Question: Interpro Enrichment - Any Organism
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gravatar for boczniak767
7.3 years ago by
boczniak767640
Poland
boczniak767640 wrote:

Among many tools for over-/under-representation analysis there are few which are not constrained to fixed list of species.

For my knowledge it is Ontologizer and ASCA-Functional from SEA suite.

There one have to just provide already available association of genes with functional categories.
I wonder if you know any other "open-species" enrichment analysis tools.
I'm mostly interested in analysis of InterPro enrichment tools, where analysis rely on user submitted population and experimantal sets with IDs and file with IDs' association with InterPro IDs.

EDIT

I ended with creation of GO-like association and obo files for InterPro and use Ontologizer program. Much work to do  but works fine.

enrichment function • 3.7k views
ADD COMMENTlink modified 4.6 years ago • written 7.3 years ago by boczniak767640
1
gravatar for Casual
7.2 years ago by
Casual90
Casual90 wrote:

I just found this one ,http://wego.genomics.org.cn/cgi-bin/wego/index.pl ,WEGO by BGI in China. It can accept interpro scan results(raw ,xml,txt) as input.

ADD COMMENTlink written 7.2 years ago by Casual90
0
gravatar for ALchEmiXt
7.3 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

Not sure if I understand your question completely but maybe DAVID can do that for you. It can show enriched Interpro domains...

ADD COMMENTlink written 7.3 years ago by ALchEmiXt1.9k
1

I saw this program at GO website along with similar software.
The problem with it is that it requires specification of type of IDs used. I have a mixed list so it doesn't work for me.

ADD REPLYlink written 7.3 years ago by boczniak767640
1

I learned that mgsa package allows what I need to do http://www.bioconductor.org/packages/release/bioc/html/mgsa.html

ADD REPLYlink written 7.3 years ago by boczniak767640
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