Pathway analysis of Mouse

Question

[arpa530]

Hello,

I am working on RNA-seq analysis of mouse. I have found significantly differentiated gene through cuff diff analysis. After doing that I have performed the Gene Ontology and Pathview analysis. Here is my next question how can I identify which genes are linked to multiple pathways? Because Pathview gives the individual pathway result. It is very esoteric to do this work manually by looking all those genes. Your suggestion will be highly appreciated.

Thanks.

Answer 1

[Guangchuang Yu]

see this RNA workflow which use clusterProfiler.

Answer 2

[EagleEye]

Gene Set Clustering based on Functional annotation (GeneSCF)