Over Representation Analysis over one specific pathway

Question

[Manuel Sokolov Ravasqueira]

Hi!

Let's say I would like to analyse if a particular pathway is enriched how would I do that given that I have a set of DGE genes resulting from 1500 genes of RNA Seq?

I do not want to analise any of the default pathways such as C2..C9 or ALL (MF, CC, BP)

go_enrich_1 <- enrichGO(gene = genes,
                  universe = names(gene_list_1),
                  OrgDb = org.Hs.eg.db,
                  keyType="SYMBOL",
                  ont = "ALL",
                  pAdjustMethod = "fdr",
                  pvalueCutoff = 0.05,
                  readable = TRUE)

Here I analyze ALL the CC, MF and BP and below cancer related pathways.

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

I would like to just analyze if the glicolysis is altered between groups, how can I do that?

[GenoMax]

You have not validated answers on past questions you have asked so far. Accepting answers (green checkmark) is one way of appreciating help you receive here. It also provides closure to the threads. Please consider checking your past questions and accepting the answers/upvoting helpful comments.

[Manuel Sokolov Ravasqueira]

Thank you for notice @genomax. I added green checkmark in all the solved threads and added feedback to the questions.

Answer 1

[Manuel Sokolov Ravasqueira]

SOLVED. I did this:

hs_kegg_df <- msigdbr(species = "Homo sapiens") %>%
dplyr::filter(
gs_cat == "C2", # This is to filter only to the C2 curated gene sets
gs_subcat == "CP:KEGG" # This is because we only want KEGG pathways
)
hs_kegg_df <- hs_kegg_df[,c("gs_name","gene_symbol","gs_exact_source")]
# Get the ones related to glycolisis
hs_kegg_df <- subset(hs_kegg_df, grepl("^hsa00|^hsa01, gs_exact_source))
hs_kegg_df <- hs_kegg_df[,c("gs_name","gene_symbol")]
em <- enricher(genes, minGSSize=1, maxGSSize = 20,  universe = names(gene_list), TERM2GENE=hs_kegg_df,pAdjustMethod = "bonferroni")