Hierarchical networks. (a) Dendrogram derived from complete-linkage clustering analysis using Euclidean distance on the gene expression matrix of all genes differently expressed at 3 h (related to 0 h) in estrogen-treated MCF-7 cells (Carroll et al.  dataset). (b) Hierarchical network obtained by superimposing the dendrogram onto the corresponding co-expression gene network. The co-expression associations were computed for the same set of genes (for additional details on the pre-processed data please see Additional file 1 and Figure 3). Node coloring depicts differential expression as log2 fold-change (logFC) and node size indicates the kilobase distance of the transcription start site to the nearest ER binding site. Out-edge width represents the sum of all edges between modules divided by the total possible edges.