Mouse Phenome Database: an integrative database and analysis suite for curated empirical phenotype data from laboratory mice - PubMed (original) (raw)

. 2018 Jan 4;46(D1):D843-D850.

doi: 10.1093/nar/gkx1082.

Stephen C Grubb 1, David O Walton 1, Vivek M Philip 1, Georgi Kolishovski 1, Tim Stearns 1, Matthew H Dunn 1, Daniel A Skelly 1, Beena Kadakkuzha 1, Gregg TeHennepe 1, Govindarajan Kunde-Ramamoorthy 1, Elissa J Chesler 1

Affiliations

Mouse Phenome Database: an integrative database and analysis suite for curated empirical phenotype data from laboratory mice

Molly A Bogue et al. Nucleic Acids Res. 2018.

Abstract

The Mouse Phenome Database (MPD; https://phenome.jax.org) is a widely used resource that provides access to primary experimental trait data, genotypic variation, protocols and analysis tools for mouse genetic studies. Data are contributed by investigators worldwide and represent a broad scope of phenotyping endpoints and disease-related traits in naïve mice and those exposed to drugs, environmental agents or other treatments. MPD houses individual animal data with detailed, searchable protocols, and makes these data available to other resources via API. MPD provides rigorous curation of experimental data and supporting documentation using relevant ontologies and controlled vocabularies. Most data in MPD are from inbreds and other reproducible strains such that the data are cumulative over time and across laboratories. The resource has been expanded to include the QTL Archive and other primary phenotype data from mapping crosses as well as advanced high-diversity mouse populations including the Collaborative Cross and Diversity Outbred mice. Furthermore, MPD provides a means of assessing replicability and reproducibility across experimental conditions and protocols, benchmarking assays in users' own laboratories, identifying sensitized backgrounds for making new mouse models with genome editing technologies, analyzing trait co-inheritance, finding the common genetic basis for multiple traits and assessing sex differences and sex-by-genotype interactions.

© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

PubMed Disclaimer

Figures

Figure 1.

Figure 1.

Search results tables are filterable by dataset, procedure, treatment, strain panel, or sex (see blue facet panel to the left); sortable (up/down arrowheads for each column); and searchable (search box for each column). A quick primer for getting the most out of these pivot tables is available through the link at the top of the table: ‘Help/filtering’. In this search result for ‘cocaine’ we have chosen datasets Tarantino1 and Thomsen1 in the facets panel (left). Measures in a set are indicated by the down arrowhead (red circle) in the ‘Phenotype Measure’ column. Clicking on the down arrowhead reveals a listing of measures that make up the set ‘ambulatory episodes’. Green text indicates variable names for single measures.

Figure 2.

Figure 2.

Phenotype measure information is at the top and includes measure ID, variable name, description, units, intervention (if applicable), project to which it is associated (link to project information and associated publication), population type, number of strains (link to table of strains tested with source links, if available), sex, age, method (direct link to protocol), and ontology mappings (clicking on link opens listing of annotated terms). Plot, summary statistics, ANOVA results, and Q–Q plot are available by expanding on the blue bars. Strain means and individual animal data points are shown in the plot. Dashed lines represent ±1 standard deviation, making it easy to identify outlier strains. Plotting options are shown above the plot along with download options. Data are from project Tarantino1 (MPD:459).

Figure 3.

Figure 3.

ANOVA results (upper panel) and Q–Q normality plots (lower panel) are available. Hovering (yellow highlight) over data points reveals strain, sex and animal identification number.

Figure 4.

Figure 4.

MPD toolbox provides a collection of tools for analysis on user selected measures. In this example the ‘Ratios and differences’ tool is ineligible (since three measures are selected) and the ‘Correlations matrix’ and ‘Strain means pivot table’ have been selected (darker background). Results are shown below, in this case, side-by-side. A toggle allows the user to view the results in a stacked manner as well. Each tool can be open or closed independently by clicking on the blue bar. Measures can be selected/deselected and results are automatically updated. Data are from project Yuan3 (MPD:244).

Figure 5.

Figure 5.

The MPD SNP tool allows comparison of multiple strain sets across several SNP data resources. Only the first five rows of this retrieval are shown. There are linkouts to NCBI dbSNP per rs number. The ‘VCF’ link retrieves data from the Sanger website for a particular location. Users can download SNP retrievals in .csv format.

Figure 6.

Figure 6.

The strain hub page contains an image of a representative mouse, links to phenotype and genotype data, as well as provides a search box for data relevant to that strain. Users may also identify measures where their strain of interest is an outlier.

Similar articles

Cited by

References

    1. Blake J.A., Eppig J.T., Kadin J.A., Richardson J.E., Smith C.L., Bult C.J. the Mouse Genome Database, G. . Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse. Nucleic Acids Res. 2017; 45:D723–D729. - PMC - PubMed
    1. Park C.A., Bello S.M., Smith C.L., Hu Z.L., Munzenmaier D.H., Nigam R., Smith J.R., Shimoyama M., Eppig J.T., Reecy J.M.. The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. J. Biomed. Semantics. 2013; 4:13. - PMC - PubMed
    1. Smith C.L., Eppig J.T.. The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. Mamm. Genome. 2012; 23:653–668. - PMC - PubMed
    1. Hayamizu T.F., Mangan M., Corradi J.P., Kadin J.A., Ringwald M.. The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biol. 2005; 6:R29. - PMC - PubMed
    1. Shimoyama M., Nigam R., McIntosh L.S., Nagarajan R., Rice T., Rao D.C., Dwinell M.R.. Three ontologies to define phenotype measurement data. Front. Genet. 2012; 3:87. - PMC - PubMed

Publication types

MeSH terms

LinkOut - more resources