Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets
Fig 5
Cis regulatory networks (CRNs) and joint clustering of expression and regulation.
(A) CRN for the TF cluster set. The genes are represented as nodes and directed edges show the genes that are co-expressed and also bound by the TF of one gene (source) to a predicted CRE of the other gene (target). The cell type at which the expression of the gene is highest is shown as colours on the node. The size of the node name is proportional to its degree. (B) The CRN for the TF set (colours as A). (C) Joint clustering of genes in the TF cluster set. Genes cluster together according to the relatedness of both gene expression patterns (red-blue heatmap) and the binary pattern of TF binding (green-white heatmap) at their main predicted (co)CRE. Each cluster is distinguished by a colour coded bar above the GEP heatmap (highlighted as “Joint cluster ID”). For each cluster, the average of the TF binding profile is shown as the TF binding propensity, where 0 represents absence of TF binding and 1 represents binding of that specific TF in all the regions belonging to that cluster (green = TF binding; white = no TF binding).