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XiaoTaoWang / NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
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Could you give me some guidelines to manually review and validate the neoloops and neotads #16

Open wzhang42 opened 2 years ago

wzhang42 commented 2 years ago

Xiaotao, I am using neoloop to produce some neo-loops and neo-tads (some rows with the last columns as "1"). But I am interested in validate whether they are really neo-loops/ neo-tads that are really relevant to enhancer hijacking events. Could you give me some guideline to manually validate them? Thank you

XiaoTaoWang commented 2 years ago

Hi, to further identify enhancer hijacking events from neo-loops, first check if there are enhancer marks (e.g. H3K27ac) in one anchor of the neoloop, and gene promoters in the other anchor of the neoloop; if yes, then check if these genes are up-regulated in cancer compared with their expressions in normal control cells; if yes, it's very likely that the neoloop is inducing an enhancer hijacking to activate the target gene expression in the cancer sample/cell line.