[BioC] over-representation of specific transcription factors in gene lists

[Seth Falcon]

Mark W Kimpel <mwkimpel at gmail.com> writes:
> This seems very similar to what we go with analysis for GO category 
> over-representation, without the parent-child complication of the GO 
> structure, but with the 1 TF: many genes issue.

I can see the similarity.  I don't know whether the annotation data
you are interested in is available -- perhaps an expert will chime
in.  I can tell you that we are working on extensions to the Category
package that will integrate with the new GSEAbase package and make it
"easy" to plug in a custom gene set collection (like TFs) and carry
out the Hypergeometric analysis (as well as other analysis
approaches).  The code isn't ready yet, but is on the schedule.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/