Biochemical Protein Protein Interactions

$716 / year

This dataset includes all protein-protein interactions as well as associated annotation data obtained from the Biological General Repository for Interaction databases (BIOGRID) for major model organisms species, including involved experimental systems used to disclose the interaction. The data is a curation of thousands of publications of research experiments that found a link (interaction) between two proteins.

Complexity

BioGRID interactions are recorded as relationships between two proteins or genes (i.e. they are binary relationships) with an evidence code that supports the interaction and a publication reference. The term “interaction” includes, as well as direct physical binding of two proteins, co-existence in a stable complex and genetic interaction. It should not be assumed that the interaction reported in BioGRID is direct and physical in nature; the experimental system definitions below indicate the nature of the supporting evidence for an interaction between the two biological entities. It should also be noted that some interactions in BioGRID have various levels of evidential support. BioGRID simply curates the result of the experiment from the publication and does not guarantee that any individual interaction is true, well-established or the current consensus view of the community. Curating all available evidence supporting an interaction enables orthogonal data from various sources to be collated, allowing users of the database to decide confidence in the existence and/or physiological relevance of that interaction.

The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (thebiogrid.org). BioGRID currently holds over 980,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 55,000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. BioGRID provides interaction data from several model organism databases, resources such as Entrez-Gene, SGD, TAIR, FlyBase and other interaction meta-databases.

The dataset contains protein-protein interactions, noting the official symbol and aliases for every interactor as well as the experimental system used to disclose the interaction. Reference of the publication is given as first author and PubMed ID and the organisms involved are also specified.
Description source: Chatr-Aryamontri A, Oughtred R, Boucher L, Rust J, Chang C, Kolas NK, O’Donnell L, Oster S, Theesfeld C, Sellam A, Stark C, Breitkreutz BJ, Dolinski K, Tyers M. The BioGRID interaction database: 2017 update. Nucleic Acids Res. 2016 Dec 14;2017(1) [ Pubmed, NAR ]

Date Created

2015-12-25

Last Modified

2017-06-30

Version

3.4.150

Update Frequency

Quarterly

Temporal Coverage

N/A

Spatial Coverage

N/A

Source

John Snow Labs; Biological General Repository for Interaction Datasets;

Source License URL

Source License Requirements

N/A

Source Citation

Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID a general repository for interaction datasets. Nucleic Acids Res. 2006 Jan 1;34(Database issue)D535-9. PubMed PMID 16381927.

Keywords

PPI, Interactome, Protein protein docking, Interactor, Protein database, Protein science, Protein Database, Protein Analysis, Protein Expression, Protein C

Other Titles

Protein-protein interaction database, Species wide interactome, Annotated major model systems protein-protein interaction, Protein Database Protein Protein Interactions, Protein Analysis Protein Protein Interactions, Protein Expression Protein Protein Interactions, Protein C Protein Protein Interactions

NameDescriptionTypeConstraints
BioGRID_Interaction_IDIdentification number of the registered interaction in the BioGRID database.integerunique : 1 required : 1 level : Nominal
Entrez_Gene_Interactor_AEntrez identifier for protein A. Unique identifier for the gene of the National Center for Biotechnology Information (NCBI)’s Entrez Gene database.integerlevel : Ratio
Entrez_Gene_Interactor_BEntrez identifier for protein B. Unique identifier for the gene of the National Center for Biotechnology Information (NCBI)’s Entrez Gene database.integerlevel : Ratio
BioGRID_ID_Interactor_AIdentification number of protein A in the BioGRID database.stringrequired : 1
BioGRID_ID_Interactor_BIdentification number of protein B in the BioGRID database.stringrequired : 1
Systematic_Name_Interactor_AName of protein A given for the experimentstring-
Systematic_Name_Interactor_BName of protein A given for the experimentstring-
Official_Symbol_Interactor_AOfficial symbol name for interacting protein Astring-
Official_Symbol_Interactor_BOfficial symbol name for interacting protein Bstringrequired : 1
Synonyms_Interactor_AOther names for interacting protein Astring-
Synonyms_Interactor_BOther names for interacting protein Bstring-
Experimental_SystemLaboratory method used to find the interaction.stringrequired : 1
Experimental_System_TypeLaboratory method type used to find the interaction.stringrequired : 1
AuthorPublication in which interaction was reported presented as first author and datestring-
Pubmed_IDIdentification number of the text describing the experiment published in PubMed database as evidence of the interaction. PubMed is a US National Library of Medicine citation database that contains millions of abstracts, references and full text links of biomedical literature from different trusted sources.integerrequired : 1 level : Nominal
Organism_Interactor_AOrganism in which interactor A was foundintegerrequired : 1 level : Nominal
Organism_Interactor_BOrganism in which interactor B was foundintegerrequired : 1 level : Nominal
ThroughputThroughput level of the experiment used to disclose the interaction. High-throughtput means that the experiment was carried out with multiple simultaneous protein identifications.stringrequired : 1
ScoreRelative score of the involved interaction. The greater the score the stronger the interaction.string-
ModificationBiological change resulting from the interaction.string-
PhenotypesPhenotype (observed change) resulting from the interaction due to the modification.string-
QualificationsDescription of the experimental requirements to consider the interaction possiblestring-
Source_DatabaseDatabase from which the data was obtainedstringrequired : 1
BioGRID_Interaction_IDEntrez_Gene_Interactor_AEntrez_Gene_Interactor_BBioGRID_ID_Interactor_ABioGRID_ID_Interactor_BSystematic_Name_Interactor_ASystematic_Name_Interactor_BOfficial_Symbol_Interactor_AOfficial_Symbol_Interactor_BSynonyms_Interactor_ASynonyms_Interactor_BExperimental_SystemExperimental_System_TypeAuthorPubmed_IDOrganism_Interactor_AOrganism_Interactor_BThroughputScoreModificationPhenotypesQualificationsSource_Database
882607274055530109002120701GLP1RSVOPPCAphysicalHuang X (2013)2386465196069606Low ThroughputBIOGRID
88260827409143109002114590GLP1RSYNGR3PCAphysicalHuang X (2013)2386465196069606Low ThroughputBIOGRID
893327847847107297107297CATCATTwo-hybridphysicalWang J (2011)2198883296069606High ThroughputBIOGRID
94866827842787109046109049GNB3GNG5FRETphysicalSun Z (2012)2294062896069606Low ThroughputBRETBIOGRID
32823327852783109047109045GNG3GNB2Two-hybridphysicalYan K (1996)863615096069606Low ThroughputBIOGRID
32823427852784109047109046GNG3GNB3Two-hybridphysicalYan K (1996)863615096069606Low ThroughputBIOGRID
32823727862783109048109045GNG4GNB2Two-hybridphysicalYan K (1996)863615096069606Low ThroughputBIOGRID
32823827862784109048109046GNG4GNB3Two-hybridphysicalYan K (1996)863615096069606Low ThroughputBIOGRID
32824127872783109049109045GNG5GNB2Two-hybridphysicalYan K (1996)863615096069606Low ThroughputBIOGRID
32824227872784109049109046GNG5GNB3Two-hybridphysicalYan K (1996)863615096069606Low ThroughputBIOGRID