Question: Are maps of regulatory regions available for hg38?
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gravatar for JJ
2.3 years ago by
JJ510
JJ510 wrote:

Hi,

Does anyone know if there are maps (preferable as bed file) of (candidate) regulatory regions available for hg38? I found i-cisTarget but it's just for hg19.

Thanks!

sequence • 820 views
ADD COMMENTlink modified 2.3 years ago by ATpoint36k • written 2.3 years ago by JJ510
1

You can get a lot of bed files from the UCSC table browser, including regulatory features.

ADD REPLYlink written 2.3 years ago by WouterDeCoster44k
2
gravatar for ATpoint
2.3 years ago by
ATpoint36k
Germany
ATpoint36k wrote:

Check ReMap, a collection of transcription factor binding sites as well as the regulatory data from UCSC/ENCODE for hg38 (UCSC/ENCODE).

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by ATpoint36k

Thank you, I know about remap but that's basically a collection of TFBS peaks. I was looking for a bed file as provided by i-cis-target for hg38. They provide:

General Binding Preference models, CpG islands, proximal promoters, conserved non-coding sequences, ultra-conserved elements, regulatory elements from OregAnno, VistaEnhancers, predicted cis-regulatory modules and DNAseI Hypersensitive (DHS) uniform clustered peaks across 125 cell lines from ENCODE.

ADD REPLYlink written 2.3 years ago by JJ510
1

The i-cis-target website seems to last updated in 2015. Would a liftover or crossmap work to lift these coordinates to hg38 ?

ADD REPLYlink written 2.3 years ago by microfuge1.7k

Thanks - I figured this would be the only solutions if nothing else more updated is out there. What tool would you recommend for liftover of a bed file?

ADD REPLYlink written 2.3 years ago by JJ510
1

UCSC liftOver: https://genome.ucsc.edu/cgi-bin/hgLiftOver

ADD REPLYlink written 2.3 years ago by Alex Reynolds30k
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