Question

Statistical significance of ChIP-seq metaplot data

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7.5 years ago

loonyfly ▴ 20

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 • 1.9k views

ADD COMMENT • link updated 7.5 years ago by datascientist28 ▴ 560 • written 7.5 years ago by loonyfly ▴ 20

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

ADD REPLY • link 7.5 years ago by datascientist28 ▴ 560

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That the total enrichment is different on these genes

ADD REPLY • link 7.5 years ago by loonyfly ▴ 20

score 0 · Answer 1 · 2016-10-13

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