Evaluation scheme.

<p>In each leave-one-out cross-validation fold for a given disease, a different gene is retained from the set of known disease genes (red, blue, orange). The remaining genes known to be associated with that particular disease are mapped onto the network and used as prior knowledge (training set) to compute gene-disease scores for all the genes in the network. A test set, including the left-out gene and a set of candidates previously sampled from a pool of genes (the genes in a network or the intersection of the sets of genes in different networks), is sorted according to the obtained gene-disease scores. The performance is then determined by assessing the position of the left-out gene in the ranked test set. We average the overall and per disease results obtained in 10 complete leave-one-out cross-validation runs, each using a distinct set of candidate genes.