lasseignelab · lizzyjoan · Apr 10, 2026 · Mar 4, 2025 · Mar 4, 2025 · Mar 4, 2025
diff --git a/.gitignore b/.gitignore
@@ -241,6 +241,9 @@ bin/conda/work/
 bin/conda/work/*
 bin/conda/.nextflow/
 bin/container/*
+results/permutation_analysis/aggregate_gene_exp_mat.csv
 Rplots.pdf
 src/lint_and_style.sh
 megalinter-reports
+lintr_styler.R
+run_lintr_styler.sh
diff --git a/config/environments/lasseignelab.sh b/config/environments/lasseignelab.sh
@@ -11,3 +11,7 @@ cap_data_link "$LASSEIGNE_LAB_PATH/PROJECT_dir/setbp1_hd/tanaka"
 
 # Wong et al 2025 source data to validate DEGs
 cap_data_link "$LASSEIGNE_LAB_PATH/PROJECT_dir/setbp1_hd/wong"
+
+# Brainspan and GTEx counts data
+cap_data_link "$LASSEIGNE_LAB_PATH/DATASET_dir/brainspan"
+cap_data_link "$LASSEIGNE_LAB_PATH/DATASET_dir/gtex"
diff --git a/data/260403_setbp1_targets.csv b/data/260403_setbp1_targets.csv
diff --git a/results/figures/SETBP1_target_exp_gtex_heatmap.png b/results/figures/SETBP1_target_exp_gtex_heatmap.png
diff --git a/results/figures/SETBP1_target_sex_bytissue_boxplot.png b/results/figures/SETBP1_target_sex_bytissue_boxplot.png
diff --git a/results/figures/SETBP1_temporal_trajectory.png b/results/figures/SETBP1_temporal_trajectory.png
diff --git a/results/figures/supplementary_figure_1.png b/results/figures/supplementary_figure_1.png
diff --git a/results/permutation_analysis/SETBP1_target_coexpression_brainspan.csv b/results/permutation_analysis/SETBP1_target_coexpression_brainspan.csv
diff --git a/results/permutation_analysis/brainspan_metadata_dev_windows.csv b/results/permutation_analysis/brainspan_metadata_dev_windows.csv
diff --git a/results/permutation_analysis/brainspan_metadata_donors_by_age.png b/results/permutation_analysis/brainspan_metadata_donors_by_age.png
diff --git a/results/permutation_analysis/brainspan_permutation_stats.csv b/results/permutation_analysis/brainspan_permutation_stats.csv
@@ -0,0 +1,8 @@
+window,observed,z_score,p_val_enrichment,p_val_depletion,p_val_two_sided,p_val_adj
+Early_Prenatal,0.2782844072238795,9.513247816942267,0,1,0,0
+Mid_Prenatal,0.05721022647250982,3.232294998967253,5e-4,0.9995,0.001,0.0011666666666666668
+Late_Prenatal,-0.004742432008853141,-3.6816059627598166,1,0,0,0
+Infancy,0.011847699853442256,-1.290811243133021,0.9027,0.0973,0.1946,0.1946
+Early_Childhood,-0.46119475587906517,-9.240283685093617,1,0,0,0
+Childhood,-0.01752909962056895,-3.71473952786009,0.9997,3e-4,6e-4,0.00105
+Adult,-0.06636122622906972,-3.3594444884762438,0.9996,4e-4,8e-4,0.00112
diff --git a/results/permutation_analysis/brainspan_window_gene_means.csv b/results/permutation_analysis/brainspan_window_gene_means.csv
diff --git a/results/permutation_analysis/gtex_metadata_donors.png b/results/permutation_analysis/gtex_metadata_donors.png
diff --git a/results/permutation_analysis/gtex_permutation_results.csv b/results/permutation_analysis/gtex_permutation_results.csv
@@ -0,0 +1,75 @@
+Tissue,Age,N_Samples,Observed,Z_Score,P_Value,FDR
