Chemical Pathway Enriched Associations

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This dataset contains the results of pathway enrichment analyses performed for gene groups that are in some way affected by a chemical. The enrichment analysis system permits to find common pathways between genes. Each analysis is based in the list of genes related to the specified chemical, resulting in the output of pathways shared between the genes, creating information used in the biological processes that might be involved in the effect of the chemical over the genes or disease mechanism.

Complexity

Genome annotation is the description of a gene correlated with a structure, function, products, regulation and other enriching information. “The “unit” of genome annotation is the description of an individual gene and its protein (or RNA) product, and the focal point of each such record is the function assigned to the gene product. The record may also include a brief description of the evidence for this assigned function.” (1) One of the elements that can be annotated to a gene is the pathway(s) of biological processes in which the gene participate or generate.

Gene enrichment is a statistical analysis to identify over-represented (overexpressed) genes from a large pool of genes or proteins that share a common characteristic (i.e. microarray); these over-represented genes could be associated with a disease. Enrichment is statistically comparing descriptions to the genes set to understand the biological processes of those genes. The test determines if the pathway is enriched for the genes calculating the statistical significance of each annotation to find significantly enriched pathways associated with the list of genes. By performing this analysis scientists can determine if the genes share a common characteristic by finding the annotated pathways that are more strongly associated (by annotation significance) to the group of genes. The hypergeometric distribution statistical formula is used to find the significance of the pathways.

1. Koonin EV, Galperin MY. Sequence – Evolution – Function: Computational Approaches in Comparative Genomics. Boston: Kluwer Academic; 2003.

Date Created

2004-01-20

Last Modified

2019-10-02

Version

2019-05

Update Frequency

Monthly

Temporal Coverage

N/A

Spatial Coverage

N/A

Source

John Snow Labs; Comparative Toxicogenomics Database;

Source License URL

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

Gene Pathway Enrichment, Gene Pathway Analyses, Gene Common Pathways, Pathways Between Genes, Genome Annotation, Gene Enrichment

Other Titles

Chemical Effect Integrated into Pathways, Pathways Response to Chemical Exposure, Pathway Involved and Affected Upon Chemical Exposure, Chemical Pathway Enriched Associations Gene Ontology, Chemical Pathway Enriched Associations Kegg Pathway, Chemical Pathway Enriched Associations Enrichment, Chemical Pathway Enriched Associations Gene Set Enrichment Analysis (GSEA)

NameDescriptionTypeConstraints
Chemical_NameName of the chemical associated with the group of genes in the pathway analysis.stringrequired : 1
Chemical_IDIdentification number of the chemical by the US National Library of Medicine’s Medical Subject Headings (MeSH). MeSH is a controlled vocabulary of thousands of biomedical terms that serves to standardize the terminology used in published texts that belong to life sciences. Each MeSH term has a unique identifier, which can be from 7 to 8-character length. The MeSH unique identifier was changed to 10-character length after November 2013.stringrequired : 1
Cas_Registry_NumberUnique numeric identifier designated by CAS for the chemical substance. 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-
Pathway_NameThe official 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.stringrequired : 1
P_ValueRaw p-value. The p-value indicates how significant is the pathway to the group of genes related to the chemical; the closer to zero, the greater the probability that the pathway is shared by these genes due to reasons other than by chance. The p-value is calculated using hypergeometric distribution method, which compares the pathways shared by the genes with the background distribution of the annotation.stringrequired : 1
Corrected_P_ValueP-value after applying Bonferroni adjustment. Bonferroni correction is made when a group of variables (in this case a group of genes) is being tested, to give a more accurate significance.stringrequired : 1
Target_Match_QuantityNumber of genes that interact with the chemical and are annotated to the pathway.integerrequired : 1 level : Ratio
Target_Total_QuantityTotal number of genes that interact with the chemical.integerrequired : 1 level : Ratio
Background_Match_QuantityTotal number of genes that are annotated to the pathway.integerrequired : 1 level : Ratio
Background_Total_QuantityTotal number of human genes.numberrequired : 1 level : Ratio
Chemical NameChemical IDCas Registry NumberPathway NamePathway IDP ValueCorrected P ValueTarget Match QuantityTarget Total QuantityBackground Match QuantityBackground Total Quantity
10074-G5C534883Cell Cycle, MitoticREACT:R-HSA-692780.000140999999999999980.009162251443249
10074-G5C534883Cyclin A:Cdk2-associated events at S phase entryREACT:R-HSA-696562.66e-060.000173227143249
10074-G5C534883Cyclin E associated events during G1/S transitionREACT:R-HSA-692022.73e-060.000178227243249
10074-G5C534883G1/S TransitionREACT:R-HSA-692067.51e-060.0004882211943249
10074-G5C534883MAPK signaling pathwayKEGG:hsa040103.46e-050.002252225543249
10074-G5C534883Mitotic G1-G1/S phasesREACT:R-HSA-4532791.09e-050.00070599999999999992214343249
10074-G5C534883Pathways in cancerKEGG:hsa052008.32e-050.005412239543249
10074-G5C534883Small cell lung cancerKEGG:hsa052223.73e-060.000242228443249
10074-G5C534883S PhaseREACT:R-HSA-692428.97e-060.0005832213043249
10074-G5C534883Transcriptional misregulation in cancerKEGG:hsa052021.7e-050.001112217943249