Question

Find Tfbs Associated With A List Of Genes

0

Entering edit mode

12.4 years ago

User 2624 • 0

Trying to use DAVID to find TFBS associated with some microarray data. Added the probe id list to DAVID, clicked Functional Annotation Tool, and it puts me on the Annotation Summary Results page. Click to expand the "Protein_Interactions" section, and there is no UCSC_TFBS option that appears for me. This is the tool that I'm using: http://david.abcc.ncifcrf.gov/summary.jsp

How can I get TFBS to show up as an option? Is there a better tool for running this?

transcription binding • 5.8k views

ADD COMMENT • link updated 10.4 years ago by Charles Warden 8.2k • written 12.4 years ago by User 2624 • 0

0

Entering edit mode

What is the list you uploaded? And what did you use as background?

ADD REPLY • link 12.4 years ago by Bert Overduin ★ 3.7k

0

Entering edit mode

List of AFFYMETRIX 3PRIME IVT IDs. Background is Drosophila melanogaster.

ADD REPLY • link 12.4 years ago by User 2624 • 0

score 1 · Answer 1 · 2011-11-13

1

Entering edit mode

12.4 years ago

Bert Overduin ★ 3.7k

Looking at the UCSC Genome Browser I can see that there are some tracks with regulation data, but I don't really see TFBSs annotated. So, I guess that is the reason that DAVID doesn't offer you the UCSC_TFBS option. But as I am no UCSC expert, I may be wrong ....

ADD COMMENT • link 12.4 years ago by Bert Overduin ★ 3.7k

score 1 · Answer 2 · 2013-05-31

1

Entering edit mode

10.9 years ago

kristenbeck527 ▴ 10

DAVID used to have a UCSC TFBS option and it appears that now they don't. I'm running into the same issue trying to look up enriched terms for RNA-Seq data, but I was previously able to look up transcripts enriched for transcription factor binding sites. Does anyone knows if that option is only available for some data sets or if that option has been retired?

ADD COMMENT • link 10.9 years ago by kristenbeck527 ▴ 10

0

Entering edit mode

Follow up: I found that TFBS is only available for some species. Human yes. Cow no.

ADD REPLY • link 10.9 years ago by kristenbeck527 ▴ 10

score 0 · Answer 3 · 2011-11-14

0

Entering edit mode

12.4 years ago

Repineme ▴ 120

This link might help.

http://asia.ensembl.org/info/docs/funcgen/index.html

ADD COMMENT • link 12.4 years ago by Repineme ▴ 120

score 0 · Answer 4 · 2013-11-21

I prefer GATHER to DAVID. It is easy to interpret the enriched TRANSFAC motifs:

http://gather.genome.duke.edu/

If you have an institutional license, my favorite tool is actually the upstream regulator function in IPA (although that is based more on literature associations than predicting binding sites).

I also list a few other tools in this blog post:

http://cdwscience.blogspot.com/2013/03/bioinformatics-101-gene-expression.html