The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data

Abstract

The International Mouse Phenotyping Consortium (IMPC) web portal (http://www.mousephenotype.org) provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous highly structured and standardized protocols for the experimentation, collection and dissemination of data. Dedicated 'data wranglers' work with each phenotyping center to collate data and perform quality control of data. An automated statistical analysis pipeline has been developed to identify knockout strains with a significant change in the phenotype parameters. Annotation with biomedical ontologies allows biologists and clinicians to easily find mouse strains with phenotypic traits relevant to their research. Data integration with other resources will provide insights into mammalian gene function and human disease. As phenotype data become available for every gene in the mouse, the IMPC web portal will become an invaluable tool for researchers studying the genetic contributions of genes to human diseases.

Figure 1.

A view of the gene and phenotype data for Cib2, a calcium and integrin-binding family protein. The phenotype heatmap shows significant phenotypes for auditory and brainstem and behavioral tests (P < 0.0001). Users can explore underlying data by clicking on phenotype names. The graph shows Cib2 homozygous knockout animals have impaired response to sound stimulus indicating a significant hearing defect as well as abnormal ear morphology. A stock image of an abnormal ear is provided for reference.

Figure 2.

iMITS (https://www.mousephenotype.org/imits) stores and provides summary and detailed production information: Users can view high-level allele information on the IMPC portal gene pages. The iMITS tab of the IMPC portal shows detailed IMPC production information, e.g. for Sdha. Information to access iMITS is provided on the IMPC homepage.

Figure 3.

A schematic overview of data flows into the web portal for IMPC data. Currently, eight mouse clinics are involved in IMPC and produce phenotype data. These are then collected, validated and processed to produce curated data available from the project portal. Legacy data from EuroPhenome and Sanger MGP were directly transferred to the Central Data Archive at EMBL-EBI for direct integration on the portal.