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Table 1 Genomic interaction dataset

From: A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

AssayReference
3D chromatin interactions
 Hi-CHigh-resolution in situ Hi-C: identifies chromatin loops anchored by convergent CTCF binding sites[14]
 RNAPII ChIA-PETChromatin interaction analysis by paired-end tag sequencing targeting RNAPII: identifies chromatin interactions enriched for RNAPII binding[16]
 CTCF ChIA-PETChromatin interaction analysis by paired-end tag sequencing targeting CTCF: identifies chromatin interactions enriched for CTCF binding[16]
 CHi-CPromoter capture Hi-C: identifies chromatin interactions between promoters and other loci[17]
Genetic interactions
 eQTLsExpression quantitative trait loci: identifies genetic variants correlated with changes of gene expression of individuals in a human population[18, 19]
CRISPR/Cas9 perturbations
 crisprQTLsIdentifies loci that when targeted with CRISPR/Cas9 correlate with changes in gene expression measured in single cells[20]