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  • Promoter or enhancer regions BED format

    Hi all, One can download a BED file of human genome with exonic and intronic chromosomal coordinates.

    I wanted to know if there is such a file for promoter or enhancer sites, best if it was in BED format.

    Thanks in advance. A

  • #2
    UCSC genome browser -> genome of choice (hg18 or hg19) -> Tables -> Groups(Genes...) -> Track (RefSeq)

    When you output you have the option of selecting the format (bed) and can pick whether you want the whole gene (you can then parse out the exons) or some distance up or downstream of the genes (so, say 2000bp upstream of the 5' end would be a promoter area).

    If you want enhancers you can use a track with the histone methylation/acetylation marks that correspond to enhancers (I always forget which one it is - h3k27acetylation?)

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    • #3
      enhancer associated gene

      hello,

      I have peaks which are overlapping with enhancer regions. Now, my question is which gene are regulated by these enhancers. Therefore, I need idea how can I retrieve information of genes of related enhancers. (any tool or something!!)

      Thanks.

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      • #4
        Try using the more recent Encode-derived annotation at Ensembl. ensembl.org/info/data/ftp/index.html

        Comment


        • #5
          Usually the closest genes surrounding the enhancer region are more likely to be regulated by such enhancer. This is the general assumption used in most papers I read about enhancers.

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