Get Gene families from Mus musculus
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Entering edit mode
22 months ago
JulianC ▴ 20

Hi! I need to have a table of all gene families from Mus musculus with the relative genes that compose each of them. For human it is very simple with HGNC database (https://biomart.genenames.org/martform/#!/default/HGNC?datasets=hgnc_family_mart). For mouse I found the MGI database but I am not able to identify specifically the total number of gene families and the corresponding genes. Do you have a solution for that? Thank you!

gene families • 499 views
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Entering edit mode
22 months ago

Not sure if this is what you need (to which gene families are you referring?), but you can generate an annotation table in R:

require(biomaRt)

mart <- useMart('ENSEMBL_MART_ENSEMBL', host = 'useast.ensembl.org')
mart <- useDataset('mmusculus_gene_ensembl', mart)

annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'mgi_symbol',
    'ensembl_gene_id',
    'entrezgene_id',
    'gene_biotype',
    'family',
    'family_description',
    'superfamily',
    'wikigene_description'))

head(annotLookup)
  mgi_symbol    ensembl_gene_id entrezgene_id   gene_biotype         family
1     mt-Nd1 ENSMUSG00000064341         17716 protein_coding  PTHR11432_SF3
2     mt-Nd2 ENSMUSG00000064345         17717 protein_coding PTHR22773_SF41
3     mt-Co1 ENSMUSG00000064351         17708 protein_coding      PTHR10422
4     mt-Co2 ENSMUSG00000064354         17709 protein_coding      PTHR22888
5     mt-Co2 ENSMUSG00000064354         17709 protein_coding      PTHR22888
6    mt-Atp8 ENSMUSG00000064356         17706 protein_coding      PTHR13722
                                                              family_description
1 NADH UBIQUINONE OXIDOREDUCTASE CHAIN 1 EC_7.1.1.2 NADH DEHYDROGENASE SUBUNIT 1
2 NADH UBIQUINONE OXIDOREDUCTASE CHAIN 2 EC_7.1.1.2 NADH DEHYDROGENASE SUBUNIT 2
3   CYTOCHROME C OXIDASE SUBUNIT 1 EC_1.9.3.1 CYTOCHROME C OXIDASE POLYPEPTIDE I
4             CYTOCHROME C OXIDASE SUBUNIT 2 CYTOCHROME C OXIDASE POLYPEPTIDE II
5             CYTOCHROME C OXIDASE SUBUNIT 2 CYTOCHROME C OXIDASE POLYPEPTIDE II
6                                                                 ATP SYNTHASE 8
  superfamily            wikigene_description
1                NADH dehydrogenase subunit 1
2                NADH dehydrogenase subunit 2
3    SSF81442  cytochrome c oxidase subunit I
4    SSF49503 cytochrome c oxidase subunit II
5    SSF81464 cytochrome c oxidase subunit II
6                   ATP synthase F0 subunit 8

Then, write it out and date-stamp the filename:

write.table(
  annotLookup,
  paste0('Mouse_', gsub("-", "_", as.character(Sys.Date())), '.tsv'),
  sep = '\t',
  row.names = FALSE,
  quote = FALSE)

Kevin

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Entering edit mode

Thank you Kevin! I am just looking for all the gene families in the mouse for some analyses on them. I will try with your suggestion!

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Okay, let me know if this solution helps you.

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