CTD contains curated and inferred chemical–disease associations.
Curated associations are extracted from the published literature by CTD curators.
Inferred associations are established via curated chemical–gene interactions (e.g., chemical A is associated with disease B because chemical A has a curated interaction with gene C, and gene C has a curated association with disease B).
The following data is presented for these associations:
A disease, GO term, or pathway is considered enriched if the proportion of genes annotated to it in a test set is significantly larger than the proportion of all genes annotated to it in the genome.
The inference score reflects the degree of similarity between CTD chemical–gene–disease networks and a similar scale-free random network. The higher the score, the more likely the inference network has atypical connectivity.
Many biological networks, such as disease and metabolic networks, have been shown to be scale-free random networks. The inference score is calculated as the log-transformed product of two common-neighbor statistics used to assess the functional relationships between proteins in a protein–protein interaction network. The first statistic takes into account the connectivity of the chemical and disease along with the number of genes used to make the inference. The second statistic takes into the account the connectivity of each of the genes used to make the inference.
For more information about inference scores, please refer to our publication:
King BL, Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ.Ranking Transitive Chemical-Disease Inferences Using Local Network Topology in the Comparative Toxicogenomics Database.PLoS One. 2012;7(11):e46524. PMID:23144783
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