Question: Estimate transcription factors binding sites for Drosophila genes
0
gravatar for EvoGen
5.1 years ago by
EvoGen10
Germany
EvoGen10 wrote:

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.


 

ADD COMMENTlink modified 3.7 years ago by Joseph Pearson430 • written 5.1 years ago by EvoGen10

You can look at the ChIPseq data for different TFs

ADD REPLYlink written 5.1 years ago by Bharat Iyengar260
1
gravatar for Richard Smith
5.1 years ago by
Richard Smith400
Cambridge, UK
Richard Smith400 wrote:

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.

ADD COMMENTlink written 5.1 years ago by Richard Smith400
0
gravatar for pengchy
3.7 years ago by
pengchy410
China/Beijing
pengchy410 wrote:

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.

ADD COMMENTlink written 3.7 years ago by pengchy410
0
gravatar for Joseph Pearson
3.7 years ago by
UNC Chapel Hill
Joseph Pearson430 wrote:

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.

ADD COMMENTlink written 3.7 years ago by Joseph Pearson430
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