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  • How to find enhancer for tss-promoter

    Hi all,
    Now I got the location of a TSS-promoter for one gene.
    chr1 :198906525 - 198906959

    And I want to use the Homer to find enhancers for this promoter.

    Finding Super Enhancers using Homer:
    $ findPeaks <tag directory> -i <input tag directory> -style super -o auto

    I can using makeTagDirectory to get the <input tag directory> from alignment as follows:
    makeTagDirectory Test/ 31513_TH0.rmdup.bam

    But I don't know how to get the "tag directory", I try:
    makeTagDirectory Promoter/ TSS.bed

    In the TSS.bed, only one location of the TSS :
    chr11 198906525 198906959

    My question is how to get the TSS tag directory, please?

    Best,
    Jenny

  • #2
    Hi Jenny,
    From my understanding, HOMER findPeaks identifies transcription factor binding sites given a ChIP-SEQ dataset as input. The "super enhancers" option simply identifies those regions that are dense with lots of TF binding sites. What you are trying to do - that is, find those enhancers that associate with a given TSS-promoter is not done using findPeaks. Usually promoter-associated enhancers are discovered with techniques such as Hi-C/3C (chromatin conformation capture).

    As far as the tag directory, you just do the following:
    $ makeTagDirectory [myDirectory] [my BAM file]
    $ findPeaks [myDirectory/] -options > myOutputFile.bed

    Hope that helps!
    -Jerry
    ------------------------------------------------
    Jerry Chen, Ph.D.
    Bioinformatics Scientist
    Encoded Genomics, Inc.

    Comment


    • #3
      Enhancer prediction software tools

      Hi Jerry,
      Thanks for you reply.You know, I want to predict the enhancers of a given TSS-promoter, and then check them in the wet lab.
      I think the promoter is a regions with lots of TF binding sites , and not the enhancer is. But the enhancer will help TSS-promoter to binding TFs.

      BTW, if the HOMER can't get the enhancers' location, how to get them by bioinformatic method.
      I found some enhancer prediction software tools form this link :
      http://omictools.com/enhancer-prediction-c1691-p1.html . Which one do you think it's best one, please?

      Thanks,
      Jenny
      Postdoc in the Stanford U.
      Last edited by JennyHu; 11-12-2015, 01:40 PM.

      Comment


      • #4
        Hi Jenny,
        I work with promoter-enhancer interactions as well, but I actually haven't done any research on any good bioinformatics tools for finding enhancers associated with a given promoter. If any of the ones you listed or other ones are good, please let me know - thanks!

        -Jerry
        --------------------------------------------------------
        Jerry Chen, Ph.D.
        Bioinformatics Scientist, Encoded Genomics Inc.

        Comment


        • #5
          Ok, thanks Jerry.

          Comment

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