,,Intracellular signal transduction
-MGAT2,Brainspan_Coexpr; GO:0009059,0.724337445865331,Macromolecule_biosynthetic_process
-MT-ND1,GO:0005739; GO:0007005,,Mitochondrion; Mitochondrion_organization
-MT-ND6,GO:0005739; GO:0007005,,Mitochondrion; Mitochondrion_organization
-NDUFAB1,GO:0010467; GO:0009059; GO:0005739; GO:0007005,,Gene_expression; Macromolecule_biosynthetic_process; Mitochondrion; Mitochondrion_organization
-NDUFS5,GO:0005739; GO:0007005,,Mitochondrion; Mitochondrion_organization
-NFE2L2,GO:0010467; GO:0051254; GO:0035556; GO:0043043; GO:0009059,,Gene_expression; Positive_regulation_RNA_metabolic_process; Intracellular signal transduction; Peptide_biosynthetic_process; Macromolecule_biosynthetic_process
-PARG,GTEx_Coexpr; GO:0005739,0.689870605098776,Mitochondrion
-PBRM1,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0006325; GO:0003682; GO:0010564; GO:0009059,0.784728267921418; 0.899652829181532,Gene_expression; Chromatin_organization; Chromatin_binding; Regulation of cell cycle process; Macromolecule_biosynthetic_process
-PDE4D,Brainspan_Coexpr; GO:0010467; GO:0035556; GO:0009059,0.746948212122413,Gene_expression; Intracellular signal transduction; Macromolecule_biosynthetic_process
-PHF8,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682; GO:0009059,0.664580654846671,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Chromatin_binding; Macromolecule_biosynthetic_process
-PITRM1,GTEx_Coexpr; GO:0010467; GO:0009059; GO:0005739,0.800958901344844,Gene_expression; Macromolecule_biosynthetic_process; Mitochondrion
+MGAT2,Brainspan_Coexpr,0.724337445865331,
+NDUFAB1,GO:0010467,,Gene_expression
+NFE2L2,GO:0010467; GO:0051254; GO:0035556,,Gene_expression; Positive_regulation_RNA_metabolic_process; Intracellular signal transduction
+PARG,GTEx_Coexpr,0.689870605098776,
+PBRM1,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0006325; GO:0003682; GO:0010564,0.784728267921418; 0.899652829181532,Gene_expression; Chromatin_organization; Chromatin_binding; Regulation of cell cycle process
+PDE4D,Brainspan_Coexpr; GO:0010467; GO:0035556,0.746948212122413,Gene_expression; Intracellular signal transduction
+PHF8,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682,0.664580654846671,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Chromatin_binding
+PITRM1,GTEx_Coexpr; GO:0010467,0.800958901344844,Gene_expression
 PKN2,GTEx_Coexpr; GO:0035556; GO:0010564,0.682733654788693,Intracellular signal transduction; Regulation of cell cycle process
-PRKACB,GO:0010467; GO:0035556; GO:0009059,,Gene_expression; Intracellular signal transduction; Macromolecule_biosynthetic_process
-PTGS2,GO:0010467; GO:0035556; GO:0009059,,Gene_expression; Intracellular signal transduction; Macromolecule_biosynthetic_process
+PRKACB,GO:0010467; GO:0035556,,Gene_expression; Intracellular signal transduction
+PTGS2,GO:0010467; GO:0035556,,Gene_expression; Intracellular signal transduction
 PTPN13,GO:0051896; GO:0035556; GO:0007416,,Regulation of protein kinase B signaling; Intracellular signal transduction; Synapse_assembly
-PTPRC,GO:0010467; GO:0035556; GO:0009059,,Gene_expression; Intracellular signal transduction; Macromolecule_biosynthetic_process
+PTPRC,GO:0010467; GO:0035556,,Gene_expression; Intracellular signal transduction
 RAD52,GTEx_Coexpr,0.713643644110946,
 STK17B,GO:0035556,,Intracellular signal transduction
 TFPI,GTEx_Coexpr,0.670779105480738,
diff --git a/results/permutation_analysis/prioritized_target_pathways.csv b/results/permutation_analysis/prioritized_target_pathways.csv
index 71b0dfb..275a7a8 100644
--- a/results/permutation_analysis/prioritized_target_pathways.csv
+++ b/results/permutation_analysis/prioritized_target_pathways.csv
@@ -292,178 +292,3 @@ GO:0007416,PTEN
 GO:0007416,ERBB4
 GO:0007416,MEF2C
 GO:0007416,RAP2A
-GO:0043043,NFE2L2
-GO:0043043,AASDH
-GO:0009059,NDFIP2
-GO:0009059,PPP5C
