TY - JOUR TI - A computational interactome and functional annotation for the human proteome AU - Garzón, José Ignacio AU - Deng, Lei AU - Murray, Diana AU - Shapira, Sagi AU - Petrey, Donald AU - Honig, Barry A2 - Ben-Tal, Nir VL - 5 PY - 2016 DA - 2016/10/22 SP - e18715 C1 - eLife 2016;5:e18715 DO - 10.7554/eLife.18715 UR - https://doi.org/10.7554/eLife.18715 AB - We present a database, PrePPI (Predicting Protein-Protein Interactions), of more than 1.35 million predicted protein-protein interactions (PPIs). Of these at least 127,000 are expected to constitute direct physical interactions although the actual number may be much larger (~500,000). The current PrePPI, which contains predicted interactions for about 85% of the human proteome, is related to an earlier version but is based on additional sources of interaction evidence and is far larger in scope. The use of structural relationships allows PrePPI to infer numerous previously unreported interactions. PrePPI has been subjected to a series of validation tests including reproducing known interactions, recapitulating multi-protein complexes, analysis of disease associated SNPs, and identifying functional relationships between interacting proteins. We show, using Gene Set Enrichment Analysis (GSEA), that predicted interaction partners can be used to annotate a protein’s function. We provide annotations for most human proteins, including many annotated as having unknown function. KW - protein interactions KW - function annotation KW - machine learning JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -