ComPPI, a cellular compartment-specific database for protein-protein interaction network analysis
Daniel V. Veres,David M. Gyurko,Benedek Thaler,Kristof Z. Szalay,Dávid Fazekas,Tamas Korcsmaros,Peter Csermely +6 more
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TLDR
Due to its novel features, ComPPI is useful for the analysis of experimental results in biochemistry and molecular biology, as well as for proteome-wide studies in bioinformatics and network science helping cellular biology, medicine and drug design.Abstract:
Here we present ComPPI, a cellular compartment specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis (this http URL). ComPPI enables the user to filter biologically unlikely interactions, where the two interacting proteins have no common subcellular localizations and to predict novel properties, such as compartment-specific biological functions. ComPPI is an integrated database covering four species (S. cerevisiae, C. elegans, D. melanogaster and H. sapiens). The compilation of nine protein-protein interaction and eight subcellular localization data sets had four curation steps including a manually built, comprehensive hierarchical structure of more than 1600 subcellular localizations. ComPPI provides confidence scores for protein subcellular localizations and protein-protein interactions. ComPPI has user-friendly search options for individual proteins giving their subcellular localization, their interactions and the likelihood of their interactions considering the subcellular localization of their interacting partners. Download options of search results, whole proteomes, organelle-specific interactomes and subcellular localization data are available on its website. Due to its novel features, ComPPI is useful for the analysis of experimental results in biochemistry and molecular biology, as well as for proteome-wide studies in bioinformatics and network science helping cellular biology, medicine and drug design.read more
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Integrated interactions database: tissue-specific view of the human and model organism interactomes
TL;DR: IID (Integrated Interactions Database) is the first database providing tissue-specific protein–protein interactions (PPIs) for model organisms and human, with larger PPI networks, tissue annotations for interactions, and new query, analysis and data visualization capabilities.
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IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species.
TL;DR: 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, and now supports topology and enrichment analyses of returned networks.
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Predicting protein-protein interactions from primary protein sequences using a novel multi-scale local feature representation scheme and the random forest.
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