The PHEs were obtained by a supervised-learning method . Columns CNEs and PCRMs display the number of overlaps between the CNEs and PHEs, and the PCRMs (putative CRMs) and PHEs, respectively. The expected number of overlaps between the CNEs and the PHEs was calculated experimentally in 10000 trials. In each trial, a set was randomly selected from the input CNEs. These CNEs are located in the 154 heart-specific gene loci and comprise the mixed sets that CrmMiner analysed. The number of CNEs in a random set is the same as the number of the PCRMs. Then, the overlaps between a random set and the PHEs were counted. The expected number is the average overlap in the 10000 trials. The Z-scores were based on the distribution of the overlaps in the 10000 trials. The P-values associated with the nine Z-scores are 0.