Do you know of any informatic tool that can predict the effect on gene expression levels of the removal of a particular transcription factor binding site (TFBS)? I'm analysing DHS regions and have learnt that in my subject several TFBS have been removed. I would like to know if I should expect some functional consequence (at the very least, changes in transcription levels). Thanks a lot for your help!
"ConSite" and "Match" are two license-free softwares to predict transcription factor binding sites within gene regulatory regions.
Based on gene proximity (UCSC browser), and knowing the specific TF, you can partially predict the targets. I am not aware/expert about more techinical tools.
Best
W
You can do all the computer gazing you like, but that is no substitute for doing an actual experiment.
Thanks, Wanda and Gregory, for your interesting contributions!
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