+Bladder,20-29,12,0.629887434713362,8.66390676456396,0,0
+Bladder,30-39,9,0.5963425563821171,8.819840656548296,0,0
+Bladder,40-49,20,0.632628563700223,12.682318664332676,0,0
+Bladder,50-59,23,0.5559105702233601,12.29565515178114,0,0
+Bladder,60-69,12,0.6103384427466958,14.46125843258219,0,0
+Blood,20-29,107,-0.2928615607953293,-6.498049977617908,0,0
+Blood,30-39,98,-0.2789229017670139,-6.634352220183157,0,0
+Blood,40-49,174,-0.3200596457433215,-7.109456620145368,0,0
+Blood,50-59,358,-0.3960609156006221,-8.711245604477888,0,0
+Blood,60-69,359,-0.4690473118584052,-10.052931299894192,0,0
+Blood,70-79,34,-0.547994246581826,-11.39035740051524,0,0
+Blood Vessel,20-29,114,0.5570541625996318,18.399965014080287,0,0
+Blood Vessel,30-39,115,0.5687121551111108,17.119122970462055,0,0
+Blood Vessel,40-49,237,0.5698929666957444,16.73004475224162,0,0
+Blood Vessel,50-59,490,0.5692976447518249,15.924171114187578,0,0
+Blood Vessel,60-69,439,0.5701985061976234,14.629926465057906,0,0
+Blood Vessel,70-79,36,0.5772857902871267,12.083308376100728,0,0
+Blood Vessel,Pediatric,6,0.2557857064330933,2.660016292058988,0.0142,0.019826415094339623
+Brain,20-29,72,0.04837394938260908,-1.9618936911022566,0.0452,0.05766896551724138
+Brain,30-39,97,0.038187301253474075,-1.4996189548629095,0.1284,0.1461784615384615
+Brain,40-49,296,-0.14004247068484024,-6.174480902397588,0,0
+Brain,50-59,980,-0.14530204985356157,-6.537259424989032,0,0
+Brain,60-69,1619,-0.21953940101871083,-8.473769291665958,0,0
+Brain,70-79,170,-0.18445126415290114,-8.321486164684487,0,0
+Brain,Pediatric,4,0.47776784496862396,2.2442961754292985,0.0414,0.05470714285714286
+Esophagus,20-29,168,0.2964451571884536,14.170755062266103,0,0
+Esophagus,30-39,147,0.29215437586069604,13.337036265037288,0,0
+Esophagus,40-49,287,0.2956182328782232,13.217373201514226,0,0
+Esophagus,50-59,514,0.29827787748928414,12.347673840200544,0,0
+Esophagus,60-69,420,0.24866221405105235,9.738129168834572,0,0
+Esophagus,70-79,42,0.21287770926002259,7.807966855404763,0,0
+Esophagus,Pediatric,18,0.06971897423985696,2.0193800825590738,0.056,0.0679344262295082
+Heart,20-29,35,-0.41431243232214354,-6.038902905873551,0,0
+Heart,30-39,42,-0.50880913702201,-8.9023152363792,0,0
+Heart,40-49,130,-0.5169781942743059,-10.298063560500907,0,0
+Heart,50-59,325,-0.5485777978598463,-11.343663108037303,0,0
+Heart,60-69,348,-0.6198073849596628,-13.66959608028685,0,0
+Heart,70-79,33,-0.7054333501420444,-16.123402005741617,0,0
+Heart,Pediatric,7,-0.485578542906318,-4.346459138879867,0,0
+Kidney,20-29,4,0.14084468941024123,0.38563491101901126,0.665,0.6884055555555555
+Kidney,30-39,10,0.08244802710537895,-0.584049963468136,0.5862,0.619697142857143
+Kidney,40-49,10,-0.3138919708716714,-5.749160583444764,0,0
+Kidney,50-59,41,-0.2510334791333261,-5.1107954675881,0,0
+Kidney,60-69,43,-0.28732312956762607,-5.389963321949304,0,0
+Kidney,70-79,7,-0.02101643129416891,-1.8419320956038823,0.0424,0.055045614035087724
+Kidney,Pediatric,3,0.260214084248171,1.6540546138318921,0.1164,0.13672380952380953
