Gene pathway analysis of my list of genes
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?
• 2,618 views
•
link
updated
by
GenoMax
•
written
by
Pin.Bioinf
•
written
by
Pin.Bioinf
2 answers
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
• 0 views
•
link
written
by
Kevin Blighe
GeneSCF. Described here: Gene Set Clustering based on Functional annotation (GeneSCF)
Log in to answer this question.
There are a couple of R packages which work together called Gage and Pathview, they use KEGG pathway information.