IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species

TLDR

Context‑specific protein–protein interactions are crucial for understanding tissue‑ or disease‑specific biology, yet such data are scarce, especially for non‑human species. IID aggregates interactions from multiple databases to deliver the most extensive set of context‑specific human PPI networks—covering 133 tissues, 91 disease states, and 17 non‑human species—and annotates over 4.8 million PPIs with tissue, subcellular, disease, and druggability information. The 2018 update expands the database from 6 to 18 species, from ~1.5 million to ~4.8 million PPIs, and from 30 to 133 tissues, while adding topology and enrichment analysis capabilities. IID is accessible at http://ophid.utoronto.ca/iid.

Abstract

Knowing the set of physical protein–protein interactions (PPIs) that occur in a particular context—a tissue, disease, or other condition—can provide valuable insights into key research questions. However, while the number of identified human PPIs is expanding rapidly, context information remains limited, and for most non-human species context-specific networks are completely unavailable. The Integrated Interactions Database (IID) provides one of the most comprehensive sets of context-specific human PPI networks, including networks for 133 tissues, 91 disease conditions, and many other contexts. Importantly, it also provides context-specific networks for 17 non-human species including model organisms and domesticated animals. These species are vitally important for drug discovery and agriculture. IID integrates interactions from multiple databases and datasets. It comprises over 4.8 million PPIs annotated with several types of context: tissues, subcellular localizations, diseases, and druggability information (the latter three are new annotations not available in the previous version). This update increases the number of species from 6 to 18, the number of PPIs from ∼1.5 million to ∼4.8 million, and the number of tissues from 30 to 133. IID also now supports topology and enrichment analyses of returned networks. IID is available at http://ophid.utoronto.ca/iid.