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 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please)

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/