How to find transcription factor downstream binding

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5.7 years ago

Alex Gibbs ▴ 90

Hi all,

I would like to find out what the mouse Stat3 transcription factor binds to and the full signalling pathway(s) that it is involved in.

So far, I have only managed to find a signalling pathway that ends in Stat3, and subsequently genes that bind to Stat3.

I have tried JASPAR, but the website is down. Does anyone have any suggestions?

Thanks in advance!

Alex

RNA-Seq gene • 851 views

ADD COMMENT • link updated 5.6 years ago by Biostar 20 • written 5.7 years ago by Alex Gibbs ▴ 90

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If you want actual binding data, search for Stat3 ChIP-seq on GEO/NCBI. JASPAR is just a database for motifs but a motif presence does not imply binding.

ADD REPLY • link 5.7 years ago by ATpoint 86k

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Well I would say TF (for e.g stat3) binding and its target genes would be cell type specific. you may have in general stat3 binding motif and known putative targets, I am not sure about your objectives, however if you are interested in some type regulation in particular cell type, you may have to look for ChIPseq data for that particular TF.

ADD REPLY • link 5.7 years ago by Prakash ★ 2.2k

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