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gene list annotation

i have a list of gene (~5000) chromosome wise and i want to know that which gene involved in what pathway and to which disease it is mostly related. can anybody suggest from where to do such kind of thing. any webserver is mostly welcomed if anybody knows which can annotate my whole gene list. thank....

genome gene software error
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updated by EagleEye EagleEye • written by rajesh rajesh

There are many different tools. To name a few DAVID, GOrilla will be somewhere to start

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written by Sam Sam

Thanks for your answer, i have tried on these softwares, but the problem with GOrilla and DAVID is that they dont annotate whole gene list, some gene remain exempted from their annotataion list.

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written by rajesh rajesh

Please use ADD REPLY or ADD COMMENT to answer to earlier reactions, as such this thread remains logically structured and easy to follow.

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written by WouterDeCoster WouterDeCoster

Hello rajesh !

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written by Ram Ram

2 answers

I think this would take some manual work, but you could check and download that information from several biological pathways databases:

NCBI Biosystems database (Geer et al., 2010) includes gene set databases from:

  1. KEGG (Kanehisa et al., 2012)
  2. REACTOME (Matthews et al., 2009)
  3. The Pathway Interaction Database (PID) (Shaefer et al., 2009)
  4. Wikipathways (Kelder et al. 2011)
  5. BIOCYC (REF?? hehe).

For diseases check OMIM? Also you can download all the GWAS catalog database and check for the traits associated to the reported genes?

OMIM: https://www.omim.org/ GWAS catalog (download link): https://www.ebi.ac.uk/gwas/docs/file-downloads

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written by GabrielMontenegro GabrielMontenegro

Try, Gene Set Clustering based on Functional annotation (GeneSCF)

(NOT web-based)

OR

Try this solution (need some scripting), A: How to look up GO terms in BioMart using GI ID or Accession ID

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written by EagleEye EagleEye

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