Application of DRMNs to the cellular reprogramming sequencing data set using histone marks, accessibility, and Q-motifs. (A) Shown are gene expression (log 1 + TPM) patterns of the k = 7 modules for each cell state (major row). The number above the heatmap is the number of genes in that module. The color corresponds to the level of expression, with more red denoting high expression and more blue denoting low expression. (B) Inferred regulators for each module across time. Only modules with highest expression and that had TFs as regulators (5, 6, and 7) are shown. The red intensity is proportional to the z-score significance of the regression weight of a regulator. For all values, see Supplemental Table S6. (C) Transitioning gene sets showing changes into the high expression modules (5, 6, 7). Shown are the mean expression levels of genes in the gene set (left; red–blue heatmap), the module assignment (second), the number of genes in each module (third), and the set of regulators for each gene set (white–red heatmap). Red arrows depict gene sets discussed in the text. (D) Selected transitioning gene set C216 in the cellular reprogramming data set. The panel shows the member genes of the transitioning gene set. The columns show the module assignment of each gene, followed by its expression level in each cell state (Expression). The subsequent groups of columns are the levels of the regulator on the gene promoters. The name of the regulator is specified at the bottom of the heatmap.
