Question: How Can I Plot Go Data Using R Or Any Tools?
8
gravatar for Bebo
6.2 years ago by
Bebo90
Bebo90 wrote:

Hi all, I want to know how to use R or any tools else for plotting Gene Ontology data.

what I mean is, I made sequence for my plant species transcriptome using 454 sequencer and I annotate the GO terms by blast2GO software, now I want to plot these data using R or any tools. do you know any tools which I can use it to produce nice graph for GO term.

gene visualization • 8.4k views
ADD COMMENTlink modified 6.2 years ago by jhc2.5k • written 6.2 years ago by Bebo90

What do you mean exactly with "Gene Ontology data". Is that information from the Gene Ontology itself. Or do you have another type of data that you analyzed using the Gene Ontology and that you would like to show in the context of that ontology?

ADD REPLYlink written 6.2 years ago by Chris Evelo9.9k
8
gravatar for Pablo Pareja
6.2 years ago by
Pablo Pareja1.6k
Granada, Spain
Pablo Pareja1.6k wrote:

Hi,

if you are interested on graph visualization of protein-go annotations you can take a look into Bio4j Go Tools. Here you have a link to a blog post for this:

http://blog.bio4j.com/2011/04/go-annotation-graph-visualizations-with-bio4j-go-tools-gephi-toolkit-sigma-project/

I forgot to provide some extra links:

Sample GO Annotation results XML file: (from Era7 Automatic annotation of E. coli TY2482)

https://s3-eu-west-1.amazonaws.com/pablo-tests/EHECAnnotationVersion2.xml

Link to a quick tutorial on how to use the graph visualization: http://www.bio4j.com/videos/Bio4jGoToolsGraphUseTutorial.htm

Displaying whole Gene Ontology with Gephi:

http://blog.ohnosequences.com/2011/03/playing-with-gephi-bio4j-and-go/

Cheers,

Pablo

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Pablo Pareja1.6k
3
gravatar for jhc
6.2 years ago by
jhc2.5k
Germany
jhc2.5k wrote:

If you are planning to visualize GO terms obtained from a over/under-representation test, take a look at REVIGO. Pretty handy tool that mitigates the problem of having very similar GO terms in your lists. Visualization is also very good, so you can inspect GO terms as kind of clusters.

[?]

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by jhc2.5k

It looks like the link you provided 'http://revigo.irb.hr/Blockquote' is wrong. I guess the 'Blockquote' part got somehow pasted there ;)

ADD REPLYlink written 6.2 years ago by Pablo Pareja1.6k

fixed! thanks Pablo.

ADD REPLYlink written 6.2 years ago by jhc2.5k

You're welcome. Your platform looks pretty cool! are the services/viewers' implementations open-source? If so, where can the code be found?

ADD REPLYlink written 6.2 years ago by Pablo Pareja1.6k

Pablo, I'm not a developer of REVIGO, so I'm not sure whether the implementation is freely available or not. I know some of the authors, although. Let me forward your question :)

ADD REPLYlink written 6.2 years ago by jhc2.5k

Thanks, I'd appreciate that ;)

ADD REPLYlink written 6.2 years ago by Pablo Pareja1.6k

Hello all, I'm the developer of REVIGO. Regarding code availability - for visualizers, REVIGO uses Google Motion Chart, and Drastic Treemap (which are free but AFAIK not open source), and Cytoscape Web (which is free and open source).

I still haven't released the code that does the semantic-similarity based clustering/redundancy elimination of GO categories, but I'm willing to share, please drop me a note if you're interested in this part.

ADD REPLYlink written 6.2 years ago by fran supek40

Hi Fran, I'd be interested on that part, as well as the one dealing with Cytoscape Web ;)

ADD REPLYlink written 6.2 years ago by Pablo Pareja1.6k
1
gravatar for David Quigley
6.2 years ago by
David Quigley10k
San Francisco
David Quigley10k wrote:

See also the answers to this question on the same topic.

ADD COMMENTlink written 6.2 years ago by David Quigley10k
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