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Sunil Kamalakar 09-05-2012 07:09 PM

Figuring out gene pathway/interaction after gene annotation
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.


TiborNagy 09-06-2012 07:19 AM

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 09-06-2012 08:48 AM

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

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