Others 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
Keywords
- Protein Database
- Drugs Interaction
- Drugs Interaction Database
- Interaction Drugs
- Gene Druggable Pathways
- Phenotypic Ratio
- Epistasis
- Phenotypic Ratio
- Genotype Example
Gene Chemical Interactions
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.
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Description
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 ]
About this Dataset
Data Info
Date Created | 2015-12-25 |
---|---|
Last Modified | 2022-02-28 |
Version | 4.4.207 |
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 |
N/A |
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 |
Data Fields
Name | Description | Type | Constraints |
---|---|---|---|
Biogrid_Chemical_Interaction_ID | Identification number of the registered interaction in the BioGRID database. | integer | level : Nominalrequired : 1unique : 1 |
Biogrid_Gene_ID | Identification number of the gene in the BioGRID database. | integer | level : Nominalrequired : 1 |
Entrez_Gene_ID | Entrez 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. | integer | level : Nominalrequired : 1 |
Gene_Systematic_Name | Name of the gene given for the experiment. | string | - |
Gene_Official_Symbol | Short-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. | string | required : 1 |
Gene_Synonyms | Synonyms for the gene name. A “|” separated list of alternate identifiers for the interacting gene. | string | - |
Organism_ID | Identification number of the organism in which the interaction was tested. | integer | level : Nominalrequired : 1 |
Organism | Name of the organism in which the interaction was tested. | string | required : 1 |
Action | Type of effect of the chemical over the gene. | string | required : 1 |
Chemical_Interaction_Type | Indicates the type of chemical interaction. | string | required : 1 |
Author | First 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). | string | required : 1 |
Pubmed_ID | PubMed Id identifier for the publication in which the gene chemical interaction was shown | integer | level : Nominalrequired : 1 |
Biogrid_Publication_ID | Identification number of the evidence publication in the BioGRID database. | integer | level : Nominalrequired : 1 |
Biogrid_Chemical_ID | Identification number of the chemical in the BioGRID database. | integer | level : Nominalrequired : 1 |
Chemical_Name | The official name for the chemical involved in the interaction. | string | required : 1 |
Chemical_Synonyms | Synonyms for the name of the chemical involved in the interaction. A “|” separated list of synonyms for this chemical. | string | - |
Chemical_Brands | The brand name for the chemical involved in the interaction. A “|” separated list of brand names for this chemical. | string | - |
Chemical_Source_ID | Identification number for the chemical in its source database. | string | - |
Chemical_Molecular_Formula | Molecular formula for the chemical involved in the interaction | string | - |
Chemical_Type | Type of chemical involved in the interaction | string | required : 1 |
Chemical_ATC_Codes | ATC codes for the chemical involved in the interaction. A “|” separated list of ATC codes for the chemical. "The Anatomical Therapeutic Chemical (ATC) Classification System is used for the classification of active ingredients of drugs according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties." (Wikipedia) | string | - |
Chemical_CAS_Number | Unique 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 | - |
Data Preview
