Transcriptional regulation in eukaryotes

Supplementary material and resources from "Identification of sparsely distributed clusters of cis regulatory elements in sets of co-expressed genes" by Gabriel Kreiman

Supplemental figure 2 Probability of false alarms, PFA, as a function of the proportion of genes with correct predictions of the known regulatory region (see Methods for the definitions). Each plot corresponds to a different set of parameters for the maximum distance between motifs, maxd, and the maximum number of motifs in a module, nmotifs. From left to right, those combinations are (25,2), (25,3), (25,4), (50,2), (50,3), (50,4), (100,2), (100,3), (100,4), (200,2), (200,3), (200,4) for maxd and nmotifs respectively. (A) Drosophila pattern formation set, all predictions. (B) Drosophila pattern formation set, top 10 predictions. (C) Human skeletal muscle set, all predictions. (D) Human skeletal muscle set, top 10 predictions.