In addition to providing downloads of phenotype and genotype data, MPD provides a number of analysis tools to support exploratory data analysis and discovery. The ability to choose strains for a specific experiment by accessing and analyzing existing phenotype data can bypass the need for investigators to invest time and resources (re)characterizing strains. This functionality, in turn, accelerates research and leverages existing community resources. To assist researchers in data analysis, summary statistics are computed from submitted per-animal data and are available in tabular format. Tools are provided for visualizing measurement data, comparing strains and correlating measurements across all submitted datasets. Researchers can also use MPD to create customized datasets of phenotype measurements. contains a description of selected MPD tools with reference to thumbnail views shown in . Four demos have been prepared to illustrate these tools and other MPD features and displays (Supplementary Data 8–11, indexed in ).
Figure 1 MPD displays and graphics from selected tools. Thumbnail images illustrate a variety of MPD visualization and analysis tools. The key for A through M is shown in Table 4. Learn more about these tools and graphic output options in MPD Demos 1–4 (more ...)
In addition to the standard statistical analysis tools, MPD provides a number of more advanced user tools. Find Mouse Models, a powerful criteria-fit tool, enables the identification of those strains best matching a set of user-defined criteria [ (I), ]. Using the best mouse model for a particular research application helps optimize phenotype-driven approaches to functionally define the genome. illustrates the power of the Find Mouse Models tool (see more details in MPD Demo 3, Supplementary Data 10). This tool aids in finding mouse strains with certain traits or complex phenotypes, and further, it helps choose control strains for specific applications. As the power of this tool is data-dependent (quantity and quality), data representing other medically relevant phenotypic domains and data from additional levels of comprehensive phenotyping are needed to identify new, possibly improved, mouse models that more accurately emulate human disease.
Figure 2 Find mouse models—criteria fit tool. This tool helps identify strains best matching user-specified criteria. Users choose measurements of interest and specify criteria for each. A search is issued across the entire MPD and the strains giving the (more ...)
An important goal of the Mouse Phenome Project is to provide online tools to help researchers link genotype and phenotype. MPD recently updated a data display whereby phenotypic data may be viewed alongside SNPs from specified genes or regions. This interactive tool, illustrated in Figure 1 (M) and MPD Demo 2 (Supplementary Data 9) is useful for a quick assessment of possible phenotype–genotype associations and for selecting strains harboring specific polymorphisms in candidate genes or regions of interest. Strains identified this way are valuable for hypothesis testing, candidate gene validation and follow-on research. More sophisticated tools for in silico haplotype association mapping will be developed when a consensus is determined regarding the most effective algorithms to accurately associate genotype and phenotype.
Additional information about MPD tools and features can be found in the FAQ (Supplementary Data 12).