SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   Figuring out gene pathway/interaction after gene annotation (http://seqanswers.com/forums/showthread.php?t=23091)

Sunil Kamalakar 09-05-2012 06:09 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.

Thanks.

TiborNagy 09-06-2012 06:19 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 07:48 AM

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


All times are GMT -8. The time now is 06:29 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.