> library(msigdbr)
> msigdbr_species()
# A tibble: 11 x 2
species_name species_common_name
<chr> <chr>
1 Bos taurus cattle
2 Caenorhabditis elegans roundworm
3 Canis lupus familiaris dog
4 Danio rerio zebrafish
5 Drosophila melanogaster fruit fly
6 Gallus gallus chicken
7 Homo sapiens human
8 Mus musculus house mouse
9 Rattus norvegicus Norway rat
10 Saccharomyces cerevisiae baker's or brewer's yeast
11 Sus scrofa pig
> temp=msigdbr(species = "Mus musculus")
> head(temp)
# A tibble: 6 x 17
gs_cat gs_subcat gs_name entrez_gene gene_symbol human_entrez_ge~
<chr> <chr> <chr> <int> <chr> <int>
1 C3 MIR:MIR_~ AAACCA~ 239273 Abcc4 10257
2 C3 MIR:MIR_~ AAACCA~ 109359 Abraxas2 23172
3 C3 MIR:MIR_~ AAACCA~ 60595 Actn4 81
4 C3 MIR:MIR_~ AAACCA~ 11477 Acvr1 90
5 C3 MIR:MIR_~ AAACCA~ 11502 Adam9 8754
6 C3 MIR:MIR_~ AAACCA~ 23794 Adamts5 11096
# ... with 11 more variables: human_gene_symbol <chr>, gs_id <chr>,
# gs_pmid <chr>, gs_geoid <chr>, gs_exact_source <chr>, gs_url <chr>,
# gs_description <chr>, species_name <chr>, species_common_name <chr>,
# ortholog_sources <chr>, num_ortholog_sources <dbl>
> a=data.frame(temp[,1],temp[,2])
> table(a)
gs_subcat
gs_cat CGN CGP CM CP CP:BIOCARTA CP:KEGG CP:PID
C1 18362 0 0 0 0 0 0 0
C2 0 0 363345 0 4343 4761 12525 8017
C3 0 0 0 0 0 0 0 0
C4 0 41371 0 47519 0 0 0 0
C5 0 0 0 0 0 0 0 0
C6 29262 0 0 0 0 0 0 0
C7 921461 0 0 0 0 0 0 0
C8 52047 0 0 0 0 0 0 0
H 7309 0 0 0 0 0 0 0
gs_subcat
gs_cat CP:REACTOME CP:WIKIPATHWAYS GO:BP GO:CC GO:MF HPO
C1 0 0 0 0 0 0
C2 84995 25514 0 0 0 0
C3 0 0 0 0 0 0
C4 0 0 0 0 0 0
C5 0 0 630418 92266 99925 352419
C6 0 0 0 0 0 0
C7 0 0 0 0 0 0
C8 0 0 0 0 0 0
H 0 0 0 0 0 0
gs_subcat
gs_cat MIR:MIR_Legacy MIR:MIRDB TFT:GTRD TFT:TFT_Legacy
C1 0 0 0 0
C2 0 0 0 0
C3 33873 363011 142328 151761
C4 0 0 0 0
C5 0 0 0 0
C6 0 0 0 0
C7 0 0 0 0
C8 0 0 0 0
H 0 0
http://bioinf.wehi.edu.au/software/MSigDB/
image.png
提取KEGG,GO_BP dataframe
> KEGG_df = msigdbr(species = "Mus musculus",category = "C2",subcategory = "CP:KEGG")
> GO_df = msigdbr(species = "Mus musculus",category = "C5",subcategory = "GO:BP")
