Estimate transcription factors binding sites for Drosophila genes

Question

[EvoGen]

I have a list of genes for Drosophila melanogaster, for which I would like to get the all the TFBS for each gene. It would be very helpful if anybody could suggest the resources, databases or any relevant literature that would help me annotate TFBS my gene list.

[Bharat Iyengar]

You can look at the ChIPseq data for different TFs

Answer 1

[Richard Smith]

FlyMine includes Drosophila TF binding sites from a couple of sources, you can upload a list of genes then use it in a pre-defined Template Query that searches for TF binding sites, maybe this one.

You could also look at modENCODE which included several projects to identify TF binding sites. You can search modENCODE data using modMine, a similar interface to FlyMine.

Answer 2

[pengchy]

Another resource suggest:

http://redfly.ccr.buffalo.edu/

Gallo, S.M., Gerrard, D.T., Miner, D., Simich, M., Des Soye, B., Bergman, C.M. and Halfon, M.S. (2010). REDfly v3.0: Toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res.; doi: 10.1093/nar/gkq999

REDfly has 5577 CRMs associated with 552 genes, and 2058 TFBSs bound by 158 transcription factors acting on 212 target genes. These data are based on 680 curated publications.

Answer 3

[Joseph Pearson]

Redfly is a great curated list of enhancers from publications, highly recommend. As a reliable database of PWMs for in vitro binding specificity (to find candidate factors for individual enhancers/binding sites), I've found FlyFactorSurvey to be incredibly useful.