Hi all,
Hoping someone could give me a bit of direction here.

I have a set of genes which are all members of the same pathway.

I want to identify if there are any transcription factor binding sites
(TFBS) in the "promoters" (so far defined as 5kb upstream of the TSS) that
are more common to genes among the pathway.

I have managed to get the 5kb upstream using biomaRt (although the query
throws an intermittent error, moaning about the upstream_flank filter,
doesn't happen all the time, it's weird!)

I also managed to download all the JASPAR matrices, parse the file for only
human ones and convert them into position weight matrices.

Lastly, I have produced a table of counts of each human TFBS motif in each
of my genes using countPWM(pwm, seq, cutoff="90%")

This is as far as I have gotten and am simply wondering what do I do next.
>From some reading the hypergeometric distribution is used in this situation
but I am not sure what metrics to place in as the white balls drawn, total
white balls, black balls etc., for those of you familiar with the
hypergeometric distribution.

I read that perhaps I should compare to a background set of genes, some
sources say all other genes. This seems like overkill.

Any help is appreciated.
Cheers,
Davy

-- 
David Kavanagh
Nephrology Research, Centre of Public Health, Queen's University Belfast, A
floor, Tower Block,
City Hospital, Lisburn Road, BT9 7AB, Belfast, United Kingdom

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