Gene Pathways

$79 / year

This dataset from the Comparative Toxicogenomics Database (CTD) contains the biological pathways on which the analyzed genes are part of. These pathways are useful on inferring relationships between chemicals, genes and diseases when the gene and the disease or chemical in some way share independent relationships with the same pathway. The dataset contains different types of standardized identifications for the pathway and the gene to provide a cross-platform compatibility making able to identify the pathway and the gene in major science databases and to locate the references for the research in which the inference was based.

Complexity

Chemicals are among the main environmental factors that influence health and the way these can cause disease is not totally understood. The Comparative Toxicogenomics Database purpose is to provide a tool to generate new hypotheses on the mechanism of chemicals in the development of diseases by collecting curated data reported in the scientific literature on chemicals, genes and diseases and making inferences on the relationships of these three elements. This is accomplished through transitive inference, which happens when for example a chemical and a disease share interactions with one or more genes, thus inferring that there is a relationship between the chemical and the disease linked to a process or product of the particular genes, with this information could be inferred the mechanism of action of the chemical upon the gene to produce the disease, the genes linked to the disease, the physiopathology of the disease and other inferences. “For example, if chemical A interacts with gene B, and independently gene B is associated with disease C, then chemical A is inferred to have a relationship with disease C (via gene B).” (1) These inferences could be given in other directions, for example, a gene and a disease could share the same group of chemicals; also the inferences could have direct evidence in which there are published research with evidence of the relationship, while other inferences don’t have direct evidence in the literature and can be used to create new testable hypothesis about the mechanism of disease, initiate new research on the relationship and potentially predict disease treatment and prevention.

1. Davis AP, Grondin CJ, Johnson RJ, Sciaky D, King BL, McMorran R, Wiegers J, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database: update 2017. Nucleic Acids Res. 2016 Sep 19;[Epub ahead of print]

Date Created

2004-01-20

Last Modified

2016-04-04

Version

2016-04-04

Update Frequency

Monthly

Temporal Coverage

N/A

Spatial Coverage

N/A

Source

John Snow Labs => Comparative Toxicogenomics Database

Source License URL

John Snow Labs Standard License

Source License Requirements

Publicly available and free for research application but citation is required. Permission asked for commercial uses

Source Citation

Davis AP, Grondin CJ, Johnson RJ, Sciaky D, King BL, McMorran R, Wiegers J, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database update 2017. Nucleic Acids Res. 2016 Sep 19;[Epub ahead of print]

Keywords

Analyzed Genes Biological Pathways, Relationship Between Chemicals Genes and Diseases, Gene and Disease Relationship, Heterogeneous Exposure Information, Comparative Toxicogenomics Database, Relationships Between Genes and Diseases, Chemical and Disease Inferences, Chemical Disease Hypotheses, Taxogenomics

Other Titles

Genes to Pathway Definitions, Database of Relationships Between Pathways and Genes

Name Description Type Constraints
Gene_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 for other species.stringrequired : 1
Gene_IDUnique 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.string-
Pathway_NameOfficial name of the pathway involved in the interaction. A pathway is a series of steps in biological processes at a molecular level that leads to a biological change; a pathway is possible due to the activities of multiple gene products and other elements. Pathways involve molecular interactions and reactions pertaining to metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems, human diseases and drug development. Every pathway has a generic or standardized name that helps on obtaining an overview of the pathway’s nature, others have unique but well-known names, for example, the Krebs cycle.stringrequired : 1
Pathway_IDKEGG or REACTOME identifier. Alphanumerical code that identifies the pathway in the lookup of the KEGG or the REACTOME databases. KEGG Pathway Database is a collection of manually drawn pathway maps representing the knowledge on the molecular interaction and reaction networks for metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems, human diseases and drug development. The Reactome Pathway Database is a curated database of pathways and reactions (pathway steps) in human biology. The Reactome definition of a 'reaction' includes many events in biology that are changes in state, such as binding, activation, translocation and degradation, in addition to classical biochemical reactions. Information in the database is authored by expert biologist researchers, maintained by Reactome editorial staff, and extensively cross-referenced to other resources e.g. NCBI, Ensembl, UniProt, UCSC Genome Browser, HapMap, KEGG (Gene and Compound), ChEBI, PubMed and GO.stringrequired : 1
Gene_SymbolGene_IDPathway_NamePathway_ID
A2M2HemostasisREACT:604
AKT1207GliomaKEGG:05214
AKT2208GliomaKEGG:05214
ARAF369GliomaKEGG:05214
BRAF673GliomaKEGG:05214
CD40958AsthmaKEGG:05310
EGF1950GliomaKEGG:05214
EPX8288AsthmaKEGG:05310
FAS355MeaslesKEGG:05162
IL33562AsthmaKEGG:05310