Fig. 3

Simulation of both gene expression and activity of a synthetic GRN. a The synthetic GRN consisting of 30 TFs and 447 target genes. An edge of transcriptional activation is shown as black line with an arrowhead; an edge of transcriptional inhibition as red line with a blunt head; an edge of signaling interaction as green line with an arrowhead. Transcription factor labeled as TF9 was selected for knockdown simulations. b The summary of the correlation analyses of the simulated expression and activity. The left, middle, and right columns represent the outcomes for TF and target activities, TF and target expressions, and TF activities and target expressions, respectively. For each category, the histograms of Spearman correlations are shown for non-interacting gene pairs (first row), interacting gene pairs (second row), gene pairs of excitatory transcriptional regulation (third row), gene pairs of excitatory signaling regulation (fourth row), and gene pairs of inhibitory transcriptional regulation (fifth row). Here, the target activity is set to be the same as the target expression for non-TF genes. c The histograms of Spearman correlations for gene pairs of target genes from the same TF. d Jaccard indices between the ground truth regulons of the synthetic GRN and the regulons inferred by ARACNe using either the simulated expression (red) or activity data (blue)