Tools For Pathway/Gene Set Analysis Of Gwas (Genome-Wide Association Study) Data

Question

[Larry_Parnell]

I am reading the thorough review by Wang, et al entitled "Analysing biological pathways in genome-wide association studies" and as this will become an important aspect of our research, I thought to solicit opinions and advice from BioStar members.

Which approach(es) do you take toward pathway or gene-set analysis of GWAS data? Do you prefer to work with a list of SNP p-values as input or raw SNP genotypes? Or something else? What are your primary sources of pathways and gene-sets? Which software tools do you prefer for the actual analysis?

Lastly, can you offer any advice regarding caveats or pitfalls to the analysis of GWAS data with pathways?

Thanks much - responses will certainly help in guiding our research in the near term.

Answer 1

[Ryan D]

Hi Larry,

For this, I like to run my list of genes through my favorite Pubmed abstract searching tool: Chilibot. It practically writes paper discussions for you.

If using P-values, we also like to use GRAIL . Mary has a nice little tutorial on how it works over at OpenHelix.

GSA-SNP is very handy since it uses permutations.

Most recently our group has been using our own eQTL database compiled from a bunch of studies done by others, but we've also enjoyed using RegulomeDB and HaploReg. We've downloaded RegulomeDB since we use it quite frequently, but it only has a subset of the eQTL studies in the database I've built.

My colleague also has built a couple tools including GWAR which try to tap in to GWAS, ENCODE, eQTL, and other data types.