species "Mus musculus" returns human sets

[l-ko]

Find GOBP_FEMALE_SEX_DIFFERENTIATION set:

# load mouse DB
msdb <- msigdbr(species = "Mus musculus") # 2023.1.1

# find all GOBP_FEMALE_SEX_DIFFERENTIATION genes and group into set
results <- msdb %>%
    filter(grepl(tolower('GOBP_FEMALE_SEX_DIFFERENTIATION'), tolower(gs_name))) %>%
    group_by(gs_name, gs_description) %>%
    summarise(
      genes = list(ensembl_gene),
      .groups = 'drop'
    )

print(results)

# A tibble: 1 × 3
  gs_name                         gs_description                                                                          genes      
  <chr>                           <chr>                                                                                   <list>     
1 GOBP_FEMALE_SEX_DIFFERENTIATION The establishment of the sex of a female organism by physical differentiation. [GOC:bf] <chr [122]>

There are 122 genes in a set which looks like a human set https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/GOBP_FEMALE_SEX_DIFFERENTIATION.html

since mouse one contains 156 genes https://www.gsea-msigdb.org/gsea/msigdb/mouse/geneset/GOBP_FEMALE_SEX_DIFFERENTIATION.html

I tried few other sets with the same results.

Find all fibrosis related sets:

# A tibble: 16 × 3
   gs_name                                        gs_description                             genes      
   <chr>                                          <chr>                                      <list>     
 1 HP_CONGENITAL_FIBROSIS_OF_EXTRAOCULAR_MUSCLES  Congenital fibrosis of extraocular muscles <chr [6]>  
 2 HP_CONGENITAL_HEPATIC_FIBROSIS                 Congenital hepatic fibrosis                <chr [47]> 
 3 HP_ENDOCARDIAL_FIBROSIS                        Endocardial fibrosis                       <chr [6]>  
 4 HP_HEPATIC_BRIDGING_FIBROSIS                   Hepatic bridging fibrosis                  <chr [9]>  
 5 HP_HEPATIC_FIBROSIS                            Hepatic fibrosis                           <chr [142]>
 6 HP_INTERSTITIAL_CARDIAC_FIBROSIS               Interstitial cardiac fibrosis              <chr [10]> 
 7 HP_MYELOFIBROSIS                               Myelofibrosis                              <chr [13]> 
 8 HP_MYOCARDIAL_FIBROSIS                         Myocardial fibrosis                        <chr [18]> 
 9 HP_PANCREATIC_FIBROSIS                         Pancreatic fibrosis                        <chr [22]> 
10 HP_PERIPORTAL_FIBROSIS                         Periportal fibrosis                        <chr [10]> 
11 HP_PORTAL_FIBROSIS                             Portal fibrosis                            <chr [15]> 
12 HP_PULMONARY_FIBROSIS                          Pulmonary fibrosis                         <chr [72]> 
13 HP_RENAL_FIBROSIS                              Renal fibrosis                             <chr [16]> 
14 REACTOME_DEFECTIVE_CFTR_CAUSES_CYSTIC_FIBROSIS Defective CFTR causes cystic fibrosis      <chr [61]> 
15 WP_LUNG_FIBROSIS                               Lung fibrosis                              <chr [63]> 
16 WP_NITRIC_OXIDE_METABOLISM_IN_CYSTIC_FIBROSIS  Nitric oxide metabolism in cystic fibrosis <chr [13]> 

returns lots of human sets. There is only one WP_LUNG_FIBROSIS might be mouse one, but it is likely the human because it has 63 genes, and mouse one should be 60.

It seems that either older MSigDB had no mouse sets (idk) or they are not loaded correctly.