By pairwise distance calculations between CAGE enhancers, we identified clusters of densely positioned enhancers in the genome. 815 regions of length >=2kb containing >2 enhancers were identified. Of these, 198 regions contained enhancers whose average pairwise expression correlation (Pearson's r) were >=0.75. The expression of associated Refseq genes (see ‘Linking TSSs and enhancers by expression correlations’) as well as their enrichment of gene ontology biological process terms (via the DAVID tool66) were compared to that of genes associated with non-clustered enhancers.
