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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.

  • #2
    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.

    Comment


    • #3
      Thank you TiborNagy. I will have a look at these packages.

      Comment

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