Perturbation networks of both pro-differentiative and anti-differentiative TF genes were selected as nodes for this network. To depict the putative network, only significant edges (mean of ΔΔCT > 2 SD and P < 0.05) were extracted based on Matrix RNAi data (Additional data file 5). The networks were drawn by Cytoscape . In these networks, TFs and TF genes regulated by them are not distinguished from each other, but the nodes emitting and accepting an arrow represent putative regulators and regulated genes, respectively. Arrowheads and blue lines indicate stimulatory regulation. T-shaped heads and red lines indicate repressive regulation. Line widths indicate perturbation magnitude.
Tomaru et al. Genome Biology 2009 10:R121 doi:10.1186/gb-2009-10-11-r121