Figure 3.

Cell cycle TF prediction. Figure 3A: Significance scores for 46 predicted TFs for cell cycle genes (FDR p ≤ 0.05). Red bars represent nine core cell cycle TFs and blue bars show secondary cell cycle TFs. Figure 3B: Predicted phase specificity for cell cycle TFs. Cell cycle phases are shown clockwise from top right, and TF activities across phases are shown in concentric circles (not drawn to scale). Intensity of red tone shows predicted proportion of TF activity from scaled regression coefficients. TF names are coloured according to their known phase of action, confirming the agreement between known and predicted functions of TFs. Figure 3C: Contribution of regulatory evidence in recovering 13 known cell cycle TFs. Bar color denotes class of evidence and bar height shows proportion of weight assigned to this class. Figure 3D: Performance and robustness comparison of m:Explorer and other methods. X-axis corresponds to proportion of genes presented to method, and Y-axis shows performance with the Area Under Curve statistic for 18 cell cycle TFs (AUC, 95% confidence intervals for 100 runs). m:Explorer values are plotted in wider, black lines. Numbers at the right end of curves reflect method performance with the full yeast dataset of 6253 genes. AUC, area under curve; G1, gap-1; G2, gap-2; M, mitosis; S, synthesis; TFs, transcription factors; TFBS, transcription factor binding site.