How Can I Plot Go Data Using R Or Any Tools?

Question

[Bebo]

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.

[Chris Evelo]

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?

Answer 1

[Pablo Pareja]

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

Answer 2

[jhc]

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.

[?]

[Pablo Pareja]

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

[jhc]

fixed! thanks Pablo.

[Pablo Pareja]

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

[jhc]

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 :)

[Pablo Pareja]

Thanks, I'd appreciate that ;)

[fran supek]

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.

[rishi.dasroy]

I have many groups of GO terms and for each group using a server is not very easy. It would be nice to have it as an R package or like biomaRt .

[Pablo Pareja]

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

Answer 3

[David Quigley]

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