Question: Download gene list associated with GO terms from DAVID
1
gravatar for qwzhang0601
17 months ago by
qwzhang060150
United States
qwzhang060150 wrote:

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

go • 843 views
ADD COMMENTlink modified 17 months ago by jin80 • written 17 months ago by qwzhang060150
0
gravatar for EagleEye
17 months ago by
EagleEye5.1k
Sweden
EagleEye5.1k wrote:

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/'.

ADD COMMENTlink modified 17 months ago • written 17 months ago by EagleEye5.1k

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.

ADD REPLYlink written 17 months ago by qwzhang060150

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.

ADD REPLYlink written 17 months ago by emblake40

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

ADD REPLYlink written 17 months ago by EagleEye5.1k
0
gravatar for jin
17 months ago by
jin80
jin80 wrote:

For Plant GO annotation and enrichment analysis, try PlantRegMap.

ADD COMMENTlink written 17 months ago by jin80

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

ADD REPLYlink written 17 months ago by Ram15k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1978 users visited in the last hour