Question: How To Get Gene List From Each Gene Ontology Term?
4
gravatar for Omid
6.3 years ago by
Omid560
Netherlands
Omid560 wrote:

Hi,

I have a long list of Gene Ontology(GO) term like below and I would like to put this list in a on-line free available webpage and then receive the genes which categorize in each GO term ID.

Thanks

GO:0007099 GO:0043516 GO:0045665 GO:0051651 GO:0007017 GO:0051235 GO:0007059 GO:0046777 GO:0051640 GO:0000278 GO:0051301 GO:0048285 GO:0007049

go • 7.1k views
ADD COMMENTlink modified 4 months ago by EagleEye6.5k • written 6.3 years ago by Omid560
5
gravatar for Emily_Ensembl
6.3 years ago by
Emily_Ensembl19k
EMBL-EBI
Emily_Ensembl19k wrote:

You can do this in BioMart on Ensembl.

There's a help video on using BioMart here:

<iframe></iframe>

The tool is here: http://www.ensembl.org/biomart/martview/c7904f8b46d31846e072964b3ca0955a

You can just filter by GO accessions, then get gene names as attributes.

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Emily_Ensembl19k

I really appreciate

ADD REPLYlink written 6.3 years ago by Omid560

Dear Emily,

I think there is some discordance. For example GO:0044702 is: single organism reproductive process

But when I put it in Biomart I got GO:0001541 which is:ovarian follicle development

Do you know what the resoan? is and how can I solve the problem?

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Omid560
1

I assume that you're filtering by GO:0044702, then selecting GO term accession as an attribute?

What's happening here is that the GO terms that you get out of BioMart are the most specific ones available. GO terms are hierarchical, so GO:0044702 is a very general term, and GO:0001541 is a more specific term which is a subset of GO:0044702. So everything with the GO term GO:0001541 will pass the filter for GO:0044702, but only GO:0001541, or other more specific GO terms, such as GO:0001554 and GO:0007276, will be displayed.

ADD REPLYlink written 6.3 years ago by Emily_Ensembl19k

Thanks,

But for my calculation I need just GO:0044702 and the genes which located in this GO term not the others.

ADD REPLYlink written 6.3 years ago by Omid560
1
gravatar for EagleEye
4 months ago by
EagleEye6.5k
Sweden
EagleEye6.5k wrote:

Hi, since this thread is live again. Feel like I must also contribute with some updated/easy solution. (Note: Sorry, this is command-line solution)

You can retrieve complete list of GO terms with corresponding genes as plan text table format using GeneSCF's prepare_database module.

Download all GO terms and list of genes from human:

./prepare_database -db=GO_all -org=goa_human

If you like to retrieve genes only for you GO term list, grep your terms against GeneSCF downloaded table.

grep -fF PATH/YOUR_TERMS_oneTermPerLine.list PATH/geneSCF-master-source-v1.1-p2/class/lib/db/goa_human/GO_all_sym.txt >  PATH/YOUR_TERMS_withGenes.table.txt
ADD COMMENTlink modified 4 months ago • written 4 months ago by EagleEye6.5k
0
gravatar for murshad.60ali
4 months ago by
murshad.60ali10 wrote:

library(GO.db)

Term("GO:0006281")

GO:0006281 "DNA repair"

ADD COMMENTlink written 4 months ago by murshad.60ali10

While your contribution to an old thread for completeness is valued, this barely constitutes an answer in its present form. This is presumably some R code based on the use of library(), but it isn't at all clear. As a minimum, please format the code (if that is what it is) with proper code highlighting (the 101010 button).

ADD REPLYlink written 4 months ago by Joe14k
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