Fig. 2

Modulators affect the pattern of the transcriptional regulation. a Expression pattern of HAC1 and AG. Each dot corresponds to the gene expression of HAC1 and AG in one sample. MI represents the mutual information score. b Top, expression pattern of a modulator–TF–target triplet: HFR1, HAC1, and AG. Each column represents a sample, which is sorted according to the expression level of the modulator (HFR1). The mutual information (MI) score of the AG and HAC1 on all the samples is 0.53. Middle, expression pattern of TF-target (HAC1 and AG) in HFR1 lowly expressed samples (bottom 35% samples). MI score is 0.34. Bottom, expression pattern of TF-target (HAC1 and AG) in HFR1 highly expressed samples (top 35% samples). TF and target gene are strongly correlated across those samples and the MI score is 0.72. The conditional mutual information (CMI) score is 0.38. c Significance test of the conditional mutual information of the HFR1-HAC1-AG. We randomly chose two groups of samples (each group contains 35% samples) and computed the mutual information between TF and target (HAC1-AG) in each group. We repeated this procedure 1000 times to generate the null distribution. Given HFR1’s expression level, the mutual information of HAC1 and AG is significantly changed (p-value < 0.001). d A summary for the example of the HFR1-HAC1-AG