Dissecting Early Differentially Expressed Genes in a Mixture of Differentiating Embryonic Stem Cells
Figure 3
A regulatory network in differentiating ES cells.
Modules and regulatory relationships. Yellow and blue nodes represent genes that are up- and down-regulated in differentiated cells. All blue and yellow nodes are collectively termed as pluripotency and differentiation modules, respectively. Edges (plain edges, activators ↑ and repressors ⊤) represent evidence of regulatory relationships. Plain edges: the regulatory relationship is supported by the binding of the regulator to the target gene (ChIP-seq or ChIP-chip data). Activators: the regulatory relationship is supported by both the binding of the regulator to the target gene (ChIP-seq or ChIP-chip data) and down-regulation of the target gene expression when the regulator is knocked down (RNAi microarray data). Repressors: the regulatory relationship is supported by both the binding of the regulator to the target gene (ChIP-seq or ChIP-chip data) and up-regulation of the target gene expression when the regulator is knocked down (RNAi microarray data).