-GO:0009059,BRCA1
-GO:0009059,SARS2
-GO:0009059,RPS16
-GO:0009059,ZNF862
-GO:0009059,FKTN
-GO:0009059,ZMYND11
-GO:0009059,TRDMT1
-GO:0009059,ACTA2
-GO:0009059,PITRM1
-GO:0009059,HGF
-GO:0009059,CDKN1B
-GO:0009059,BMP5
-GO:0009059,PDE4D
-GO:0009059,ST8SIA4
-GO:0009059,INO80D
-GO:0009059,WDR75
-GO:0009059,NFE2L2
-GO:0009059,NDUFAB1
-GO:0009059,ZNHIT6
-GO:0009059,KMT2A
-GO:0009059,SET
-GO:0009059,EPC1
-GO:0009059,BAZ2B
-GO:0009059,NCOA5
-GO:0009059,CDKN1A
-GO:0009059,HDAC9
-GO:0009059,FOXP2
-GO:0009059,MRPS12
-GO:0009059,NSUN5
-GO:0009059,CTNNBL1
-GO:0009059,CDK8
-GO:0009059,ELP3
-GO:0009059,CCNH
-GO:0009059,ZC3H10
-GO:0009059,EPC2
-GO:0009059,KAT7
-GO:0009059,DNAJC1
-GO:0009059,MRPL15
-GO:0009059,RIOK2
-GO:0009059,FGF5
-GO:0009059,BMPR1B
-GO:0009059,TMTC3
-GO:0009059,NAA30
-GO:0009059,EIF4B
-GO:0009059,PRKACB
-GO:0009059,PIGK
-GO:0009059,MED29
-GO:0009059,HAX1
-GO:0009059,MEIS1
-GO:0009059,RBMS3
-GO:0009059,ZMAT2
-GO:0009059,ABT1
-GO:0009059,GOLGA7
-GO:0009059,CDKN2A
-GO:0009059,ZEB1
-GO:0009059,TAF5
-GO:0009059,CHEK1
-GO:0009059,ARID5B
-GO:0009059,ANK3
-GO:0009059,ZC3H15
-GO:0009059,CWF19L2
-GO:0009059,MBNL1
-GO:0009059,HS2ST1
-GO:0009059,TSEN2
-GO:0009059,SFR1
-GO:0009059,UTP14A
-GO:0009059,CNOT11
-GO:0009059,SNF8
-GO:0009059,RUNX1
-GO:0009059,DPY30
-GO:0009059,GNL3
-GO:0009059,PBRM1
-GO:0009059,PITX2
-GO:0009059,NOL6
-GO:0009059,BAG5
-GO:0009059,LEO1
-GO:0009059,E4F1
-GO:0009059,MGAT2
-GO:0009059,BMI1
-GO:0009059,ZFPM2
-GO:0009059,RNF139
-GO:0009059,BPTF
-GO:0009059,PTEN
-GO:0009059,JMJD1C
-GO:0009059,PAF1
-GO:0009059,AFF1
-GO:0009059,PTGS2
-GO:0009059,PHF8
-GO:0009059,CHD2
-GO:0009059,EED
-GO:0009059,NR2F1
-GO:0009059,ERBB4
-GO:0009059,CSRNP3
-GO:0009059,EIF3K
-GO:0009059,ALX1
-GO:0009059,MRPS16
-GO:0009059,RBM33
-GO:0009059,HOXA9
-GO:0009059,MLLT10
-GO:0009059,TCEA1
-GO:0009059,LIN28B
-GO:0009059,SUPT5H
-GO:0009059,MEF2C
-GO:0009059,PTPRC
-GO:0009059,DDI2
-GO:0009059,TAF13
-GO:0009059,CEP290
-GO:0009059,KAT6A
-GO:0009059,MECOM
-GO:0009059,CHERP
-GO:0009059,RBM20
-GO:0009059,BMPR2
-GO:0009059,DNAJC19
-GO:0009059,MT-TL1
-GO:0009059,ZFHX4
-GO:0009059,MT-TF
-GO:0009059,MT-TT
-GO:0009059,DENND1B
-GO:0009059,MCTS1
-GO:0009059,MZF1
-GO:0009059,SNORD13
-GO:0009059,NSUN6
-GO:0009059,HOXA10
-GO:0009059,EEF1G
-GO:0009059,EIF3D
-GO:0009059,HM13
-GO:0005739,DLAT
-GO:0005739,RPIA
-GO:0005739,PDSS2
-GO:0005739,NDUFAB1
-GO:0005739,NOL6
-GO:0005739,BAG5
-GO:0005739,NDUFS5
-GO:0005739,NUDT9
-GO:0005739,ETFDH
-GO:0005739,METAP1D
-GO:0005739,ERBB4
-GO:0005739,MRPS16
-GO:0005739,NBR1
-GO:0005739,TOMM7
-GO:0005739,MT-ND6
-GO:0005739,MT-ND1
-GO:0005739,TIMM23B
-GO:0005739,DNAJC19
-GO:0005739,PARG
-GO:0005739,TIMM23
-GO:0005739,CRLS1
-GO:0005739,USP48
-GO:0005739,PDPR
-GO:0005739,NDFIP2
-GO:0005739,SARS2
-GO:0005739,PITRM1
-GO:0005739,PPP3CC
-GO:0005739,MRPS12
-GO:0005739,COX4I1
-GO:0005739,DCAF8
-GO:0005739,MRPL15
-GO:0005739,PSMB6
-GO:0005739,HAX1
-GO:0005739,TMEM177
-GO:0005739,MPC1
-GO:0005739,CDKN2A
-GO:0007005,HGF
-GO:0007005,CDKN2A
-GO:0007005,NDUFS5
-GO:0007005,ERBB4
-GO:0007005,TOMM7
-GO:0007005,MT-ND6
-GO:0007005,MT-ND1
-GO:0007005,NEURL4
-GO:0007005,NDUFAB1
diff --git a/src/permutation_analysis/04_prioritize_targets.R b/src/permutation_analysis/04_prioritize_targets.R
index e2a3a71..4f415db 100644
--- a/src/permutation_analysis/04_prioritize_targets.R
+++ b/src/permutation_analysis/04_prioritize_targets.R
@@ -77,12 +77,7 @@ pathway_map <- list(
   # Neurodevelopment and circuitry
   "Regulation of neural precursor cell proliferation" = "GO:2000177",
   "Synapse_assembly" = "GO:0007416",
-  "Prostaglandin_receptor_activity" = "GO:0004955",
-  # Metabolism and bioenergetics
-  "Peptide_biosynthetic_process" = "GO:0043043",
-  "Macromolecule_biosynthetic_process" = "GO:0009059",
-  "Mitochondrion" = "GO:0005739",
-  "Mitochondrion_organization" = "GO:0007005"
+  "Prostaglandin_receptor_activity" = "GO:0004955"
 )
 
