Question: Score Over/Under Representation Of Chipseq Marks In A Set Of Regions And Combine With A Heatmap?
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gravatar for daniel.soronellas
5.9 years ago by
Spain
daniel.soronellas330 wrote:

Dear all,

I come to you to ask for suggestions in order to do this kind of representation.

The initial situation: I have a set of specific genomic regions (for example: promoters, exons, intergenic regions, etc...) I want to characterize using some ChIPseq data. I do not want to cluster data on this set of regions, I want to see which marks are under/over represented compared to an input or total histone.

So I thought it could be interesting to represent this as a heatmap where each square has also the score in order to show overrepresentation or underrepresentation of TF or Histone Marks in certain genomic regions. For this analysis I was thinking to compute the Zscore based on reads per sample and then divide each mark (TF or Histone Mark) by the input or total desired histone; then using R try to plot the figure.

So far I looked at the literature and could not find anything like this, but I remember once I saw some paper figure showing this kind of heatmap I describe but unfortunately I cannot remember the publication.

  1. Do you know any paper where this has been shown?
  2. Or even better, could you give me any suggestion/correction to the strategy on how to do this?
  3. Is also possible to calculate the statistical significance of each enrichment nor depletion?

Thanks for your help once more.

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by daniel.soronellas330
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