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?
•
written
by
User 2624 •
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 ....
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?
Follow up: I found that TFBS is only available for some species. Human yes. Cow no.
This link might help.
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
Log in to answer this question.
What is the list you uploaded? And what did you use as background?
List of AFFYMETRIX 3PRIME IVT IDs. Background is Drosophila melanogaster.