Help & Documentation

Disease models on gene page

The ‘Disease models’ section on the Gene page summarizes the phenotypic similarity between mouse models (with that particular gene knocked out), described using MP terms, and the curated annotations of human diseases, described using HP terms. Data for mouse phenotypes originates from the IMPC and from the MGI database, a repository of mouse models generated by the scientific community. Definitions and phenotypic profiles of human diseases originate from several online databases: OMIM, ORPHANET, DECIPHER.

The section consists of a table with two tabs.

The first tab displays all diseases with which the gene has an established association via orthology, between human and mouse genes. Orthologues are determined using Ensembl Compara. The second tab displays diseases based on phenotypic similarity. In either case, phenotypic similarity is evaluated by the Phenodigm algorithm.

Each tab displays a table with disease name, annotation source, and numerical scores.

Rows in the table are expandable; clicking an expansion button should reveal a detailed sub-table.

The detailed view lists all mouse models that have been generated with a one-gene knockout. The view includes models profiled by the IMPC (marked with the IMPC logo), as well as those described by MGI. All models list their measured phenotypes.

The detailed view also contains an interactive heatmap, which summarizes individual phenotype matches.

The heatmap matrix provides insight as to which phenotypes are deemed similar. These similarities are then aggregated into numerical scores using the Phenodigm algorithm.

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