Question: Standard methods for filtering enriched GO terms based on similarity scores?
0
gravatar for mbrando17
4.5 years ago by
mbrando170
United States
mbrando170 wrote:

I have a list of enriched GO terms computed using any gene enrichment tool. I can compute similarity scores for my list of enriched terms using GOSim. And then based on the GOSim similarity scores, I would like to filter my list of enriched terms to remove redundant terms and reduce to a smaller, more meaningful sublist. Are there any precedents or standards for doing this? I can't seem to find anything.

R gene • 2.0k views
ADD COMMENTlink modified 4.5 years ago by Woa2.7k • written 4.5 years ago by mbrando170
0
gravatar for Renesh
4.5 years ago by
Renesh1.6k
United States
Renesh1.6k wrote:

You can use Q-value for filtering enriched GO-terms.

ADD COMMENTlink written 4.5 years ago by Renesh1.6k

I'm assuming my list of enriched GO terms already consists of those enriched terms with adj. p-value (or other statistic) < threshold. I would like to further filter (or essentially re-rank) the list using term similarity scores so that if a set of terms is very similar, one term is kept and the others are removed (or given a lower ranking). I'd like to avoid making arbitrary choices if possible, so I'm just wondering if anyone has seen this done before.

ADD REPLYlink written 4.5 years ago by mbrando170
0
gravatar for Woa
4.5 years ago by
Woa2.7k
United States
Woa2.7k wrote:

See if ReviGo can solve your problem:
http://revigo.irb.hr/

ADD COMMENTlink written 4.5 years ago by Woa2.7k

That's just what I'm looking for. Thanks!

ADD REPLYlink written 4.5 years ago by mbrando170
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