BioGRID: a general repository for interaction datasets

Published in

(2005)

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TL;DR

BioGRID is a freely accessible database of physical and genetic interactions that includes >116 000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens.

Abstract

Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at . BioGRID release version 2.0 includes >116 000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. Over 30 000 interactions have recently been added from 5778 sources through exhaustive curation of the Saccharomyces cerevisiae primary literature. An internally hyper-linked web interface allows for rapid search and retrieval of interaction data. Full or user-defined datasets are freely downloadable as tab-delimited text files and PSI-MI XML. Pre-computed graphical layouts of interactions are available in a variety of file formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID.

Authors

Chris Stark

1 papers

Bobby-Joe Breitkreutz

1 papers

T. Reguly

1 papers

References33 items

MINT: the Molecular INTeraction database

MIPS: analysis and annotation of proteins from whole genomes in 2005

The synthetic genetic interaction spectrum of essential genes

The Biomolecular Interaction Network Database and related tools 2005 update

FlyBase: genes and gene models

BioGRID: a general repository for interaction datasets

Published in

(2005)

External Links:

Generate Graph DownloadPDF

TL;DR

Abstract

Authors

Chris Stark

1 papers

Bobby-Joe Breitkreutz

1 papers

T. Reguly

1 papers

References33 items

MINT: the Molecular INTeraction database

MIPS: analysis and annotation of proteins from whole genomes in 2005

The synthetic genetic interaction spectrum of essential genes

The Biomolecular Interaction Network Database and related tools 2005 update

FlyBase: genes and gene models

Lorrie Boucher

1 papers

A. Breitkreutz

1 papers

A Drosophila protein-interaction map centered on cell-cycle regulators

A robust toolkit for functional profiling of the yeast genome.

Global Mapping of the Yeast Genetic Interaction Network

The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data

A Map of the Interactome Network of the Metazoan C. elegans

A Protein Interaction Map of Drosophila melanogaster

Development of human protein reference database as an initial platform for approaching systems biology in humans.

Functional genomics and proteomics: charting a multidimensional map of the yeast cell.

Assembly of Cell Regulatory Systems Through Protein Interaction Domains

The GRID: The General Repository for Interaction Datasets

Osprey: a network visualization system

Analyzing yeast protein–protein interaction data obtained from different sources

Comparative assessment of large-scale data sets of protein–protein interactions

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

Functional organization of the yeast proteome by systematic analysis of protein complexes

Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants

A comprehensive two-hybrid analysis to explore the yeast protein interactome

A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins.

From molecular to modular cell biology

From the Cover : Conserved patterns of protein interaction in multiple species

IntAct: an open source molecular interaction database

The Database of Interacting Proteins: 2004 update

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms

TL;DR

Abstract

Authors

References33 items

MINT: the Molecular INTeraction database

MIPS: analysis and annotation of proteins from whole genomes in 2005

The synthetic genetic interaction spectrum of essential genes

The Biomolecular Interaction Network Database and related tools 2005 update

FlyBase: genes and gene models

TL;DR

Abstract

Authors

References33 items

MINT: the Molecular INTeraction database

MIPS: analysis and annotation of proteins from whole genomes in 2005

The synthetic genetic interaction spectrum of essential genes

The Biomolecular Interaction Network Database and related tools 2005 update

FlyBase: genes and gene models

A Drosophila protein-interaction map centered on cell-cycle regulators

A robust toolkit for functional profiling of the yeast genome.

Global Mapping of the Yeast Genetic Interaction Network

The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data

A Map of the Interactome Network of the Metazoan C. elegans

A Protein Interaction Map of Drosophila melanogaster

Development of human protein reference database as an initial platform for approaching systems biology in humans.

Functional genomics and proteomics: charting a multidimensional map of the yeast cell.

Assembly of Cell Regulatory Systems Through Protein Interaction Domains

The GRID: The General Repository for Interaction Datasets

Osprey: a network visualization system

Analyzing yeast protein–protein interaction data obtained from different sources

Comparative assessment of large-scale data sets of protein–protein interactions

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

Functional organization of the yeast proteome by systematic analysis of protein complexes

Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants

A comprehensive two-hybrid analysis to explore the yeast protein interactome

A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins.

From molecular to modular cell biology

From the Cover : Conserved patterns of protein interaction in multiple species

IntAct: an open source molecular interaction database

The Database of Interacting Proteins: 2004 update

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms

GermOnline, a cross-species community knowledgebase on germ cell differentiation

Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource

Harvesting the genome's bounty: integrative genomics.

DIP: The Database of Interacting Proteins: 2001 update

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