Functional Annotation With Ensembl Gene Ids

Question

[jackuser1979]

I have a set of gene of interest with ensembl Gene ids and I want to do functional annotation for each and to categorize them based on function. I am interested to do other than doing with blast2GO. I have tried with DAVID tool, but I don't find any functional annotation for my set of genes. Can I try with eggNOG?. Any suggestion for using better tool for functional annotation.

Answer 1

[Zev.Kronenberg]

You might find BioMarts ID conversion tool very handy. You can get GO terms and much more.

http://central.biomart.org/converter/#!/ID_converter/gene_ensembl_config_2

also check out Amigo:

http://amigo.geneontology.org/cgi-bin/amigo/go.cgi

Answer 2

[Giulietta - Ensembl Helpdesk]

BioMart is a useful tool for this, as mentioned.

The Ensembl Core Perl API can also be used to retrieve GO terms.

Installation instructions are here:

http://www.ensembl.org/info/docs/api/api_installation.html

Modules are here:

http://www.ensembl.org/info/docs/Doxygen/core-api/index.html

Specifically, you would want the ontologyterm adaptor methods.

If you have more questions about how to get GO terms for Ensembl transcripts, email us at [e-mail]