Enhancer distance cutoff
How far can be the enhancer peaks (H3K27ac) associated with TSS of the protein coding gene. As enhancer can act at long distance, I want to concentrate on Cis-acting enhancers and use it for Geneset enrichment analysis
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That is a question we cannot answer as there is no max distance. We even know of enhancers that act on different chromosomes - but those are naturally rare events.
From a more practical orientation a possible cold be features within the same TAD (topological associated domain) or features within +/-2e5 nucleotides. Generally I would not suggest going larger than that.
Hope this helps.
Kristoffer
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