Figure 4.

PanomiR deconvolutes coordinate clusters of differentially regulated pathways in liver cancer. The network displays a pathway co-expression map of liver cancer pathways. PanomiR detected three major groups of pathways, defined by the direction of differential regulation and clusters of coexpression. The three classes are (i) activation of transcription in tumors (cluster A); (ii) activation of cellular replication (cluster B); and (iii) deactivation of specific signaling pathways (cluster C). Each node in the network represents a differentially regulated pathway (Table 2). Edges represent canonical coexpression between two pathways, obtained from an independent compendium of gene expression data, derived from the PCxN method. Node colors represent unsupervised network clusters found by the Louvain algorithm. Clusters were manually labeled according to the functional consensus of their pathways.