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

[Mark W Kimpel]

I have a list of about 300 rat genes that are differentially expressed 
in an experiment. Irrespective of what transcription factors (TFs) are 
in my list, I would like to test to see if any of the known TFs in the 
affy chipset I am using (rat2302) are over-represented in the promotor 
regions of my list of sig. genes.

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.

It seems that what is needed is an annotation package with a list that 
contains all the genes with all the TF's associated with each gene. A 
Google search reveals several proprietary databases with this type of 
information but one then has to use a proprietary tool to access. Is 
there anything in BioC or some other open-source repository to address 
my need? Remember, I am working with rat genes. I have seen some stuff 
for human and mouse, but not for rat.

Thanks,
Mark

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

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