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Gene functional annotation

I have ~ 5000 gene and i want to annotate them that in which pathway they belongs to but the existing software like DAVID and PANTHER only annotate ~ 3000 gene from my list. So can anyone suggest me that from where i can functionally annotate all my gene list which are in ensembl ID form. Thanks....

genome gene blast
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updated by Elisabeth Gasteiger Elisabeth Gasteiger • written by rajesh rajesh

Hello rajesh !

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written by Ram Ram

2 answers

  • Convert your Ensembl ids to genesymbols (HGNC) or EntrezIds using Biomart

1) Select dataset

2) click Filters on left side -> Gene -> Input External reference IDs (paste your ensembl IDs)

3) click Attribute on left side -> External -> Entrez Gene ID or HGNC symbol

4) Results

  • Use GeneSCF tool for functional annotation (check the advantages of using GeneSCF).

Gene Set Clustering based on Functional annotation (GeneSCF)

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written by EagleEye EagleEye

You can also try UniProt's IDmapping tool (http://www.uniprot.org/uploadlists) to map to UniProtKB, and once you have your results, use the "Customize" button to add a column for pathway, to see which of your proteins have pathway annotations.

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written by Elisabeth Gasteiger Elisabeth Gasteiger

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