Enricher with Gene Symbols

Question

[Manuel Sokolov Ravasqueira]

Hi!

I have a list of genes with abs(logfc) >= 0.9 like this:

> genes
[1] "MDM2"      "CDK4"      "CCND2"     "FLNA"      "RBP7"      "EDNRB"     "EPHA4"     "PTPRB"     "PPP1R13L"  "TPM1"      "INSR"     
[12] "DLC1"      "WNT7B"     "SFRP1"     "IFI16"     "ZMAT3"     "MEST"      "AKT3"      "CD36"      "SRD5A1"    "KIF23"     "EPOR"  

So the list has the gene symbols. When doing enrichGO i can set the option keyType="Symbol" and use the genes without having to convert to entrez id or other representation like this:

 go_enrich <- enrichGO(gene = genes,
                  universe = names(gene_list),
                  OrgDb = org.Hs.eg.db,
                  keyType="SYMBOL",
                  ont = "ALL",
                  pAdjustMethod = "fdr",
                  pvalueCutoff = 0.05,
                  readable = TRUE)

Currently I am using enricher like this which i don't believe to be right:

C3_t2g <- msigdbr(species = "Homo sapiens", category = "C3") %>% 
dplyr::select(gs_name, gene_symbol)
em <- enricher(genes, TERM2GENE=C3_t2g)

How can I sent the arguments for enricher in order to the list of genes to be symbols and not entrez id?

Thank you!

[bk11]

Enricher is using gene symbols here: em <- enricher(genes, TERM2GENE=C3_t2g) because you have gs_name and gene_symbol columns in your C3_t2g table. So I don't see there is any problem here.

Here is the illustration-

genes=c("MDM2","CDK4","CCND2","FLNA","RBP7","EDNRB","EPHA4","PTPRB","PPP1R13L","TPM1","INSR",   
 "DLC1","WNT7B","SFRP1","IFI16","ZMAT3","MEST","AKT3","CD36","SRD5A1","KIF23","EPOR")

C3_t2g <- msigdbr(species = "Homo sapiens", category = "C3") %>% 
dplyr::distinct(gs_name, gene_symbol) %>% as.data.frame()

head(C3_t2g)
gs_name gene_symbol
1 AAACCAC_MIR140       ABCC4
2 AAACCAC_MIR140    ABRAXAS2
3 AAACCAC_MIR140       ACTN4
4 AAACCAC_MIR140       ACVR1
5 AAACCAC_MIR140       ADAM9
6 AAACCAC_MIR140     ADAMTS5

em <- enricher(genes, TERM2GENE=C3_t2g)

head(em)
                                                         ID                   Description GeneRatio   BgRatio       pvalue    p.adjust      qvalue                 geneID Count
MIR4524A_5P                                     MIR4524A_5P                   MIR4524A_5P      4/21 240/27978 2.817928e-05 0.007955666 0.006073365 CCND2/ZMAT3/AKT3/KIF23     4
MIR4524B_5P                                     MIR4524B_5P                   MIR4524B_5P      4/21 240/27978 2.817928e-05 0.007955666 0.006073365 CCND2/ZMAT3/AKT3/KIF23     4
MIR646                                               MIR646                        MIR646      4/21 247/27978 3.152840e-05 0.007955666 0.006073365   CCND2/INSR/DLC1/AKT3     4
MIR503_5P                                         MIR503_5P                     MIR503_5P      3/21  99/27978 5.457081e-05 0.010327526 0.007884046       CCND2/AKT3/KIF23     3
LET_7A_5P_LET_7C_5P_LET_7E_5P LET_7A_5P_LET_7C_5P_LET_7E_5P LET_7A_5P_LET_7C_5P_LET_7E_5P      4/21 401/27978 2.050963e-04 0.015974030 0.012194594  CCND2/EPHA4/INSR/DLC1     4
LET_7B_5P                                         LET_7B_5P                     LET_7B_5P      4/21 403/27978 2.090303e-04 0.015974030 0.012194594  CCND2/EPHA4/INSR/DLC1     4