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  • Chip-Seq and Gene expression data

    Dear All,

    I am processing Chip-Seq data for 4 histone modifications in 3 samples.
    I would like to find a way to correlate histone modifications to gene expression data,
    any hint on how to do it?

    thanks,
    p

  • #2
    Depending on what you mean by "correlate" (and if you are an R user), we have a R/Bioconductor package called Repitools that can do some of this.

    See (for general info):
    Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.


    The user's guide contains some examples:


    For example, binPlots() or clusterPlots (or their output) can be useful for various exploratory tasks.

    Best regards,
    Mark

    Comment


    • #3
      Hi,
      I mean that I have some list of genes found to be differentially expressed between two conditions with microarray analysis.

      I have also some list of genes whose histone modifications ( activating and repressing transcription) vary betweend the two conditions.

      I would like to find a way to check wheter they correlate, for example,

      gene condition A condition B
      x 10 8
      y 98 200

      histone mod gene condition A condition B

      H3K4me(act) x 20 reads 12 reads
      H3K27me3(rep) x 34 reads 50 reads

      In this case gene x is found to be turned off with microarray data and also ChipSeq data confirm that these genes is subjected to histone repression ( decrase of H3K4me3 and increase of H3K27me3)


      any hint?

      thanks,
      p

      Comment

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