 target_pathway_ids <- unlist(pathway_map)
diff --git a/verifications/permutations_prioritize.out b/verifications/permutations_prioritize.out
index a677973..4a9a9fb 100644
--- a/verifications/permutations_prioritize.out
+++ b/verifications/permutations_prioritize.out
@@ -1,3 +1,3 @@
-f8da1713d0477c4362a2fffe798af60c  results/permutation_analysis/prioritized_setbp1_targets.csv
+5fde0c81c9c2c299781457a69b2bf3c5  results/permutation_analysis/prioritized_setbp1_targets.csv
 78f4b96de1889ad86651415c78abf5e1  results/permutation_analysis/prioritized_target_coexpression.csv
-7948a1fafc5fb54f1c3db0eaac857252  results/permutation_analysis/prioritized_target_pathways.csv
+ca26594f3f6cf15910ef2f0ca872c0d3  results/permutation_analysis/prioritized_target_pathways.csv

From f42d9bfa68f8a48a9659f6fabab2dc0b1940ae2b Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Wed, 8 Apr 2026 14:04:19 -0500
Subject: [PATCH 14/16] cleanup table (replace '_' with ' ' in GO terms)

---
 .../prioritized_setbp1_targets.csv            | 50 +++++++++----------
 .../04_prioritize_targets.R                   |  3 +-
 2 files changed, 27 insertions(+), 26 deletions(-)

