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Help: Chemical Enriched Pathways


CTD contains curated interactions between chemicals and genes/proteins. Many of the genes/proteins are represented in KEGG and REACTOME pathway maps that represent molecular interaction and reaction networks. To provide insight into the pathways and networks that may be affected by a particular chemical, this report provides a list of pathways that are statistically enriched among the genes/proteins that interact with a chemical (the subject of this page or one of the subject term's descendants). Pathways 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 pathway is significantly higher than the fraction of all human genes annotated to that pathway in the genome.

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

  1. The name of the pathway, linked to additional information about the pathway.
  2. The ID of the pathway from KEGG or REACTOME.
  3. The raw p-value.
  4. The corrected p-value calculated using the Bonferroni multiple testing adjustment (see above).
  5. The number of interacting genes with the associated pathway. Each number is linked to a list of the specific genes/proteins that comprise the pathway.
  6. The genome frequency: the fraction of genes in the genome annotated to the pathway.

Sorting

Sort these data differently by clicking a column heading.

Download

Save these data into a comma-separated values (CSV), Excel, XML, or tab-separated values (TSV) file by clicking a Download link at the bottom of the table.