This dataset from the Comparative Toxicogenomics Database (CTD) contains different types of standardized identifications for the gene and the disease to provide a cross-platform compatibility making able to identify the gene and the disease in major science databases and to locate the references for the research in which the inference was based. It also provides the inference score that allows determining the importance of the inference.
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 (CTD) 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.
The CTD datasets can be used to create a tool for input of queries to obtain inferred relationships between genes, chemicals and diseases and the significance of the inferences. To prioritize inferences CTD uses the inference score, which ranks how true is the inferred relationship; this is accomplished by a network diagram where the chemicals, genes and disease are nodes and the relationships between them (inferences) are edges (lines), then the statistical analysis takes into account the number of nodes (genes, diseases or chemicals) that interact with the node of interest (gene, disease or chemical), the number of inferences with direct evidence, and the location of the node of interest using the hypergeometric clustering coefficient and common neighbor statistics. Finally, the inferences should be ranked from higher to lower inference score, being the ones with higher score the most significant ones.
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]