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Fig. 7 | Genome Biology

Fig. 7

From: Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data

Fig. 7

User guidelines for selecting an appropriate enhancer-to-gene assignment method (LocDef) for GSE testing. Depending on the specific research questions, three types of LocDefs can be selected for GSE testing from the chipenrich R package: (1) “5 kb” or “1 kb” for promoter regulation, (2) “enhancer” for distal regulation, and (3) “enhancer.5kb” for whole genome regulation. Different LocDefs have different genome coverages as shown in the last column. Options in other GSE testing software for genomic regions will differ. We no longer recommend using nearest TSS method for Poly-Enrich analysis

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Genome Biology

ISSN: 1474-760X

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