Pathway analysis programs

Question

[benzhang]

Hello all,

Can anyone recommend me some softwares for pathway analysis? Basically, I have 100 genes and I would like to know which pathways they are involved in. So far, I've tried DAVID, and Reactome pathway database. DAVIA seems to give me a list of known pathway of each gene in the list. However Reactome gives me a list of pathways that contains genes in my list, which is what I want. The problem with Reactome is that there are 20 genes that it doesn't recognize from my list. Can someone recommend me some other software that's like Reactome? Thank you!

Best, Ben

Answer 1

[HK]

Well i have always used ingunity pathway analysis (IPA) and it recognise almost all the genes.

Answer 2

[Samarth Kulshrestha]

I think you can map your genes to KEGG database (link below):

http://www.genome.jp/kegg/tool/map_pathway1.html

This should give you the list of pathways that contains your genes.

Answer 3

[pixie@bioinfo]

All genes may not be enzyme coding, and may not be annotated for biochemical pathways. GO enrichment might be another option to consider.