Schematic representation of the analysis and validation.

Sample-wise predictivity of TranNet was evaluated based on a leave-one-out test (blue-shaded, Section ‘Expression of genes in control samples informs gene expression in tumor’); Interactions inferred by TranNet were tested with enrichment of the functional interactions (green-shaded, Section ‘The transition edges inferred by TranNet are enriched in functional interaction edges’); Gene-wise prediction accuracy of TranNet was evaluated by the prediction error (mean absolute error) on the targets. (grey-shaded, Section ‘Expression of genes in control samples informs gene expression in tumor’).