Fig. 3

FFL definition and model performance. a Example Gene Regulatory Network (GRN, left) and feed-forward loops (FFLs, right). The presence of a regulatory interaction between TF1 and TF2 means that any target gene which is co-regulated by both of these TFs is part of an FFL. For example, TF1 and TF2 form an FFL with both Tar2 and Ta3, but not Tar1 or Tar4 because they are not regulated by TF2 and TF1, respectively. b Venn diagram showing the overlaps between FFLs identified across data sets similar to Fig. 1c. c AUC-ROC values for SVM classifiers of each cell-cycle expression gene set (as in Fig. 2) using TF-TF interaction information and FFLs derived from each data set. Heatmap coloring scheme is the same as that in Fig. 2b. Note the similarity and AUC-ROC value distribution here to Fig. 2b