Question: Motif Annotation
gravatar for Dataminer
7.2 years ago by
Dataminer2.6k wrote:

Dear all,

I have a set of motifs and would like to have the GO annotation for these motifs.

Something like associating motifs to GO terms through their gene targets.....

Any suggestion for an existing tool which can do this or a group of tools that can be used to achieve this....

Thank you

gene annotation motif • 2.5k views
ADD COMMENTlink modified 7.2 years ago by Charles E. Grant220 • written 7.2 years ago by Dataminer2.6k
gravatar for Alastair Kerr
7.2 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

It depends on the motifs and the reason why you wish to associate them. Protein motifs? Regulatory DNA motifs?

One approach would to perform some GO term enrichment analysis such as BINGO ( this and other tools here) on the associated genes, taking care ensure the enriched terms are appropriate

Alternatively why not link to known Interpro motifs? If applicable this may be much cleaner. Use the precalculated data from model organisms or use Interproscan if not known.

ADD COMMENTlink written 7.2 years ago by Alastair Kerr5.2k
gravatar for Charles E. Grant
7.2 years ago by
Charles E. Grant220 wrote:

If you are talking about DNA motifs, take a look at GOMO. It's part of the MEME Suite. Your motifs have to be in MEME format.

"GOMO will use the DNA binding motifs to find putative target genes and analyze their associated GO terms. A list of significant GO terms that can be linked to the given motifs will be produced."

ADD COMMENTlink written 7.2 years ago by Charles E. Grant220
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