list of genes with associated histone marks

Question

[Noyk]

Hi,

I would like to make association study between DNA methylation data with histone methylation.

Is there a processed list of genes with H3K4me3, H3K9me3, H3K27me3 and H3K36me3 marks in promoters or gene bodies?

[Jelena Aleksic]

Which organism? Which developmental point? Which tissue?

Answer 1

[PoGibas]

Noyk, you can use UCSC genome browser to get this data.

For example: select wanted histone modification (from "Table Browser -> Regulation -> SYDH Histone") and use intersection with Genes group.

This way is simple and quick - should work for primary investigation.

Answer 2

[Ming Tommy Tang]

or if you have a bed peak file, you can use http://broad-enrich.med.umich.edu/ to annotate the peaks or you can download the refgene table from UCSC, get the promoter region for each gene, and use bedtools intersect with the histone modification peaks.