diff --git a/results/permutation_analysis/prioritized_setbp1_targets.csv b/results/permutation_analysis/prioritized_setbp1_targets.csv
index 5b48f51..02a2713 100644
--- a/results/permutation_analysis/prioritized_setbp1_targets.csv
+++ b/results/permutation_analysis/prioritized_setbp1_targets.csv
@@ -1,35 +1,35 @@
 Target_Gene,Method,Spearman_Rho,GO_Term
-BAZ2B,GO:0010467; GO:0006325,,Gene_expression; Chromatin_organization
-BMPR1B,GO:0010467; GO:0051254,,Gene_expression; Positive_regulation_RNA_metabolic_process
-BMPR2,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0035556,0.7474918810946,Gene_expression; Positive_regulation_RNA_metabolic_process; Intracellular signal transduction
-BPTF,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0051254; GO:0006325,0.711537323508429; 0.810125210856751,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization
-BRCA1,GO:0010467; GO:0051254; GO:0006325; GO:0035556; GO:0010564,,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Intracellular signal transduction; Regulation of cell cycle process
-CDK8,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0051254,0.715980907220096; 0.726755256041085,Gene_expression; Positive_regulation_RNA_metabolic_process
-CDKN1A,GO:0010467; GO:0035556; GO:0010564,,Gene_expression; Intracellular signal transduction; Regulation of cell cycle process
-CHEK1,GO:0010467; GO:0006325; GO:0035556; GO:0010564,,Gene_expression; Chromatin_organization; Intracellular signal transduction; Regulation of cell cycle process
-EED,GO:0010467; GO:0006325; GO:0003682,,Gene_expression; Chromatin_organization; Chromatin_binding
-EPHA7,Brainspan_Coexpr; GO:0035556; GO:0007416,0.8350026342238,Intracellular signal transduction; Synapse_assembly
+BAZ2B,GO:0010467; GO:0006325,,Gene expression; Chromatin organization
+BMPR1B,GO:0010467; GO:0051254,,Gene expression; Positive regulation RNA metabolic process
+BMPR2,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0035556,0.7474918810946,Gene expression; Positive regulation RNA metabolic process; Intracellular signal transduction
+BPTF,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0051254; GO:0006325,0.711537323508429; 0.810125210856751,Gene expression; Positive regulation RNA metabolic process; Chromatin organization
+BRCA1,GO:0010467; GO:0051254; GO:0006325; GO:0035556; GO:0010564,,Gene expression; Positive regulation RNA metabolic process; Chromatin organization; Intracellular signal transduction; Regulation of cell cycle process
+CDK8,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0051254,0.715980907220096; 0.726755256041085,Gene expression; Positive regulation RNA metabolic process
+CDKN1A,GO:0010467; GO:0035556; GO:0010564,,Gene expression; Intracellular signal transduction; Regulation of cell cycle process
+CHEK1,GO:0010467; GO:0006325; GO:0035556; GO:0010564,,Gene expression; Chromatin organization; Intracellular signal transduction; Regulation of cell cycle process
+EED,GO:0010467; GO:0006325; GO:0003682,,Gene expression; Chromatin organization; Chromatin binding
+EPHA7,Brainspan_Coexpr; GO:0035556; GO:0007416,0.8350026342238,Intracellular signal transduction; Synapse assembly
 EPRS,Brainspan_Coexpr,0.821415914810745,
-ERBB4,GO:0010467; GO:0051254; GO:0051896; GO:0035556; GO:0007416,,Gene_expression; Positive_regulation_RNA_metabolic_process; Regulation of protein kinase B signaling; Intracellular signal transduction; Synapse_assembly
+ERBB4,GO:0010467; GO:0051254; GO:0051896; GO:0035556; GO:0007416,,Gene expression; Positive regulation RNA metabolic process; Regulation of protein kinase B signaling; Intracellular signal transduction; Synapse assembly
 GGCX,GTEx_Coexpr,0.756490182916181,
-HDAC9,GO:0010467; GO:0006325,,Gene_expression; Chromatin_organization
-HGF,GO:0010467; GO:0051254; GO:0051896; GO:0035556,,Gene_expression; Positive_regulation_RNA_metabolic_process; Regulation of protein kinase B signaling; Intracellular signal transduction
-KAT6A,Brainspan_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682; GO:0035556,0.867259060324318,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Chromatin_binding; Intracellular signal transduction
