Question: Getting hints on protein function by correlating its ChIP-seq peaks with public datasets?
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gravatar for bsksln
4 months ago by
bsksln0
bsksln0 wrote:

Hi, First of all, my apology that the question might be a little confusing. I'll try to explain. I did a ChIP-seq experiment on a novel protein and got some nice peaks. MEME motif analysis wasn't very informative (this is not a sequence-specific TF). Since there is not much known about this protein, I am thinking about correlating it with public datasets (ChIP-seqs, RNA-seqs, etc). In another word, to find what other protein/histone modifications have similar binding patterns to this protein. This will potentially tell me what are the cofactors of my protein. However, I am not able to process all the public datasets, so I am looking for such tools.

I already have .bed files with coordinates of the protein binding sites generated by MACS2. My specific question is, is there a tool that can compare this bed file with public datasets, and output factors/histone modifications that have similar binding patterns? Thanks!

ADD COMMENTlink written 4 months ago by bsksln0
0
gravatar for ATpoint
4 months ago by
ATpoint14k
Germany
ATpoint14k wrote:

I think ReMap is exactly what you are looking for.

Welcome to ReMap an integrative analysis of transcriptional regulators ChIP-seq experiments from both Public and Encode datasets. The ReMap atlas consists of 80 million peaks from 485 transcription factors (TFs), transcription coactivators (TCAs) and chromatin-remodeling factors (CRFs). The atlas is available to browse or download either for a given TF or cell line, or for the entire dataset. You can navigate ReMap on the UCSC Genome Browser [EU], [US], the Ensembl Browser [EU],[US],[Asia] or as Track Hubs.

I think it even has an interface for a kind of overlap test (Fisher's Exact or something similar) to check significant co-occurrences. Alternatively, you can download the content and use packages like LOLA from Bioconductor.

ADD COMMENTlink modified 4 months ago • written 4 months ago by ATpoint14k

The tool looks exactly what I need. I'll give a try. Thank you.

ADD REPLYlink written 3 months ago by bsksln0
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