Fig. 1: Workflow of the INMC PPI prediction project.
From: Assessment of community efforts to advance network-based prediction of protein–protein interactions
26 representative network-based methods were systematically evaluated to predict PPIs in the interactome of four different organisms: A. thaliana19, C. elegans20, S. cerevisiae21, H. sapiens: HuRI4, STRING22 and BioGRID23 (using rTRM package82). During the computational validation, the PPIs of each interactome were divided into training set and validation set through 10-fold cross-validation. The performance of each method was evaluated using four standard metrics: AUROC, AUPRC, P@500, NDCG. For each method, an overall score was defined as the sum of z-scores of three metrics (AUPRC, P@500 and NDCG) for each interactome. Top-seven methods were selected based on their performance in predicting human PPIs during the computational validation. Using the entire human interactome, each of the top-seven methods predicted the top-500 human PPIs for experimental validation using the Y2H assay. PPI: protein–protein interaction. AUROC: Area Under the Receiver Operating Characteristic curve. AUPRC: Area Under the Precision-Recall Curve. P@500: Precision of the top-500 predicted PPIs. NDCG: Normalized Discounted Cumulative Gain. Y2H: yeast two-hybrid assay. v1-v3: assay 1-assay 3.
