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CTD contains curated interactions between chemicals and genes/proteins. Many of these genes/proteins have Gene Ontology (GO) annotations that provide information about their associated biological processes, molecular functions, and cellular components. To provide insight into the biological properties that may be affected by a chemical, this report provides a list of GO terms that are statistically enriched among the genes/proteins that interact with the chemical or one of its descendants. GO terms are displayed in order of significance.

The significance of enrichment was calculated by the hypergeometric distribution and adjusted for multiple testing using the Bonferroni method.[1] The hypergeometric distribution is used to calculate the probability that the fraction of interacting genes annotated to the GO term or its descendants is significantly higher than the fraction of all human genes annotated to that GO term or its descendants in the genome.

For each enriched GO term with a Bonferroni p-value less than 0.01, the following information is displayed:

1. The ontology to which the GO term belongs (BP = Biological Process; CC = Cellular Component; MF = Molecular Function).
2. The highest level to which the GO term is assigned within the GO hierarchical ontology. Many GO terms are located at multiple levels within the ontology; only the highest level is displayed. Level 1 constitutes “children” of the most general Biological Process, Cellular Component, and Molecular Function terms.
3. The name of the enriched GO term associated with interacting genes. Each term is linked to additional information about the term.
4. The number of interacting genes with the associated GO term annotation or its descendants. Each number is linked to a list of the specific genes/proteins with this GO annotation.
5. The raw p-value.
6. The corrected p-value calculated using the Bonferroni multiple testing adjustment (see above).
7. The genome frequency: the fraction of genes in the genome annotated to the GO term or its descendants.

Top Footnotes

[1]

Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G. GO::TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics. 2004 Dec 12;20(18):3710-5. [PMID:15297299]