GO and KEGG from DESeq2 counts

Question

[devarts]

Does anyone know of a Bioconductor or other R package that can do GO and/or KEGG Gene set enrichment analysis from counts generated with DESeq2? I have a set of counts generated via DESeq2, with some very nice differential expression analysis. I was thinking of redoing the DE analysis using EdgeR which also uses a negative bionomial based normalization, as I could then use the GOana package for GO and KEGG analysis. Can that work with DESeq2, or is there a similar package that can use counts generated in DESeq2?

[Hann]

topGO R package is very good and it will work very well for your DESeq2 if you have the GO labels for your genes/proteins sequences:

https://bioconductor.org/packages/release/bioc/html/topGO.html

https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf

[Arindam Ghosh]

Just curious to know why edgeR works with GOana whille DESeq2 doesn't. Both gives a list of genes and I have performed GO analysis based on this list on web via DAVID and Panther. What's the difference with R packages?

Answer 1

[eyonesi]

GOseq is a suitable R package for GO AND KEGG enrichment. Maybe this link will help you related to DESeq2.

https://wikis.utexas.edu/display/bioiteam/GO+Enrichment+using+goseq