Method overview. (A) Gene expression data for the three plants were downloaded and (B) used to compute the mutual information and the corresponding CLR score for each gene pair. (C) A co-expression network was constructed by connecting all gene pairs with a CLR score above a certain threshold. Links from transcription factors (TFs, blue) to genes (green) were represented as directed links (arrows). Networks from different species were then compared at different CLR thresholds with respect to (D) network properties and network motifs) and (E) fraction of conserved links or conserved neighbourhoods.