Figure 2.

Summary of our final predictions. This network diagram is a graphical representation of our final predicted 177 TF-gene functional pairs between 18 TFs and 66 target genes (coherent linker genes). Dashed links show 24 literature-verified pairs. Links with white arrow heads represent 85 pairs with conserved motifs. Green and red links show additional information about expression correlation between TF-encoding genes and their target genes: high positive (Pearson coefficients > 0.661) and negative correlation (Pearson coefficients < -0.628) respectively. For example, the predicted functional pair of Rap1 and TEF1 (on the bottom right) is confirmed with respect to literature and conserved motifs. In addition, the pair shows high expression correlation between them. We use this additional information for detailed case studies by considering those pairs as high confident among all our predictions (see subsection 4 in Results). See Additional File 2 for better visibility of this figure and Additional File 3 for a list of TF-gene pairs together with Pearson coefficients. Generated by Cytoscape [36] and yED graph editor [37].