Enrichment Test between Genomic and Epigenomic Regions
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7.7 years ago

Hi all,

I have detected some interesting epigenetic regions on the genome (for example, differentially methylated regions) and I have some features on the genome (for example, I classify all the genome to 3'UTR/5'UTR/gene body/promoter/enhancer/junk region).

Different features have different lengths (i.e. junk regions occupy the majority of the genome).

How to say if my set of intervals - diff methylated regions - is enriched in one of the features? One interval can have intersection with several features. I know how to apply a proportion test, I do not know how to normalise number of intersections between features and intervals for the length of features.

enrichment • 1.7k views
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Careful with the idea of 'junk' regions. It's thought that methylation is actually majorly involved in the repression of transposable elements, that make up about 50% of the human genome and the vast majority of other genomes as well. It's entirely possible that this junk region is in fact mostly composed of insulator/TEs.

You could try a hyper geometric test to test for enrichment.

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Agree with everything, called it "junk" just in order not to specify all 30 options. It is absolutely clear how to use hypergeometric test (i.e. https://www.geneprof.org/GeneProf/tools/hypergeometric.jsp ) while having a control dataset, but I do not understand how to work in terms of features/intervals only, what is "Population", what is "Sample" and what is a success in this case.

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