If you would like to find transcription factor binding sites enriched in your list of genes, try this:
DAVID for the enrichment analysis
of TFBSs associated with your genes (given TFBS is involved in the control of the transcription of the gene). Once you uploaded your gene
list you have an option to perform
enrichment calculations using a
variety of annotations. DAVID provides
a category called "UCSCTFBS" in
default setting this option unchecked.
Please click and expand the
"ProteinInteractions" and click on
"UCSC_TFBS" PS. I am not sure about
source of this data set, so far I got
only this link the source data on
DAVID forum. It will be great if
someone can tell more about the data
This data is sourced from UCSC TFBS conserved track. See the details here and table schema here.
If you would like to know what transcription factors (in other words, transcription factor targets) may initiate transcription of your 500 genes, try this:
The data is curated from TRANSFAC, you can do a 'Compute Overlap' of
your genes with the list of genes in
the dataset. Output includes a p-value
to indicate statistical significance
and a Gene/geneset overlap matrix to
visualize the gene categorized into
different transcription factor
Transcription Factor Target Data set
is available here.
Also refer to related question on transcription factor target here.
DBD is fine. To that I would add the list of TFs that the FANTOM consortium considers as relevant for ENCODE and other projects involving transcription factors. There is also some information there on regulatory interactions, such as transcriptional regulation.