Figure 3. Identification of target-cohorts in WNT and FGF self-renewal pathways.

(A) Target propensity separation threshold used to separate genes above and below E2F target propensity thresholds. The P-values at each target propensity threshold for various measures of differential expression profiles is computed during target-cohort analysis. The average P-value at each target propensity threshold is used to determine the optimal target propensity threshold to separate high and low target propensity genes. As target propensity threshold decreased to 4.9, statistical significance increases sharply before plateau-ing off. This is called ‘target propensity separation threshold’. (B) Differential expression similarity with E2F1 (covariance measure) is plotted against the differential expression scores for genes below (pink squares) and above (blue triangles) separation threshold. For most genes below separation threshold (with the exception of one outlier), |covariance|<0.135 while differential expression <0.9. For genes above separation threshold, those with |covariance|>0.135 and differential expression >0.9 (outside red box), are called target-cohorts, and likely to be enriched in target genes. (C) E2F target-cohorts identified in WNT pathway using separation threshold = 4.9 (red circle) and 4.0 (black circle). For separation threshold = 4.9, target-cohorts are genes marked with an ‘*’ and have differential expression >0.9 and either |dot product|>3.2 or |covariance|>0.135. To explore more genes for trans-activation by E2F, target propensity separation threshold is lowered to 4.0 with the resulting criteria to identify target-cohorts being differential expression >0.55 and either |dot product|>2.0 or |covariance|>0.1. (D) Similar to the procedure highlighted in (A) and (B), target-cohorts in FGF pathways were identified using separation threshold = 5.1, with differential expression >0.617 and either |covariance|>0.126 or |dot product|>1.87.