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09-05-2012, 07:09 PM
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#1 |
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Junior Member
Location: USA Join Date: Sep 2012
Posts: 2
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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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09-06-2012, 07:19 AM
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#2 |
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Senior Member
Location: Budapest Join Date: Mar 2010
Posts: 329
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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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09-06-2012, 08:48 AM
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#3 |
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Junior Member
Location: USA Join Date: Sep 2012
Posts: 2
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Thank you TiborNagy. I will have a look at these packages.
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| Tags |
| gene annotation, gene pathway analysis, trio |
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