When trying to map PRG4 to species orthologs, CoSIA seems to only recognize human and rat. This was first noticed in the shiny app, but I have reproduced it using the package.
input_species <- c("h_sapiens")
model_comparing <- c("m_musculus")
output_species <- c(model_comparing, input_species)
map_tissues <- CoSIA::getTissues(output_species)
common_tissues <- map_tissues[["Common_Anatomical_Entity_Name"]]
mapped <- CoSIAn(
gene_set = "PRG4", input_id = "Symbol",
i_species = "h_sapiens",
o_species = c("r_norvegicus", "m_musculus", "h_sapiens"),
# o_species = c("r_norvegicus", "h_sapiens"),
output_ids = c("Ensembl_id", "Symbol"),
mapping_tool = "annotationDBI",
map_species = c("m_musculus"),
# map_species = c("r_norvegicus"),
ortholog_database = "HomoloGene",
common_tissues,
metric_type = "DS_Gene"
)
CoSIA::getConversion(mapped)
This gives the warning:
Warning messages:
1: In annotationTools::getHOMOLOG(myGenes, species_number, homologene, :
One or more gene ID/cluster with no target provided in homologue table
2: In CoSIA::getConversion(mapped) :
No orthologs were found for m_musculus across all the genes provided by the user.
And returns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Joining with `by = join_by(h_sapiens_symbol)`
Joining with `by = join_by(h_sapiens_symbol)`
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Joining with `by = join_by(h_sapiens_symbol)`
Joining with `by = join_by(h_sapiens_symbol)`
An object of class "CoSIAn"
Slot "gene_set":
[1] "PRG4"
Slot "i_species":
[1] "h_sapiens"
Slot "input_id":
[1] "Symbol"
Slot "o_species":
[1] "r_norvegicus" "m_musculus" "h_sapiens"
Slot "output_ids":
[1] "Ensembl_id" "Symbol"
Slot "mapping_tool":
[1] "annotationDBI"
Slot "ortholog_database":
[1] "HomoloGene"
Slot "converted_id":
h_sapiens_symbol r_norvegicus_ensembl_id r_norvegicus_symbol h_sapiens_ensembl_id
1 PRG4 ENSRNOG00000002385 Prg4 ENSG00000116690
Slot "map_tissues":
[1] "Ammon's horn" "adrenal gland" "adult mammalian kidney"
[4] "bone marrow" "brain" "cerebellar cortex"
[7] "cerebellum" "cerebral cortex" "colon"
[10] "cortex of kidney" "cortical plate" "duodenum"
[13] "esophagus" "frontal cortex" "ganglionic eminence"
[16] "granulocyte" "heart" "hindlimb stylopod muscle"
[19] "hypothalamus" "intestine" "islet of Langerhans"
[22] "kidney" "liver" "lung"
[25] "multicellular organism" "muscle tissue" "ovary"
[28] "pancreas" "placenta" "primary visual cortex"
[31] "skeletal muscle tissue" "spleen" "stomach"
[34] "superior frontal gyrus" "testis" "urinary bladder"
[37] "ventricular zone" "zone of skin"
Slot "map_species":
[1] "m_musculus"
Slot "gex":
X0
1 0
Slot "metric_type":
[1] "DS_Gene"
Slot "metric":
X0
1 0
The "converted_id" returns the same as in the Shiny app when selecting human, mouse, rat, and zebrafish, and regardless of mapping_tool and ortholog_database selection. PRG4 does have mouse and zebrafish orthologs, though, and there's data for them in Bgee https://www.bgee.org/search/genes?search=PRG4
This could just be an issue of needing to update the CoSIAdata, but not sure.
I tested this locally in Rstudio, sessionInfo:
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS 26.4.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] CoSIAdata_1.6.0 CoSIA_1.6.0 ExperimentHub_2.14.0 AnnotationHub_3.14.0
[5] BiocFileCache_2.14.0 dbplyr_2.5.1 BiocGenerics_0.52.0
loaded via a namespace (and not attached):
[1] rappdirs_0.3.4 generics_0.1.4 homologene_1.4.68.19.3.27
[4] BiocVersion_3.20.0 RSQLite_2.4.6 magrittr_2.0.4
[7] fastmap_1.2.0 blob_1.3.0 jsonlite_2.0.0
[10] AnnotationDbi_1.68.0 GenomeInfoDb_1.42.3 DBI_1.3.0
[13] BiocManager_1.30.27 httr_1.4.8 purrr_1.2.1
[16] org.Rn.eg.db_3.20.0 UCSC.utils_1.2.0 Biostrings_2.74.1
[19] annotationTools_1.80.0 cli_3.6.5 rlang_1.1.7
[22] crayon_1.5.3 XVector_0.46.0 Biobase_2.66.0
[25] bit64_4.6.0-1 withr_3.0.2 cachem_1.1.0
[28] yaml_2.3.12 otel_0.2.0 tools_4.4.2
[31] memoise_2.0.1 dplyr_1.2.0 GenomeInfoDbData_1.2.13
[34] filelock_1.0.3 curl_7.0.0 org.Hs.eg.db_3.20.0
[37] mime_0.13 vctrs_0.7.2 R6_2.6.1
[40] png_0.1-9 stats4_4.4.2 lifecycle_1.0.5
[43] zlibbioc_1.52.0 KEGGREST_1.46.0 S4Vectors_0.44.0
[46] IRanges_2.40.1 bit_4.6.0 pkgconfig_2.0.3
[49] pillar_1.11.1 glue_1.8.0 tibble_3.3.1
[52] tidyselect_1.2.1 org.Mm.eg.db_3.20.0 rstudioapi_0.18.0
[55] compiler_4.4.2
When trying to map PRG4 to species orthologs, CoSIA seems to only recognize human and rat. This was first noticed in the shiny app, but I have reproduced it using the package.
This gives the warning:
And returns
The "converted_id" returns the same as in the Shiny app when selecting human, mouse, rat, and zebrafish, and regardless of mapping_tool and ortholog_database selection. PRG4 does have mouse and zebrafish orthologs, though, and there's data for them in Bgee https://www.bgee.org/search/genes?search=PRG4
This could just be an issue of needing to update the CoSIAdata, but not sure.
I tested this locally in Rstudio, sessionInfo: