Integrated interactions database: tissue-specific view of the human and model organism interactomes

By M. Kotlyar, C. Pastrello, Nicholas Sheahan, Igor Jurisica. 2015

221 citations recorded by the source corpus.

IID (Integrated Interactions Database) is the first database providing tissue-specific protein–protein interactions (PPIs) for model organisms and human. IID covers six species (S. cerevisiae (yeast), C. elegans (worm), D. melonogaster (fly), R. norvegicus (rat), M. musculus (mouse) and H. sapiens (human)) and up to 30 tissues per species. Users query IID by providing a set of proteins or PPIs from any of these organisms, and specifying species and tissues where IID should search for interactions. If query proteins are not from the selected species, IID enables searches across species and tissues automatically by using their orthologs; for example, retrieving interactions in a given tissue, conserved in human and mouse. Interaction data in IID comprises three types of PPI networks: experimentally detected PPIs from major databases, orthologous PPIs and high-confidence computationally predicted PPIs. Interactions are assigned to tissues where their proteins pairs or encoding genes are expressed. IID is a major replacement of the I2D interaction database, with larger PPI networks (a total of 1,566,043 PPIs among 68,831 proteins), tissue annotations for interactions, and new query, analysis and data visualization capabilities. IID is available at http://ophid.utoronto.ca/iid.

Subfields: Cell Biology, Molecular Biology

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Citations in the corpus

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets (2018, background): “The STRING database (‘Search Tool for Retrieval of Interacting Genes / Proteins’) belongs to this latter class, along with GeneMania (22), FunCoup (23), I2D (24), ConsensusPathDb (25), IMP (26) and HumanNet (27)––most of which have recently been reviewed and benchmarked in (7).”
GeneMANIA update 2018 (2018, background): “Given query genes that are part of a protein complex, Gen-eMANIA will often find additional members of that complex and give high weight to physical interactions or predicted physical interactions – e.g. from orthologous interactions provided by I2D (9)).”
Machine learning approaches and databases for prediction of drug–target interaction: a survey paper (2020, methodology): “In total, 11 molecular interaction databases (including IntAct) were incorporated into IntAct including AgBase [ 266–269], MINT [ 270–273], UniProt [274][41], I2D [275], MBINFO, MatrixDB [276], Molecular Connections, InnateDN [ 277], IMEx [278] and GOA.”
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible (2016, methodology): “Apart from STRING, this latter group includes GeneMANIA (27), Integrated Multi-species Prediction (28), Integrated Interactions Database (29), Human-Net (17), FunCoup (30) and others.”
HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks (2016, background): “There are other resources integrating PPIs and gene functional interactions (40,41), and some of them make it possible to generate tissue-specific (42,43) or more general context-specific networks (44).”