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Lizio et al. Cell-type-specific TRNs by KD-CAGE and ChIP-seq Integration activates DACH1, SHOX2, PAX6, and PDX1. Analysis of these complementary datasets suggests the need for caution in interpreting ChIP-seq datasets. (1) A large fraction of binding sites are at distal enhancer sites and cannot be directly associated to their targets, without chromatin conformation data. (2) Many peaks may be non-functional: even when there is a peak at a promoter, the expression of the gene may not be affected in the matching perturbation experiment.doi:10.3389/fgene.2015.00331 pmid:26635867 pmcid:PMC4650373 fatcat:hwhg7gwa65hphhcmwgeyl6sm5m