Figuring out gene pathway/interaction after gene annotation

[Sunil Kamalakar]

Hi All,

We have whole genome data for a trio(mom, dad and kid), which we have annotated using snpEff.

Now after annotation, what is the best way to figure out pathway and other interaction involved? What are best tools that I could use to do the same.

Thanks.

[TiborNagy]

You can use gene ontology annotation and some tool that can find over represented GO terms. I had used NestedMica, but I think it is not up to date now. You can browse tools here.

Another solution is KEGG database. There are lots of R package to analyse a KEGG pathways:
here and here.

[Sunil Kamalakar]

Thank you TiborNagy. I will have a look at these packages.