Fig. 3

Cell cycle pathway genes are less strongly targeted by TFs in cell lines. a Group-specific gene regulatory networks were generated using PANDA. The illustrations represent subnetworks of the 1000 edges with the highest edge weight difference between a cell line and its tissue of origin around the cell cycle genes. The color indicates the edge weight strength between the TF and target gene (the edges shown have a weight greater than 2 in at least one network). b Illustration of the gene in-degree difference between each cell line and its tissue of origin. Positive values indicate higher targeting in cell lines, and negative values indicate higher targeting in tissues. c Boxplot of the gene in-degree differences for the genes in the KEGG cell cycle pathway and for genes not in this pathway (significance measured using a t-test). Reduction of gene in-degree difference indicates that the genes in the cell cycle pathway are less strongly targeted by TFs in the cell line compared to its tissue of origin