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Approaches to using MPD
Use this page as a starting point if you're considering ways of looking at the data in MPD.

Much of the information in MPD is "strain survey" data, meaning that a set of investigator-selected inbred strains is tested in a cohesive project where baseline phenotype, intervention- or aging-related phenotype effects, expression, or genotype are measured. Because all mice of a particular inbred strain are genetically uniform, analyses often use strain/sex averages or strain consensus values. These averages can be collected from a variety of labs and experiments. Strain survey data are useful in correlations and other more involved analyses, with the opportunity to leverage available high-resolution strain-specific genotype data. More recently MPD has expanded into other data paradigms such as heterogeneous populations. For more discussion of data types and study designs see the About MPD page.

Look up data for one or two strains
    Find data for a specific strain   Find phenotype, SNP/variation, or expression data for a certain strain, or list phenotypes and probesets where a certain strain is a high-end or low-end outlier.

    Compare two strains   For two strains of interest see how they compare in phenotypes, polymorphisms, and expression.

Work with a particular strain panel or set

Phenotype strain survey data
    Tools and views   [Demo]   Web-based tools for plotting, correlations, criteria-fit, finding outliers, downloading selected data, and looking at ratios and differences. Normally you navigate to phenotype data of interest, or go to your cart, then click on Apply Tools.

    Ontologies   MPD phenotype strain survey data have been mapped to MP, VT, and MA ontology terms. Find phenotype data by ontology term, or navigate the ontologies and term-specific linkouts to other resources.

    Your collection   While browsing MPD collect phenotype measurements into your shopping cart. Then go to your cart (at top of page) to work with them.

    By intervention or by phenotyping methodology
    Drug, alcohol, diet, pathogen, challenge, toxicity intervention studies are available. Data can be queried by phenotyping methodology, and each data set has associated protocol documentation with methodology details (via the symbols).

    Aging studies   MPD has comprehensive characterization of aged mice.

    Create user vectors and find correlated objects. To create a "user vector" you can input strain averages from your own assays, or take the ratio or difference of two existing MPD phenotype measurements. Then with this vector you can list correlated phenotype measurements and expression data from across MPD.

    EMMA association study   Genome-wide association studies of selected MPD phenotypes were run by the ZarLab at UCLA using their EMMA GWAS software.

    Sex differences   List measured traits by average amount of sex difference. Or if you have a set of measurements, you can use Apply Tools to list the strains that exhibit the most sex difference.

    Sampling variation over time   Several studies measured seasonal variation of C57BL/6J mice in various phenotypes.

Genotype variation strain survey data
    SNP / variation query   Retrieve SNPs, indels, or SVs from a number of data sets. View the result or download as CSV.

    Polymorphism matrix view   After running a query as above, a strain matrix of %polymorpic for the retrieval can be viewed.

    Haplotypes / strain groupings view   After running a query as above, a strain group summary can be viewed.

    Find genes where selected strains are polymorphic   Select from the 29 strains assayed in Sanger1 and list the genes where selected strains are highly polymorphic, across the entire genome or a particular chromosome. Based on tabulations made in advance on Sanger1 data.

Gene expression strain survey data
    Correlations and outliers Mathematical correlations between phenotypes and expression probesets, and finding probesets where certain strains are outliers.

    Differential expression analysis   Studies are available comparing treatments vs. controls, females vs. males, or cell types. Treatments include high-fat diet, LPS, TCE, OxPAPC.

QTL studies
    MPD includes 70+ QTL studies in various research areas, each having phenotype and genotype data for members of a population derived from a specific cross. Each study has a web page listing the phenotypes studied, as well as downloadable data files. Users download the data and run analyses locally using software such as R/qtl.

Finding data associated with a particular gene
    Use MPD's gene search page to look up specific genes of interest. MPD has gene-specific SNP/variation strain survey data, expression strain survey data, and certain phenotype strain survey and QTL data.

Capture a gene set

Data downloads


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