Transcription Factor Enrichment?

Depends on what you want to do of course--but you might find some tools in the MEME suite that could help you: http://meme.sdsc.edu/meme/

Check out the data and tools in the jasper database (Free)

The PAINT promoter analysis tool is my personal favorite. It will take a list of genes, find the upstream regions automatically, pass them through the free version of TRANSFAC and then compare the enrichment to a background set of genes ... either user provided or from a built-in choice. Everything is quite automated and very customizable.

A grad student here had this very question at the beginning of her thesis. Like others here, we used TRANSFAC motifs. I would do that again adding JASPAR to the mix. At that time, no tools were known to her. We found two important considerations:

1. What defines the "promoter" or "gene control region" in human? We settled on 5000 bp of upstream sequence + exon 1 + intron 1 (entire or up to first 1000 bp, can't recall). Why intron 1? Because many gene control elements are found here.

2. When looking for enrichment, how do you define your set of control genes? By size (given that we took exon 1 and intron 1 data)? By GO categories? By gene position (say the neighboring gene)? This was tough and your solution may be specific to the genes your examining or the question(s) you are after.

The student then ran MAPPER to identify the TRANSFAC motifs.

I would suggest you to may customize your favorite GO enrichment tool in a way that the background list of genes will only represent the TFs or genes with TF related terms and perform the enrichment calculation. I tried this one for a small analysis.

Other option is to use a published method like Modulator inference by network dynamics (MINDy) . Disclaimer: I have not tried MINDy myself.

You could try PSCAN http://159.149.109.9/pscan/ it uses TFBS from both TRANSFAC and JASPAR.