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. 2019 Jan 8;47(D1):D581-D589.
doi: 10.1093/nar/gky1037.

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

Max Kotlyar  1 , Chiara Pastrello  1 , Zara Malik  1 , Igor Jurisica  1   2   3
Affiliations

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

Max Kotlyar et al. Nucleic Acids Res. .

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.

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Figures

Figure 1.
Figure 1.
Figure shows the percentage of proteins with degree 5 or lower in each species, taking into consideration the entire set of interactions in IID (light blue) or only the experimental ones (dark blue).
Figure 2.
Figure 2.
Tissue distributions of PPIs in each IID species (A). Distribution in human of detailed joint (B) and brain tissues (C). Network of SLC22A6, a protein involved in renal sodium-dependent transport and excretion of organic anions. Blue edges indicate PPIs in kidney, yellow edges indicate PPIs in synovial macrophages, green edges indicate PPIs in both tissues, and black edges indicate PPIs without tissue annotations (D). Data from IID, network layout generated using NAViGaTOR 3.08 (48).
Figure 3.
Figure 3.
Drug target class (top) and localization (bottom) distributions of PPIs in each IID species.
Figure 4.
Figure 4.
Disease distributions of human PPIs. PPIs are annotated with a disease if both interactors are annotated with the disease in DisGeNET.
See this image and copyright information in PMC

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