Published online 18 November 2011 Nucleic Acids Research, 2012, Vol. 40, Database issue D887–D894 doi:10.1093/nar/gkr1061 Mouse Phenome Database (MPD) Terry P. Maddatu, Stephen C. Grubb, Carol J. Bult and Molly A. Bogue* The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA Received September 26, 2011; Revised October 25, 2011; Accepted October 26, 2011 ABSTRACT The Mouse Phenome Project was launched a decade ago to complement mouse genome sequencing efforts by promoting new phenotyping initiatives under standardized conditions and col- lecting the data in a central public database, the Mouse Phenome Database (MPD; http://phenome .jax.org). MPD houses a wealth of strain character- istics data to facilitate the use of the laboratory mouse in translational research for human health and disease, helping alleviate problems involving experimentation in humans that cannot be done practically or ethically. Data sets are voluntarily contributed by researchers from a variety of institu- tions and settings, or in some cases, retrieved by MPD staff from public sources. MPD maintains a growing collection of standardized reference data that assists investigators in selecting mouse strains for research applications; houses treat- ment/control data for drug studies and other interventions; offers a standardized platform for dis- covering genotype–phenotype relationships; and provides tools for hypothesis testing. MPD improve- ments and updates since our last NAR report are presented, including the addition of new tools and features to facilitate navigation and data mining as well as the acquisition of new data (phenotypic, genotypic and gene expression). INTRODUCTION Phenomics, the comprehensive study of phenotypes, com- plements advances in knowledge from genomics, pharma- cogenomics and other -omics approaches. Most human diseases are complex, polygenic and subject to modiﬁca- tions by environmental, genetic and epigenetic factors. A phenomics approach requires collecting comprehensive high-dimensional phenotypic data, integrating it with other types of diverse biological data, and evaluating it with computational tools and bioinformatic approaches. MPD is the only database of its kind—amassing, annotating, integrating and maintaining quantitative phenotypic data for the laboratory mouse, and providing online tools to access and analyze those data. MPD is an established community resource and research tool enabling investigators to access thousands of data points from hundreds of strains, saving time and money by precluding the need to (re)characterize strains. MPD provides many tools to facilitate mouse research. For example, MPD enables users to: . Compare strains to identify mouse models of human disease. . Select optimal genetic backgrounds for new or existing mutations. . Take advantage of the MPD Protocol Library contain- ing detailed, illustrated procedures that have been validated by experts in their ﬁelds (and further, to view data generated from these protocols to conﬁrm experimental results). . Discover phenotype–genotype relationships and . Validate and reﬁne results from traditional mapping studies. More powerful mapping tools are increasingly essential and indispensable in the analysis of complex traits and systems genomics to dramatically reduce the broad, unwieldy intervals of previously identiﬁed quantitative trait loci (QTL) containing hundreds (if not thousands) of genes, down to the gene level. For several years now, the community has had access to high-density SNP data for 16 inbred strains at over 8 million genome-wide loca- tions through the NIEHS-Perlegen resequencing effort (1) and for 94 strains at 132K locations provided by the Mouse HapMap Project (2). These data were used to develop a novel high-density genotyping array, the Mouse Diversity Genotyping Array (3) (see also http:// cgd/tools/diversityarray.shtml). These SNP data sets are available in MPD: Perlegen2 (4), Broad2 (5) and CGD2 (6), respectively. MPD has Mouse Diversity Array data for 123 inbred strains at 550K locations. In addition, the Wellcome Trust Sanger Institute recently released whole-genome sequence data for 17 inbred mouse strains and is generating transcriptome data (RNA-Seq) for these *To whom correspondence should be addressed. Tel: +1 207 288 6016; Fax: +1 207 288 6079; Email: molly.bogue@jax.org The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.