Comparison with other CRM detection algorithms. (a-e) Receiver operating characteristic (ROC) curves for the leave-one-out cross-validation using ModuleMiner, ModuleSearcher, CisModule, EMCMODULE, Clover, and random transcriptional regulatory models for each of the five benchmark sets: ORegAnno Erythroid (panel a), liver (panel b), muscle (panel c), ORegAnno Stat1 (panel d) and smooth muscle (panel e). (f-i) ROC curves when using transcription factor binding site (TFBS) preservation (TFBS set 2) in the genome ranking step for all algorithms, on the four benchmark sets that performed above random: liver (panel f), muscle (panel g), ORegAnno Stat1 (panel h), and smooth muscle (panel i). (j) ModuleMiner performance for the three TFBS sets on the muscle benchmark data. CRM, cis-regulatory module.