Biogrid Chemical Interaction ID | Biogrid Gene ID | Entrez Gene ID | Gene Systematic Name | Gene Official Symbol | Gene Synonyms | Organism ID | Organism | Action | Chemical Interaction Type | Author | Pubmed ID | Biogrid Publication ID | Biogrid Chemical ID | Chemical Name | Chemical Synonyms | Chemical Brands | Chemical Source ID | Chemical Molecular Formula | Chemical Type | Chemical ATC Codes | Chemical CAS Number |
1 | 108447 | 2147 | F2 | PT|RPRGL2|THPH1 | 9606 | Homo sapiens | inhibitor | target | Eriksson BI (2000) | 11055889 | 171739 | 1 | Lepirudin | Lepirudin recombinant|Hirudin variant-1 | refludan | DB00001 | C287H440N80O110S6 | biologic | B01AE02 | 138068-37-8 | |
2 | 108447 | 2147 | F2 | PT|RPRGL2|THPH1 | 9606 | Homo sapiens | inhibitor | target | Warkentin TE (2000) | 10912644 | 171738 | 1 | Lepirudin | Lepirudin recombinant|Hirudin variant-1 | refludan | DB00001 | C287H440N80O110S6 | biologic | B01AE02 | 138068-37-8 | |
3 | 108447 | 2147 | F2 | PT|RPRGL2|THPH1 | 9606 | Homo sapiens | inhibitor | target | Szaba FM (2002) | 11807012 | 171737 | 1 | Lepirudin | Lepirudin recombinant|Hirudin variant-1 | refludan | DB00001 | C287H440N80O110S6 | biologic | B01AE02 | 138068-37-8 | |
4 | 108447 | 2147 | F2 | PT|RPRGL2|THPH1 | 9606 | Homo sapiens | inhibitor | target | Fabrizio MC (2001) | 11467439 | 171736 | 1 | Lepirudin | Lepirudin recombinant|Hirudin variant-1 | refludan | DB00001 | C287H440N80O110S6 | biologic | B01AE02 | 138068-37-8 | |
5 | 108447 | 2147 | F2 | PT|RPRGL2|THPH1 | 9606 | Homo sapiens | inhibitor | target | Turpie AG (1999) | 10505536 | 171735 | 1 | Lepirudin | Lepirudin recombinant|Hirudin variant-1 | refludan | DB00001 | C287H440N80O110S6 | biologic | B01AE02 | 138068-37-8 | |
6 | 108447 | 2147 | F2 | PT|RPRGL2|THPH1 | 9606 | Homo sapiens | inhibitor | target | Chen X (2002) | 11752352 | 171740 | 1 | Lepirudin | Lepirudin recombinant|Hirudin variant-1 | refludan | DB00001 | C287H440N80O110S6 | biologic | B01AE02 | 138068-37-8 | |
7 | 108507 | 2213 | RP11-474I16.2 | FCGR2B | CD32|CD32B|FCG2|FCGR2|IGFR2 | 9606 | Homo sapiens | unknown | target | Imming P (2006) | 17016423 | 171742 | 2 | Cetuximab | Immunoglobulin G 1 (human-mouse monoclonal C 225 gamma 1 - chain anti-human epidermal growt factor receptor), disulfide wit human-mouse monoclonal C 225 kappa - chain, dimer|Ctuximab|Cetuximab|Cetuximabum | erbitux | DB00002 | C6484H10042N1732O2023S36 | biologic | L01XC06 | 205923-56-4 |
8 | 108507 | 2213 | RP11-474I16.2 | FCGR2B | CD32|CD32B|FCG2|FCGR2|IGFR2 | 9606 | Homo sapiens | unknown | target | Overington JP (2006) | 17139284 | 171741 | 2 | Cetuximab | Immunoglobulin G 1 (human-mouse monoclonal C 225 gamma 1 - chain anti-human epidermal growt factor receptor), disulfide wit human-mouse monoclonal C 225 kappa - chain, dimer|Ctuximab|Cetuximab|Cetuximabum | erbitux | DB00002 | C6484H10042N1732O2023S36 | biologic | L01XC06 | 205923-56-4 |
9 | 107177 | 716 | C1S | 9606 | Homo sapiens | unknown | target | Imming P (2006) | 17016423 | 171742 | 2 | Cetuximab | Immunoglobulin G 1 (human-mouse monoclonal C 225 gamma 1 - chain anti-human epidermal growt factor receptor), disulfide wit human-mouse monoclonal C 225 kappa - chain, dimer|Ctuximab|Cetuximab|Cetuximabum | erbitux | DB00002 | C6484H10042N1732O2023S36 | biologic | L01XC06 | 205923-56-4 | ||
10 | 107177 | 716 | C1S | 9606 | Homo sapiens | unknown | target | Overington JP (2006) | 17139284 | 171741 | 2 | Cetuximab | Immunoglobulin G 1 (human-mouse monoclonal C 225 gamma 1 - chain anti-human epidermal growt factor receptor), disulfide wit human-mouse monoclonal C 225 kappa - chain, dimer|Ctuximab|Cetuximab|Cetuximabum | erbitux | DB00002 | C6484H10042N1732O2023S36 | biologic | L01XC06 | 205923-56-4 |