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Statistical significance of ChIP-seq metaplot data

Hi,

I have analyzed ChIP-seq data of H2B-ubiquitination with ngsplot. I generated a metaplot where I see changes in the average H2B-Ub levels in the gene body of genes that are being down regulated upon treatment with a small molecule inhibitor. I have two replicates for untreated samples and two replicates with the inhibitor treated sample. I want to know if these changes in H2B-Ub signals that I observe are statistically significant. What would you suggest could be a good strategy for this? Thanks!

chip-seq
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updated by datascientist28 datascientist28 • written by loonyfly • loonyfly

What specific question are you trying to answer? That the total enrichment is different? The peak width is different?

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written by datascientist28 datascientist28

That the total enrichment is different on these genes

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written by loonyfly • loonyfly

1 answer

I think I did something similar to this for a previous paper, looking at peak width. I would recommend making a histogram of the summit total enrichment for said genes. Then do a wilcox.test to see if the distribution is different between treatment and control. Look at figure 5f http://www.cell.com/cell-reports/abstract/S2211-1247(15)01408-4

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written by datascientist28 datascientist28

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