1
$\begingroup$

I want to get transcription factor targets for my list of genes (For Human and Mouse)

I have found ENCODE Transcription Factor Targets database (The link is given below). But I am looking for some other databases also if available. I will really appreciate if anyone can suggest any other database.

http://amp.pharm.mssm.edu/Harmonizome/dataset/ENCODE+Transcription+Factor+Targets

Thank you

$\endgroup$
2
  • 1
    $\begingroup$ What is the problem with ENCODE? I am aware of the existence of TRANSFAC, but I think is a non-free resource $\endgroup$
    – plat
    Jun 7 '19 at 10:09
  • 1
    $\begingroup$ @Plat My only problem with ENCODE is that I am not sure when was it last updated (I think in 2012) $\endgroup$
    – Priya
    Jun 11 '19 at 11:25
2
$\begingroup$

JASPAR is another useful transcription factor profiling database.

The JASPAR CORE contains a curated, non-redundant set of profiles, derived from published and experimentally defined transcription factor binding sites for eukaryotes. It should be used, when seeking models for specific factors or structural classes, or if experimental evidence is paramount.

http://jaspar.genereg.net/

$\endgroup$
1
$\begingroup$

JASPAR is only based on TF motifs, which are very short sequences and not enough to precisely tell you the true TF-motif relationships, especially when multiple TFs have complex logic gates regulating overlapped targets.

An alternative way is to find some transcriptomic data upon perturbation of each TF. The drawbacks are that the redundancy of TFs will mask a lot of targets, and that the up/down regulated genes may not be direct targets but targets of targets (of targets of targets...).

Another way is to find ChIP-seq data for TFs you care about, and hopefully you can find the right biological context. But still ChIP signal isn't exactly binding pattern, which in turn isn't exactly indicating target relationship.

Overall, it's a challenging task to know what are the true targets of a TF.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.