Fig. 2
From: Core transcriptional regulatory circuits in prion diseases
TRN describing transcriptional regulation of cellular processes associated with prion diseases. A-C) Early (EU; A) and late up-regulated (LU; B) and down-regulated genes (DN; C) regulated by the TFs. In the stacked bars, the dark and light shaded areas of the target genes represent the portions of the EU, LU, and DN genes regulated by the differentially expressed TFs (DETFs) and non-DETFs, respectively, whereas the mid-color shaded areas represent the portions of the genes regulated by both DETFs and non-DETFs (see the arrows). Different colors were used to distinguish the TF-target regulatory relationships for EU (orange), LU (magenta), and DN patterns (green). The numbers regulated by the TFs are denoted. D) Percentages of the target genes regulated by the 18 key TFs in each group of 107 EU, 502 LU, and 274 DN genes. The color bar represents the gradient of Z-score reflecting the percentage of the target genes regulated by each TF (Materials and Methods). E) A TRN describing regulations of 18 key TFs with their targets. The TRN is categorized into three transcriptional regulatory subnetworks associated with PrPSc accumulation, microglial/astrocytic activation, and synaptic degeneration, respectively. The 18 key TFs are arranged in a circle surrounding the three subnetworks. Node shapes denote TFs (diamonds) and target genes (circles); node colors represent EU (orange), LU (purple), and DN (green) nodes; and edge types indicate activation (arrow), inhibition, and unspecified interactions (blunted arrow). F) Percentages of the target genes regulated by the 18 key TFs in the three subnetworks. The color bar represents the gradient of the percentage of the target genes regulated by each TF