-KMT2A,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682,0.76702022179054,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Chromatin_binding
+HDAC9,GO:0010467; GO:0006325,,Gene expression; Chromatin organization
+HGF,GO:0010467; GO:0051254; GO:0051896; GO:0035556,,Gene expression; Positive regulation RNA metabolic process; Regulation of protein kinase B signaling; Intracellular signal transduction
+KAT6A,Brainspan_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682; GO:0035556,0.867259060324318,Gene expression; Positive regulation RNA metabolic process; Chromatin organization; Chromatin binding; Intracellular signal transduction
+KMT2A,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682,0.76702022179054,Gene expression; Positive regulation RNA metabolic process; Chromatin organization; Chromatin binding
 MAP4K1,GO:0035556,,Intracellular signal transduction
 MGAT2,Brainspan_Coexpr,0.724337445865331,
-NDUFAB1,GO:0010467,,Gene_expression
-NFE2L2,GO:0010467; GO:0051254; GO:0035556,,Gene_expression; Positive_regulation_RNA_metabolic_process; Intracellular signal transduction
+NDUFAB1,GO:0010467,,Gene expression
+NFE2L2,GO:0010467; GO:0051254; GO:0035556,,Gene expression; Positive regulation RNA metabolic process; Intracellular signal transduction
 PARG,GTEx_Coexpr,0.689870605098776,
-PBRM1,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0006325; GO:0003682; GO:0010564,0.784728267921418; 0.899652829181532,Gene_expression; Chromatin_organization; Chromatin_binding; Regulation of cell cycle process
-PDE4D,Brainspan_Coexpr; GO:0010467; GO:0035556,0.746948212122413,Gene_expression; Intracellular signal transduction
-PHF8,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682,0.664580654846671,Gene_expression; Positive_regulation_RNA_metabolic_process; Chromatin_organization; Chromatin_binding
-PITRM1,GTEx_Coexpr; GO:0010467,0.800958901344844,Gene_expression
+PBRM1,GTEx_Coexpr; Brainspan_Coexpr; GO:0010467; GO:0006325; GO:0003682; GO:0010564,0.784728267921418; 0.899652829181532,Gene expression; Chromatin organization; Chromatin binding; Regulation of cell cycle process
+PDE4D,Brainspan_Coexpr; GO:0010467; GO:0035556,0.746948212122413,Gene expression; Intracellular signal transduction
+PHF8,GTEx_Coexpr; GO:0010467; GO:0051254; GO:0006325; GO:0003682,0.664580654846671,Gene expression; Positive regulation RNA metabolic process; Chromatin organization; Chromatin binding
+PITRM1,GTEx_Coexpr; GO:0010467,0.800958901344844,Gene expression
 PKN2,GTEx_Coexpr; GO:0035556; GO:0010564,0.682733654788693,Intracellular signal transduction; Regulation of cell cycle process
-PRKACB,GO:0010467; GO:0035556,,Gene_expression; Intracellular signal transduction
-PTGS2,GO:0010467; GO:0035556,,Gene_expression; Intracellular signal transduction
-PTPN13,GO:0051896; GO:0035556; GO:0007416,,Regulation of protein kinase B signaling; Intracellular signal transduction; Synapse_assembly
-PTPRC,GO:0010467; GO:0035556,,Gene_expression; Intracellular signal transduction
+PRKACB,GO:0010467; GO:0035556,,Gene expression; Intracellular signal transduction
+PTGS2,GO:0010467; GO:0035556,,Gene expression; Intracellular signal transduction
+PTPN13,GO:0051896; GO:0035556; GO:0007416,,Regulation of protein kinase B signaling; Intracellular signal transduction; Synapse assembly
+PTPRC,GO:0010467; GO:0035556,,Gene expression; Intracellular signal transduction
 RAD52,GTEx_Coexpr,0.713643644110946,
 STK17B,GO:0035556,,Intracellular signal transduction
 TFPI,GTEx_Coexpr,0.670779105480738,
diff --git a/src/permutation_analysis/04_prioritize_targets.R b/src/permutation_analysis/04_prioritize_targets.R
index 4f415db..f027795 100644
--- a/src/permutation_analysis/04_prioritize_targets.R
+++ b/src/permutation_analysis/04_prioritize_targets.R
@@ -123,7 +123,8 @@ prioritized_targets <- top_coexpr %>%
     ),
     .groups = "drop"
   ) %>%
-  filter(Target_Gene %in% pharos_druggable$Target)
+  filter(Target_Gene %in% pharos_druggable$Target) %>%
+  mutate(GO_Term = gsub("_", " ", GO_Term))
 
