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Old 09-05-2012, 06:09 PM   #1
Sunil Kamalakar
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Location: USA

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Default 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.

Thanks.
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Old 09-06-2012, 06:19 AM   #2
TiborNagy
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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.
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Old 09-06-2012, 07:48 AM   #3
Sunil Kamalakar
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Thank you TiborNagy. I will have a look at these packages.
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