ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis

@article{Veres2015ComPPIAC,
  title={ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis},
  author={Daniel V. Veres and D{\'a}vid M. Gyurk{\'o} and B. Thaler and Kristof Z. Szalay and D. Fazekas and T. Korcsm{\'a}ros and P. Csermely},
  journal={Nucleic Acids Research},
  year={2015},
  volume={43},
  pages={D485 - D493}
}
Abstract Here we present ComPPI, a cellular compartment-specific database of proteins and their interactions enabling an extensive, compartmentalized protein–protein interaction network analysis (URL: http://ComPPI.LinkGroup.hu). 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… Expand
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References

SHOWING 1-10 OF 78 REFERENCES
PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization
PA-GOSUB (Proteome Analyst: Gene Ontology Molecular Function and Subcellular Localization) is a publicly available, web-based, searchable and downloadable database that contains the sequences,Expand
Organelle DB: a cross-species database of protein localization and function
TLDR
Organelle DB is the first on-line resource devoted to the identification and presentation of eukaryotic proteins localized to organelles and subcellular structures, and annotated all protein localizations using vocabulary from the Gene Ontology consortium. Expand
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila
TLDR
Improvements have been made to the web and graphical interfaces to help biologists gain a comprehensive view of the interaction networks relevant to the genes and systems that they study. Expand
LOCATE: a mammalian protein subcellular localization database
TLDR
This database provides localization proteome for individual subcellular compartments that will underpin future systematic investigations of these regions. Expand
Analyzing protein-protein interaction networks.
TLDR
This tutorial shows how to build, visualize, and analyze a protein-protein interaction network using the molecular interaction database IntAct, the software platform Cytoscape, and its plugins BiNGO and clusterMaker. Expand
Organelle DB: an updated resource of eukaryotic protein localization and function
TLDR
The development of Organelle View is reported here the development oforganelle View, an extension of organelle DB for the interactive visualization of organelles and subcellular structures in the budding yeast Saccharomyces cerevisiae. Expand
The ConsensusPathDB interaction database: 2013 update
TLDR
ConsensusPathDB has grown mainly due to the integration of 12 further databases; it now contains 215 541 unique interactions and 4601 pathways from overall 30 databases, and has re-implemented the graph visualization feature of Consensus pathDB using the Cytoscape.js library. Expand
Human Proteinpedia: a unified discovery resource for proteomics research
TLDR
A community portal, designated as Human Proteinpedia, for sharing both unpublished and published human proteomic data through the use of a distributed annotation system designed specifically for this purpose, which allows laboratories to contribute and maintain protein annotations. Expand
Evaluation and comparison of mammalian subcellular localization prediction methods
TLDR
No individual method had a sufficient level of sensitivity across both evaluation sets that would enable reliable application to hypothetical proteins, and all methods showed lower performance on the LOCATE dataset and variable performance on individual subcellular localizations was observed. Expand
NucPred - Predicting nuclear localization of proteins
TLDR
NucPred analyzes patterns in eukaryotic protein sequences and predicts if a protein spends at least some time in the nucleus or no time at all, based on regular expression matching and multiple program classifiers induced by genetic programming. Expand
...
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3
4
5
...