What sort of experiments would you conduct, or databases would you search, in order to identify all of the transcriptional targets of a certain transcription factor of interest? For instance, say I wanted to look into all of the transcriptional targets of the ZEB1 transcription factor in cancer.
Hi Frank,
You can try using this using the collection of predicted TFBS in Harmonizome.
http://amp.pharm.mssm.edu/Harmonizome/search?t=all&q=zeb1
Prediction of target in a lot of these databases are based on motifs in promoters, what you can also try to look at is actual chip binding in cell liens:
https://www.encodeproject.org/search/?searchTerm=zeb1&type=Experiment
Or if you know the cancer cell lines you are interested in, try to find the zeb1 chip for them
best, Gen
This should help you:
http://cisbp.ccbr.utoronto.ca/
(measured and predicted TF motifs database for 59,998 TFs from 340 sequenced eukaryotes)
I would use Remap - it has compiled ChIP-seq datasets and motif searching results from a wide variety of experiments and sources to find the 'most likely' or most highly enriched sequence targets.
General link: http://tagc.univ-mrs.fr/remap/index.php
For ZEB1: http://tagc.univ-mrs.fr/remap/factor.php?TF=ZEB1&page=overview
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