Question: Tool to Visualize a list of GO- or InterPro-Terms
0
gravatar for werwulfff
3.1 years ago by
werwulfff0
werwulfff0 wrote:

Hi,

I have created my own database and blasted it against 6 metagenome samples. My output are long lists of genes and their GO- or InterPro-Terms.

Now I want to visualize these Terms with a tool or a program or something else.

I've tried REVIGO and it worked so far, but it would be nice to visualize the terms to a network. The next tool I've tried was Cytoscape, but there are only tools for fix organisms and not for hole databases (for example UniProt).

I hope someone can help me and sorry for my bad english.

visualization sequence gene • 1.3k views
ADD COMMENTlink modified 3.1 years ago by LLTommy1.2k • written 3.1 years ago by werwulfff0
0
gravatar for Tim D
3.1 years ago by
Tim D50
Belgium, Leuven
Tim D50 wrote:

I'm not sure I understand what exactly you're after. If you are trying to visualize different GO classifications and their relation to one another, you could look at GOView.

ADD COMMENTlink written 3.1 years ago by Tim D50
0
gravatar for Philipp Bayer
3.1 years ago by
Philipp Bayer6.0k
Australia/Perth/UWA
Philipp Bayer6.0k wrote:

If you don't have too many GO-terms (let's say, only for a specific condition), you can put them into a tool like DAVID or agriGO to get GO hierarchies, functional enrichment, etc.

ADD COMMENTlink written 3.1 years ago by Philipp Bayer6.0k
0
gravatar for LLTommy
3.1 years ago by
LLTommy1.2k
LLTommy1.2k wrote:

Have a look at the beta of the Ontology Lookup Service (OLS) located here. Find for example go and in there one of your terms and click on the button visualisation.

Would that be what you are looking for? Are all your terms within GO? If you have other terms, are these part of ontologies that are within the OLS?

ADD COMMENTlink written 3.1 years ago by LLTommy1.2k
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