+Lung,20-29,35,0.5384426266256427,7.887822676202136,0,0
+Lung,30-39,44,0.5393739625343046,7.592465113960132,0,0
+Lung,40-49,94,0.5447774189387334,7.7232077514039865,0,0
+Lung,50-59,211,0.5309918591684523,6.929479668000981,0,0
+Lung,60-69,198,0.5282280310350884,6.461969389575125,0,0
+Lung,70-79,22,0.5050857685016008,6.6734785411570465,0,0
+Lung,Pediatric,35,0.42602898387738,3.4889030048497838,0.002,0.00296
+Muscle,20-29,71,-0.28180604165558454,0.08228884132488537,0.9224,0.9224
+Muscle,30-39,64,-0.1765075424197575,1.9737690391826426,0.0532,0.06561333333333333
+Muscle,40-49,121,-0.20574487711945,1.1210731414533912,0.2616,0.2889313432835821
+Muscle,50-59,261,-0.23751544477142322,0.12896300162912636,0.8894,0.9015835616438357
+Muscle,60-69,273,-0.18987978167034195,0.4174585044449191,0.6698,0.6884055555555555
+Muscle,70-79,28,-0.11186930299042926,1.9558050642902811,0.0592,0.07065806451612903
+Muscle,Pediatric,48,-0.360740819223292,-1.9667978923481837,0.0364,0.04897454545454546
+Small Intestine,20-29,35,0.38935334746359135,3.734379947925299,4e-4,6.166666666666667e-4
+Small Intestine,30-39,26,0.34880959288937574,3.402636415091272,0.0018,0.002718367346938775
+Small Intestine,40-49,45,0.382965835200653,4.428718401729585,0,0
+Small Intestine,50-59,69,0.2938137511692688,2.787617739644545,0.0094,0.013376923076923078
+Small Intestine,60-69,47,0.28070415276042493,2.115894468650543,0.0466,0.05844745762711865
+Small Intestine,70-79,4,0.5129188894814712,4.844587187979415,0,0
+Small Intestine,Pediatric,24,0.2829286443055324,3.275878655691097,0.0028,0.004062745098039215
+Stomach,20-29,81,0.0860888377757927,4.574675800351846,2e-4,3.1489361702127664e-4
+Stomach,30-39,58,-0.0042363530461352154,1.4691374815566698,0.1494,0.16750909090909089
+Stomach,40-49,78,0.10545698537570726,4.0040758602221524,2e-4,3.1489361702127664e-4
+Stomach,50-59,160,0.026948435912657,2.1934104333493623,0.035,0.04796296296296297
+Stomach,60-69,107,-0.023935986338544674,0.7213455529652052,0.4614,0.4948347826086957
+Stomach,70-79,7,-0.0669752580531949,-0.8365027370536338,0.4072,0.4431294117647058
+Stomach,Pediatric,13,0.029230683531739018,1.5929711570115963,0.1252,0.14476250000000002
diff --git a/results/permutation_analysis/gtex_sex_wilcox_results.csv b/results/permutation_analysis/gtex_sex_wilcox_results.csv
@@ -0,0 +1,66 @@
+SMTS,AGE,Male_N,Female_N,P_Value,FDR
+Stomach,60-69,63,44,0.0206659221116247,0.5092749400342577
+Brain,70-79,139,31,0.03377840679817872,0.5092749400342577
+Muscle,60-69,191,82,0.03742752382310175,0.5092749400342577
+Small Intestine,60-69,29,18,0.050153286971544045,0.5092749400342577
+Muscle,50-59,176,85,0.057519043334822204,0.5092749400342577
+Muscle,40-49,71,50,0.05915226640244935,0.5092749400342577
+Blood Vessel,60-69,292,147,0.06243031017505598,0.5092749400342577
+Muscle,20-29,48,23,0.06267999261960094,0.5092749400342577
+Esophagus,70-79,27,15,0.08318487806875985,0.5545052230429
+Heart,50-59,226,99,0.08530849585275384,0.5545052230429
