Enrichment analysis/ statistical test for Epigenetic modification on SNP

Question

[BIOTIN]

Dear all,

Is there any way to Enrichment analysis/ statistical test for Epigenetic modification on SNP? Any example/method/tool would be appreciated.

Answer 1

[natasha.sernova]

Look at this paoer:

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-99

SNP-based pathway enrichment analysis for genome-wide association studies

Answer 2

[Biogeek]

you could always do manual fishers test in R along with a bit of file manipulation and manual work. Takes quite a bit of time, but an avenue worth investigating. I recently done this for IPR enrichment.