Figure 2
From: Glucocorticoid receptor coordinates transcription factor-dominated regulatory network in macrophages
Hormone-regulated genes in BMM Ф participate in highly interconnected networks with TF control nodes. (A) Ranked list of Dex-responsive genes was used as an input for GeneMania network building algorithm. The resulting combined network was partitioned using the Newman-Girvan algorithm into three Modules enriched with (A) Dex-repressed, (B) Dex-induced and (C) LPS-repressed genes. To simplify the view, the edges representing co-expression, co-localization and shared protein domains were hidden. The size of the node is proportional to the node connectivity. The nodes are colored according to the magnitude of Dex effect on respective gene expression using MulticoloredNode Cytoscape plugin. The nodes predicted by GeneMania are colored gray. Both (D) network-wide and (E) node-specific network topological parameters in Modules 1 and 2 demonstrate high level of interconnectivity with a large number of shared nodes. (F) Nodes with the highest degree of connectivity in the Modules 1 and 2. The genes coding for TFs are shown in bold.