 write_csv(prioritized_targets, paste0(outdir, "prioritized_setbp1_targets.csv"))
 cat("\nSaved final prioritized targets to: prioritized_setbp1_targets.csv\n\n")

From ededda6c518a24a2c17bd0056409124abd3bf67d Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Fri, 10 Apr 2026 10:03:56 -0500
Subject: [PATCH 15/16] update verification

---
 verifications/permutations_prioritize.out | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/verifications/permutations_prioritize.out b/verifications/permutations_prioritize.out
index 4a9a9fb..ecba849 100644
--- a/verifications/permutations_prioritize.out
+++ b/verifications/permutations_prioritize.out
@@ -1,3 +1,3 @@
-5fde0c81c9c2c299781457a69b2bf3c5  results/permutation_analysis/prioritized_setbp1_targets.csv
+fe3c2bf55ff316b8abc296e84df89a27  results/permutation_analysis/prioritized_setbp1_targets.csv
 78f4b96de1889ad86651415c78abf5e1  results/permutation_analysis/prioritized_target_coexpression.csv
 ca26594f3f6cf15910ef2f0ca872c0d3  results/permutation_analysis/prioritized_target_pathways.csv

From be2a83c39c8f7553b761103b96098763f2f8b06e Mon Sep 17 00:00:00 2001
From: Lizzy Wilk <lizzyr@uab.edu>
Date: Fri, 10 Apr 2026 11:43:32 -0500
Subject: [PATCH 16/16] fix comments

---
 src/permutation_analysis/04_prioritize_targets.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/permutation_analysis/04_prioritize_targets.R b/src/permutation_analysis/04_prioritize_targets.R
index f027795..d4e402c 100644
--- a/src/permutation_analysis/04_prioritize_targets.R
+++ b/src/permutation_analysis/04_prioritize_targets.R
@@ -60,7 +60,7 @@ write_csv(
   top_coexpr, paste0(outdir, "prioritized_target_coexpression.csv")
 )
 
-### gene functional pathway annotations ###
+### GENE-FUNCTIONAL PATHWAY ANNOTATIONS ###
 pathway_map <- list(
   # Transcriptional and epigenetic regulation
   "Gene_expression" = "GO:0010467",
@@ -101,7 +101,7 @@ setbp1_pathways <- pathway_df %>%
 write_csv(setbp1_pathways, paste0(outdir, "prioritized_target_pathways.csv"))
 
 ### COMBINED TARGET PRIORITIZATION ###
-# Targets filtered by PHAROS development leve
+# Targets filtered by PHAROS development level
 pharos_druggable <- setbp1_targets_table %>%
   filter(`Target Development Level` %in% c("Tchem", "Tclin"))