Dear ALL.

i would like to perform some transcription factor binding site enrichment analysis(/promoter analysis) but without sequences but rather geneIDs from 2 expression microarray datasets. Is this possible in any package in R or only in web-based tools ? Please excuse me if my question seems irrelevant here but my first intention is to figure out if i can use the information from my microarray datasets i have already analyzed in R . Any suggestions or ideas would be grateful !!!

Transcription factors are proteins that bind to specific DNA sequences and regulate the transcription of genetic information from DNA to messenger RNA (mRNA). They are found in all living organisms. Transcription factors bind to either the enhancer or the promoter region of the genes they regulate and function by the following three major mechanisms:

Transcription Factor Analysis is quite a vital tool to study Transcription factors.

One way to go about answering this question is to frame it as a gene set enrichment analysis.

For example, you might have a NFAT geneset which would consist of the entrez id's of the genes known to be bound by the NFAT transcription factor family.

Given several such genesets, you could then run camera, roast, whatever.

Now, where to get those genesets? Here are some places you might start to look:

• The C3 genesets from MSigDB. In particular, the C3 TFT (transcription factor targest) geneset. Gordon's lab has whipped up *.RData objects you can use for the MSigDB collections that should work pretty seemlessly with camera, roast, romer, etc.
• The factorbook might also be another place to look
• Cistrome