Gene pathway analysis of my list of genes

Question

[Pin.Bioinf]

Hello, I am new to pathway analysis and I need to do one for many lists of genes.

My list of genes looks like this: "KRTCAP3" "NDRG2" "TPPP2" "AL161668.5" "FBXO43" "CAD" "IGFALS" "ZMYND19" "SPATA6" "PITX1" "CD81" "IGFALS" "NDRG2" ... "DIRAS3" "RP11-564D11.3" "SIX1" "PCDH9" "EDIL3" "ACSL1" "ACOT12" "B3GAT1" "ZNF385B"

What tool in R can I use? Is there a code example somewhere?

[mastal511]

There are a couple of R packages which work together called Gage and Pathview, they use KEGG pathway information.

Answer 1

[Kevin Blighe]

You will hopefully get a few answers here, as there are undoubtedly many options.

• One recent one that I used for KEGG pathways is KEGGprofile.
• For Reactome pathways, there is ReactomePA

Answer 2

[GenoMax]

GeneSCF. Described here: Gene Set Clustering based on Functional annotation (GeneSCF)