A mouse informatics platform for phenotypic and translational discovery

Abstract

The International Mouse Phenotyping Consortium (IMPC) is providing the world's first functional catalogue of a mammalian genome by characterising a knockout mouse strain for every gene. A robust and highly structured informatics platform has been developed to systematically collate, analyse and disseminate the data produced by the IMPC. As the first phase of the project, in which 5000 new knockout strains are being broadly phenotyped, nears completion, the informatics platform is extending and adapting to support the increasing volume and complexity of the data produced as well as addressing a large volume of users and emerging user groups. An intuitive interface helps researchers explore IMPC data by giving overviews and the ability to find and visualise data that support a phenotype assertion. Dedicated disease pages allow researchers to find new mouse models of human diseases, and novel viewers provide high-resolution images of embryonic and adult dysmorphologies. With each monthly release, the informatics platform will continue to evolve to support the increased data volume and to maintain its position as the primary route of access to IMPC data and as an invaluable resource for clinical and non-clinical researchers.

Fig. 1

Data flow in the IMPC. The ten IMPC phenotyping centres upload data for collection and curation centrally at the DCC, followed by final statistical analysis and storage at the CDA for public dissemination and usage. Preliminary (pre-QC) data are viewable by external users immediately. Production and phenotyping processes are standardised and recorded by the use of the International Mouse Injection Tracking System (iMits) and International Mouse Phenotyping Resource of Standardised Screens (IMPReSS)

Fig. 2

The IMPC search interface. Users can search by gene, disease, phenotype and anatomy. Filters on the left of search show summaries of how many results appear in each category, and selecting a filter will return a results table for that category. Gene results include status of mouse production, availability of data and ability to register interest in a gene. Phenotype filtered results give definitions, the number of genes associated to the phenotype, and ability to register interest

Fig. 3

Diseases for which the gene Thpo is a potential model, as identified by determining if the gene is an orthologue of a human disease-causing gene (top) or by using the PhenoDigm to detect whether the phenotypes seen in IMPC Thpo-carrying mice overlap with any diseases (bottom)

Fig. 4

Text, Icon and Heatmap view for Elmod1 provide a rapid overview of the complex phenotypes and an integrated view on pre- and post-QC data (IMPC Data release 3.2)

Fig. 5

Platelet count obtained from the thrombocytopenia page. The histogram depicts the mean values for all tested strains and can be filtered by sex and by the phenotyping centre

Fig. 6

An example of micro-CT imaging of an E14.5 wild-type heart (left) and Atg3 null (right) visualised in IEV depicting a ventricular septal heart defect phenotype