E-Box Promoters In Gene List

Question

[GPR]

Hello, I have a list of genes up- and downregulated from a couple of mRNA-seq data-sets; and would like to explore if these lists are enriched in E-box containing promoters. Any suggestions on what tool is the most reliable? Thanks, GP.

[Devon Ryan]

What's the species? I only ask since there are already lists of putative/confirmed E-box binding sites for some organisms. If yours is one of those, then you get to skip the "predict E-box binding sites" step.

[dawn.zinyk]

Is there a list for mice? :-)

[Devon Ryan]

Probably, I'd have to look again (it's been a couple years...)

[dawn.zinyk]

Hi, I was wondering whether you'd had a chance to check? :-D

(Sorry if pushing ....I've just been looking for CANNTG in Word with Find for all 16 combos! lol)

[Devon Ryan]

I've not had a chance for more than a cursory look, which didn't turn up whatever I happened to know about 2.7 years ago. If you're just looking for possible motif sites then put that into a motif search tool and get all of the sites. That shouldn't take more than a couple minutes (as opposed to using find in word, which I imagine would take days to manually find everything).

Answer 1

[B. Arman Aksoy]

I thinks Gene-set Enrichment Analysis (GSEA) is the way to go: http://www.broadinstitute.org/gsea/index.jsp

I think they don't have an out-of-the-box E-Box gene set, but for example this annotation file seems to be sufficient for your case (assuming you are interested in CACGTG motif): http://www.broadinstitute.org/gsea/msigdb/cards/CACGTG_V$MYC_Q2.html