+Esophagus,50-59,355,159,0.10067462800765233,0.5645422293704044
+Heart,40-49,85,45,0.1042231808068439,0.5645422293704044
+Esophagus,40-49,167,120,0.12801864726945641,0.6400932363472821
+Stomach,50-59,107,53,0.14203368783892573,0.6474606344603329
+Blood,70-79,24,10,0.15637572175964454,0.6474606344603329
+Muscle,30-39,46,18,0.17185093871712362,0.6474606344603329
+Kidney,60-69,32,11,0.17701506240392342,0.6474606344603329
+Small Intestine,50-59,46,23,0.17929679108132293,0.6474606344603329
+Heart,30-39,25,17,0.20925400149129197,0.690354463513303
+Lung,70-79,18,4,0.21708295254888035,0.690354463513303
+Blood Vessel,70-79,26,10,0.2230375959042979,0.690354463513303
+Heart,60-69,247,101,0.29176683714741614,0.8620383824810023
+Heart,70-79,23,10,0.3178371035638304,0.869048660756857
+Blood,40-49,107,67,0.32536691382041444,0.869048660756857
+Blood,60-69,238,121,0.3342494849064835,0.869048660756857
+Small Intestine,Pediatric,14,10,0.364096429365271,0.9102410734131774
+Small Intestine,30-39,17,9,0.38849555723458407,0.9218720547768959
+Brain,20-29,45,27,0.40232378292383864,0.9218720547768959
+Blood,50-59,244,114,0.4112967629004613,0.9218720547768959
+Blood Vessel,20-29,75,39,0.44100773671252574,0.9468358974639267
+Lung,20-29,22,13,0.4629500193995568,0.9468358974639267
+Stomach,20-29,54,27,0.467627309266457,0.9468358974639267
+Kidney,40-49,7,3,0.4941245444092639,0.9468358974639267
+Blood,20-29,73,34,0.5141736623631725,0.9468358974639267
+Bladder,30-39,6,3,0.5186050164287257,0.9468358974639267
+Lung,40-49,60,34,0.536767680539281,0.9468358974639267
+Esophagus,20-29,115,53,0.5389681262486967,0.9468358974639267
+Small Intestine,20-29,22,13,0.5732301332745356,0.9805252279696004
+Muscle,Pediatric,34,14,0.5940082968848364,0.9870296233167843
+Esophagus,60-69,269,151,0.609356085562303,0.9870296233167843
+Esophagus,30-39,100,47,0.6225879162459717,0.9870296233167843
+Muscle,70-79,20,8,0.6655484706694976,0.9916383718469757
+Bladder,60-69,8,4,0.6711254583898127,0.9916383718469757
+Stomach,Pediatric,10,3,0.6726038174415166,0.9916383718469757
+Stomach,40-49,42,36,0.7144826736345963,0.9916383718469757
+Bladder,50-59,15,8,0.7225720059920624,0.9916383718469757
+Heart,20-29,20,15,0.7263386976487619,0.9916383718469757
+Blood,30-39,70,28,0.7322867976716128,0.9916383718469757
+Lung,30-39,32,12,0.8023190269653299,1
+Blood Vessel,50-59,333,157,0.8050454255075835,1
+Stomach,30-39,44,14,0.8062195680973387,1
+Lung,Pediatric,25,10,0.8408302496157976,1
+Small Intestine,40-49,29,16,0.8588536074676734,1
+Brain,50-59,732,248,0.8642750237630799,1
+Blood Vessel,40-49,143,94,0.8806881169790373,1
+Brain,40-49,197,99,0.9083288071844972,1
+Lung,50-59,150,61,0.9316185032498697,1
+Kidney,50-59,33,8,0.9344527153159942,1
+Bladder,20-29,6,6,0.9361862934730594,1
+Blood Vessel,30-39,78,37,0.949874715204563,1
+Bladder,40-49,12,8,0.9692285668393378,1
+Brain,60-69,1202,417,0.9814269825133469,1
+Lung,60-69,132,66,0.9821586405873842,1
+Brain,30-39,64,33,0.9908871859888266,1
+Esophagus,Pediatric,13,5,1,1