Gene Chemical Interactions

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This dataset includes all gene-chemical interactions with “target” interaction types as well as associated annotation data obtained from the Biological General Repository for Interaction Datasets (BioGRID) for major model organisms species, 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 organisms involved are also specified.

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 chemical-gene 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

Monthly

Temporal Coverage

N/A

Spatial Coverage

N/A

Source

John Snow Labs => Biological General Repository for Interaction Datasets

Source License URL

John Snow Labs Standard License

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. Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, Reguly T, Nixon J, Ramage L, Winter A, Sellam A, Chang C, Hirschman J, Theesfeld C, Rust J, Livstone MS, Dolinski K, Tyers M. The BioGRID interaction database 2015 update. Nucleic Acids Res. 2015 Jan;43(Database issue)D470-8. PubMed PMID 25428363

Keywords

Protein Database, Drugs Interaction, Drugs Interaction Database, Interaction Drugs, Gene Druggable Pathways, Phenotypic Ratio, Epistasis, Phenotypic Ratio, Genotype Example

Other Titles

Protein Chemical Interaction Database, Species Wide Gene-Drug Interaction, Annotated Major Model Systems Gene-Drug Interaction, Phenotypic Ratio Gene Chemical Interactions, Epistasis Gene Chemical Interactions, Phenotypic Ratio Gene Chemical Interactions

Name Description Type Constraints
Biogrid_Chemical_Interaction_IDIdentification number of the registered interaction in the BioGRID database.integerunique : 1 required : 1 level : Nominal
Biogrid_Gene_IDIdentification number of the gene in the BioGRID database.integerrequired : 1 level : Nominal
Entrez_Gene_IDEntrez database unique identifier for the gene. Unique identifier for the gene of the National Center for Biotechnology Information (NCBI)’s Entrez Gene database. This Entrez Gene unique integer can be browsed in the Entrez system online to find nomenclature, sequence, products and other specific details of the gene. The identifier is species specific, a gene ID of a human gene can’t be applied to the same gene of a different species.integerrequired : 1 level : Nominal
Gene_Systematic_NameName of the gene given for the experiment.string-
Gene_Official_SymbolShort-form abbreviation of the name of the gene. The approved symbols for human genes are collected in the HUGO Gene Nomenclature Committee database; each name and symbol is unique for every gene and can be applied to other species.stringrequired : 1
Gene_SynonymsSynonyms for the gene name. A “|” separated list of alternate identifiers for the interacting gene.string-
Organism_IDIdentification number of the organism in which the interaction was tested.integerrequired : 1 level : Nominal
OrganismName of the organism in which the interaction was tested.stringrequired : 1
ActionType of effect of the chemical over the gene.stringrequired : 1
AuthorFirst Author of the publication showing the gene chemical interaction or first author surname of the publication in which the interaction has been shown, optionally followed by additional indicators, e.g. Stephenson A (2005).stringrequired : 1
Pubmed_IDPubMed Id identifier for the publication in which the gene chemical interaction was shownintegerrequired : 1 level : Nominal
Biogrid_Publication_IDIdentification number of the evidence publication in the BioGRID database.integerrequired : 1 level : Nominal
Biogrid_Chemical_IDIdentification number of the chemical in the BioGRID database.integerrequired : 1 level : Nominal
Chemical_NameThe official name for the chemical involved in the interaction.stringrequired : 1
Chemical_SynonymsSynonyms for the name of the chemical involved in the interaction. A “|” separated list of synonyms for this chemical.string-
Chemical_BrandsThe brand name for the chemical involved in the interaction. A “|” separated list of brand names for this chemical.string-
Chemical_Source_IDIdentification number for the chemical in its source database.stringrequired : 1
Chemical_Molecular_FormulaMolecular formula for the chemical involved in the interactionstring-
Chemical_TypeType of chemical involved in the interactionstringrequired : 1
Chemical_ATC_Codesstring-
Chemical_CAS_NumberUnique numeric identifier designated by CAS for the chemical. CAS registry number also serves as a reference to find information on the specific chemical. CAS is a division of the American Chemical Society (ACS); the CAS registry collects information of millions of chemical substances identified since the early 1900’s.string-
Biogrid_Chemical_Interaction_IDBiogrid_Gene_IDEntrez_Gene_IDGene_Systematic_NameGene_Official_SymbolGene_SynonymsOrganism_IDOrganismActionAuthorPubmed_IDBiogrid_Publication_IDBiogrid_Chemical_IDChemical_NameChemical_SynonymsChemical_BrandsChemical_Source_IDChemical_Molecular_FormulaChemical_TypeChemical_ATC_CodesChemical_CAS_Number
243471074381003CDH57B4|CD1449606Homo sapiensunknownAtar D (2006)170190831819705289FX06DB05685biologic
243421089602693GHSR9606Homo sapiensunknownVenkova K (2007)174360821820015281TZP-101DB05657small molecule
2418512334781027TUBB19606Homo sapiensunknownDabydeen DA (2006)169404121819644735E7389DB04940small molecule
214081078181431CS9606Homo sapiensunknownImming P (2006)170164231717423354Malate IonDB03499C4H5O5small molecule
240951086272342FNTBFPTB9606Homo sapiensunknownWakeling AE (2005)161130951819044693AZD3409DB04893small molecule
214101078181431CS9606Homo sapiensunknownBerman HM (2000)105922351721223354Malate IonDB03499C4H5O5small molecule
243321118515916RARGNR1B3|RARC9606Homo sapiensunknownBerman HM (2000)105922351721225229R667DB05467small molecule
243431085342243FGAFib29606Homo sapiensunknownSpuentrup E (2007)179481941820585287EP-2104REP 2104RDB05675biologic
243441085342243FGAFib29606Homo sapiensunknownSpuentrup E (2007)176209421820285287EP-2104REP 2104RDB05675biologic
19979106614100ADA9606Homo sapiensunknownBerman HM (2000)105922351721222712FR236913DB02830C24H26N6O3small molecule