Download gene list associated with GO terms from DAVID

Question

[qwzhang0601]

Is there a way to download all the gene list associated with a BP GO term (e.g. 0006281) from DAVID. For a few enriched GO terms I need all genes associated with those terms as background genes for further analysis.

I tried to get such gene list from GSEA database, but it seems the gene list is larger in DAVID than that in GSEA. I also tried the methods from a previous post (such as quickGo and Biomart), but it seems those methods will not extract the genes with descending GO terms (e.g., some genes have a more specific GO term which "is-a" child term of the current term). The genes I got through those methods is much less than those in DAVID.

A previous associated post suggested some methods.
"Retrieve All Genes Associated With A Go Term" Retrieve All Genes Associated With A Go Term

Many thanks

Answer 1

[EagleEye]

GeneSCF is perl based tool where you can reterive complete GO (CURRENT) into simple tab-seperated table format (GOID GOTERM GENES).

Example :

Downloading current available database for Mus Musculus from Gene Ontology

./prepare_database -db=GO_all -org=mgi (OR)
./prepare_database -db=GO_BP -org=mgi
./prepare_database -db=GO_MF -org=mgi
./prepare_database -db=GO_CC -org=mgi

The above command downloads complete GO db as simple text file in following location, 'geneSCF-tool/class/lib/db/mgi/'.

[qwzhang0601]

Thank you. But finally I found an easy way. I uploaded all protein coding genes into DAVID and do enrichment analysis. Then download the overlapped genes with each GO terms. Although it seems the overlapped genes is a little less than those in DAVID, because I am only interested in protein coding genes, those are enough for me. Thank you all the same.

[emblake]

I would like to download GeneSCF to give it a try, but your website isn't working. Is it me or is there an issue? Thanks.

[EagleEye]

Hi emblake, it is working fine. Please check your firewall settings if that is creating any problem (othewise check with other internet/network connection source).

I cannot see any problems with the website. The download links are working fine. Please let me know if the problem persists.

GeneSCF v1.1-p1 (patch release 1) http://genescf.kandurilab.org/ftp/download-v1.1-p1.php

GeneSCF v1.1 http://genescf.kandurilab.org/ftp/download-v1.1.php

GeneSCF v1.0 http://genescf.kandurilab.org/ftp/download-v1.0.php

Answer 2

[jin]

For Plant GO annotation and enrichment analysis, try PlantRegMap.

[Ram]

You are continuing this in spite of my warning. Your user account has been suspended.