[BioC] How to compare GO term lists and create matching network?

Paul Shannon pshannon at fhcrc.org
Tue Nov 12 20:30:30 CET 2013

Hi Bernardo,

As you suggest, you have a lot of options.  Venn diagrams can be useful for a quick survey of overlapping group memberships, especially if (as in your case) you have no more than three groups.  Google "R cran venn" and you will see a few.

Your choice of technique should be guided by the scope and depth of the analysis you wish to perform.   Here at Bioconductor, we tend to think that the analysis of experimental data is a nuanced and ongoing process, in which early stage explorations often lead to questions and analyses not obvious at first blush.  R is a great language for exploring data, and may be worthwhile for you to learn: point-and-click analysis tools will take you only so far.

If you could give us a better idea of what you hope to learn from your analysis, we can probably give you more specific advice.

 - Paul


On Nov 9, 2013, at 3:08 AM, Bernardo Bello wrote:

> Hi community,
> I would like to compare three lists of GO terms, coming from an enrichment
> analysis and create a network figure and some tables with shared GO terms.
> Since a simple Venn diagram will not take into account possible parent
> absence in some samples, could someone suggest me the appropriate tool or
> refer me to a post if this has been previously asked? I've looking this
> post http://www.biostars.org/p/1277/, but I'm very new to this and don't
> know where to start.
> Cytoscape looks promising, specially because its easy to use GUI but I'm
> also open to new tools, like R/Bioconductor. Does this tool meets my needs?
> http://baderlab.org/Software/EnrichmentMap
> Last, I'm working with bacterial data, non-model organism.
> Thanks for your help. Best, Bernardo
> -- 
> *Bernardo Bello Ortí*
> PhD student
> Campus de Bellaterra-Universitat Autònoma de Barcelona
> Edifici CReSA
> 08193  Bellaterra (Barcelona, Spain)
> Tel.: 647 42 52 63 *www.cresa.es <http://www.cresa.es>  *
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