Transcription factors database

Question

[Fatemeh]

Hello everyone, I am wondering if you know how I can find which transcription factor is expressing my gene of interest. I mean whether there is a database that I can search a specific gene and find which transcription factor is regulating its expression. I would really appreciate if you can help me with this important question.

Thanks for your help.

[K.patel5]

Look into the ENCODE project. https://www.encodeproject.org/ . I believe this is one of the more well annotated databases. The Harmonize project is a good portal for TF-binding site information from several sources including ENCODE I believe https://maayanlab.cloud/Harmonizome/about.

Other than these there are other resources too, I am sure if you search around the web you will find them.

More specifically, if you know which signalling pathway your TF of interest is involved in, you can look into KEGG or Wikipathways to see for literature driven interactions.

[Fatemeh]

Thanks for your answer. However, I think these links are not meant to find what I want. I might be wrong but I could not figure it out how to find which TF is responsible for expression of "calcitonin receptor" for example. From the second link I just could search a TF and get its target genes. My problem is that I do not have a TF, I have a gene that encode a receptor, I just want to know which TF is expressing it.

[Hamid Ghaedi]

Just to add more to this post. This seems to be an option too: JASPAR

Answer 1

[jared.andrews07]

The GRNdb site offers what you want. There is also the REGnetwork site, but the search functionality on it didn't work for me.

[Fatemeh]

Thanks very much Andrew. GRNdb is great! you even searched Calcr for me. Thanks a lotttttt.

Answer 2

[pm2012]

You might find TRANSFAC database helpful. They have a public/free version of the database but it looks like it hasn't been update in a while. The commercial version should be more up to date.

[Fatemeh]

OMG! This database is perfect. I think it works perfectly. The TF candidates were correct for some of known genes. Thanks very much.