Fig. 1

Possible enhancer-gene interaction dynamics and problem definition. a Current understanding of interaction dynamics between enhancers and their target genes: (i) An enhancer can regulate a faraway gene and not necessarily the closest one. Genes with different expression patterns are marked using different colors. Enhancers associated with a specific gene (or expression pattern) are marked with the same color of the target gene. (ii) An enhancer may exist in an intron of its host or a different target gene. (iii) A gene can be regulated by multiple enhancers. b Problem definition: genes with highly similar expression patterns are grouped into clusters. Enhancers are selected from the list of unlabeled sets and assigned a gene cluster label. As a final step, a logistic regression classifier is applied to test the ability of the sequence of selected enhancers to predict the genes’ expression patterns