Network evolution after the yeast WGD. (a) The yeast coexpression networks show evidence of subfunctionalization after WGD. A co-expression network consisting of 65 pairs of WGD-produced paralogs (e.g., ohnologs) is illustrated. Each row contains a pair of ohnologs; edges join genes with co-expression correlation (Pearson’s ) ≥0.75 across >200 microarray experiments. In each row, the position of the two ohnologs can be exchanged: we searched for the arrangement that minimized the number of interactions between the two columns (central diagonal edges). The number of such “crossing edges” is much smaller than what would be expected by chance (see [34]). (b) The above patterns are at least partly driven by changes in transcriptional regulation. We have previously shown that WGD-derived duplicated transcription factors have diverged considerably since WGD [45]. Here we show the relative lack of overlap between these duplicated regulators’ functions. On the right are the transcription factors (TFs) that target other TFs but are not themselves targeted by a TF. On the left are the TFs that are regulated by other TFs. Duplicated TF pairs from WGD (e.g., ohnologs) are shown in the same color.