Best databases for Chip-Seq

Question

[JS]

Hi all,

I'm a complete novice to Chip-Seq data, so apologies for how basic this question is.

I'm interested in comparing the binding sites of two transcription factors, ideally in human adipocyte data. Where is the best place to find chip-seq peaks for a variety of transcription factors? Which are the best databases for this? I've found supplementary materials for several papers which do release the binding sites for the TFs they've looked at, but these obviously only cover a subset of TFs, and are frequently on different genome builds...etc, and so would be great if there was somewhere I could download binding sites for specific TFs of interest on the same genome build.

Thanks very much in advance for any suggestions you might have!

[Sinji]

Take a look at the ENCODE project.

[Ryan Dale]

If your data of interest are not in ENCODE, there isn't really a way around downloading supplemental data from individual papers, puzzling over why they used unconventional file formats, and converting their data into something you can use. That often includes fixing formatting, lifting over genome assemblies, editing chromosome names, etc. What we need are more standards!

[James Ashmore]

You could also try Cistrome DB

Answer 1

[ZhouK.R.]

You should try ChIPBase (details are in this post), a comprehensive database for interpreting ChIP-seq data and investigating the transcriptional regulatory maps of TFs.