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

2019-10-30

Version

3.5.178

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.integerlevel : Nominal required : 1 unique : 1
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.integerlevel : Nominal required : 1
Organism_Interactor_AOrganism in which interactor A was foundintegerlevel : Nominal required : 1
Organism_Interactor_BOrganism in which interactor B was foundintegerlevel : Nominal required : 1
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
10364162318112315108607MAP2K4FLNCJNKK|JNKK1|MAPKK4|MEK4|MKK4|PRKMK4|SAPKK-1|SAPKK1|SEK1|SERK1|SKK1ABP-280|ABP280A|ABPA|ABPL|FLN2|MFM5|MPD4Two-hybridphysicalMarti A (1997)900689596069606Low ThroughputBIOGRID
1178466588124185106603MYPNACTN2CMD1DD|CMH22|MYOP|RCM4CMD1AATwo-hybridphysicalBang ML (2001)1130942096069606Low ThroughputBIOGRID
183902339106605108625ACVR1FNTAACTRI|ACVR1A|ACVRLK2|ALK2|FOP|SKR1|TSRIFPTA|PGGT1A|PTAR2Two-hybridphysicalWang T (1996)859908996069606Low ThroughputBIOGRID
27826245371108894111384GATA2PMLDCML|IMD21|MONOMAC|NFE1BMYL|PP8675|RNF71|TRIM19Two-hybridphysicalTsuzuki S (2000)1093810496069606Low ThroughputBIOGRID
41861186774112038112651RP4-547C9.3RPA2STAT3REPA2|RP-A p32|RP-A p34|RPA32ADMIO|APRF|HIESTwo-hybridphysicalKim J (2000)1087589496069606Low ThroughputBIOGRID
58637523163106870116775ARF1GGA3Two-hybridphysicalDell'Angelica EC (2000)1074708996069606Low ThroughputBIOGRID
61237723647106872117174ARF3ARFIP2POR1Two-hybridphysicalKanoh H (1997)903814296069606Low ThroughputBIOGRID
61737727236106872118084ARF3ARFIP1HSU52521Two-hybridphysicalKanoh H (1997)903814296069606Low ThroughputBIOGRID
66354464226119970106728XRN1ALDOA1-SepALDA|GSD12|HEL-S-87pTwo-hybridphysicalLehner B (2004)1523174796069606High ThroughputBIOGRID
86635110513106848115769APPAPPBP2AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2APP-BP2|HS.84084|PAT1Two-hybridphysicalZheng P (1998)984396096069606Low ThroughputBIOGRID