I'm currently doing RNA-seq, and one of the things I would like to do is to see what genes are differentially expressed in different pathways related to the EGFR network. The pathways I'm especially interested in are the MAPK/ERK, PI3K/AKT and JAK/STAT pathways. The problem is, for me, how do I define these pathways? What I would like to do is to get a gene list of all the genes in each of the pathways, so I can say "according to <source(s)>, the JAK/STAT pathway consists of <list of genes>". The idea is then to see how the different pathways differ in terms of gene expression between my various experimental parameters, i.e. taking the analysis down from a global scale to a pathway scale.
Getting such gene lists was, apparently, all too easy, since there are so many different sources to choose from - which is the problem. I've looked at some other questions here at BioStar (A: How To Get Snps Matrix For Population Genetic Ananlysis From Snps Variant Files, Gene Pathway Association File For Kegg, Extracting List Of Genes Associated With A Pathway In Kegg) and checked some of the web-based tools to do it (KEGG, GSEA). I now have quite a few lists of the three pathways to choose from, but they are quite different. I found lists from Biocarta, KEGG, GO annotation and PID, but not a single source had genes for all three pathways, at least not that I could find.
How would one go about solving this? Just picking one of the lists at random or arbitrarily seems... iffy. I'm sure I'm not the first one to have this issue. How have you / would you solve it? Thanks in advance!