Hierarchical clustering in the context of a defined regulatory network. (A) The adjusted strength matrix was used for clustering, after which the gene expression matrix was appended. Seven major clusters which have more than five associated genes are highlighted. In the adjusted strength matrix heatmap, green color indicates that there is no prior regulatory connection in our model while white color indicates a weak regulatory influence. (B) Clustering with gene expression only. Genes in the Cluster F(regulated by STAT6) were noted with green dots, and genes in the Cluster G(regulated by MYC) were noted with orange dots. (C) Clustering with the binary regulatory relations (initial connectivity matrix) assuming all regulatory strengths are equal.