Mouse Genetic and Phenotypic Resources as Tools for Human Genetics

Abstract

The laboratory mouse community provides a rich set of data and material resources for scientists. The primary one is the Mouse Genome Informatics resource at the Jackson Laboratory (JL), supplemented by other resources at the JL and elsewhere, including a rich variety of gene expression information often presented in the form of gene expression atlases. Ordering and distribution of mutant and inbred mouse strains is well organised via the International Mouse Strain Resource. Resources such as knockout embryonic stem cells from the International Knockout Mouse Consortium (IKMC) and other nontraditional genetic resources such as the Collaborative Cross, Diversity Outbred and Chromosome Substitution lines are also available via the web. Systematic phenotyping of mouse strains, in particular knockout strains from the IKMC, is a new and developing field with a developing informatics infrastructure, which uses new approaches to data representation via ontologies to integrate data across species and to human disease information.

Key Concepts:

  • The laboratory mouse is the premier model organism for studying human disease.

  • There is a rich data infrastructure centred around the Mouse Genome Informatics project at the Jackson Laboratory.

  • Material resources (mouse strains, vector, etc) are also widely available to academic researchers, often at cost price.

  • The new systematic phenotyping projects being developed by the mouse community are developing new informatics infrastructure.

  • The development of new ontological approaches to representing phenotype data have opened up new opportunities to link mouse models to human disease.

Keywords: mouse genetics; mouse phenotyping; data resources; databases; data integration; ontologies; gene expression atlases

Figure 1.

Screen shot of the MGI web front page (accessed on 22 March 2013).

close

References

Amberger J, Bocchini C and Hamosh A (2011) A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®). Human Mutation 32: 564–7.

Armit C, Venkataraman S, Richardson L et al. (2012) eMouseAtlas, EMAGE, and the spatial dimension of the transcriptome. Mammalian Genome 23: 514–24.

Austin CP, Battey JF, Bradley A et al. (2004) The knockout mouse project. Nature Genetics 36: 921–4.

Ayadi A, Birling MC, Bottomley J et al. (2012) Mouse large‐scale phenotyping initiatives: overview of the European Mouse Disease Clinic (EUMODIC) and of the Wellcome Trust Sanger Institute Mouse Genetics Project. Mammalian Genome 23: 600–610.

Barrett T, Troup DB, Wilhite SE et al. (2011) NCBI GEO: archive for functional genomics data sets – 10 years on. Nucleic Acids Research 39(Database Issue): D1005–D1010.

Begley DA, Krupke DM, Neuhauser SB et al. (2012) The Mouse Tumor Biology Database (MTB): a central electronic resource for locating and integrating mouse tumor pathology data. Veterinary Pathology 49: 218–23.

Blake A, Pickford K, Greenaway S et al. (2010) MouseBook: an integrated portal of mouse resources. Nucleic Acids Research 38(Database Issue): D593–D599.

Bradley A, Anastassiadis K, Ayadi A et al. (2012) The mammalian gene function resource: the international knockout mouse consortium. Mammalian Genome 23: 580–6.

Brown SD and Moore MW (2012) Towards an encyclopaedia of mammalian gene function: the International Mouse Phenotyping Consortium. Disease Models and Mechanisms 5: 289–92.

Bult CJ, Eppig JT, Blake JA et al. (2013) The mouse genome database: genotypes, phenotypes, and models of human disease. Nucleic Acids Research 41: D885–91.

Chen CK, Mungall CJ, Gkoutos GV et al. (2012) MouseFinder: candidate disease genes from mouse phenotype data. Human Mutation 33: 858–866.

Churchill GA, Airey DC, Allayee H et al. (2004) The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nature Genetics 36(11): 1133–1137.

Churchill GA, Gatti DM, Munger SC et al. (2012) The diversity outbred mouse population. Mammalian Genome 23(9–10): 713–718.

Diez‐Roux G, Banfi S, Sultan M et al. (2011) A high‐resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biology 9: e1000582.

Donahue LR, Hrabe de Angelis M, Hagn M et al. (2012) Centralized mouse repositories. Mammalian Genome 23: 559–591.

Drabkin HJ, Blake JA and Mouse Genome Informatics Database (2012) Manual gene ontology annotation workflow at the mouse genome informatics database. Database (Oxford) 2012: bas045.

Eppig JT and Strivens M (1999) Finding a mouse: the International Mouse Strain Resource (IMSR). Trends in Genetics 15: 81–81.

Espinosa O and Hancock JM (2011) A gene‐phenotype network for the laboratory mouse and its implications for systematic phenotyping. PLoS One 6: e19693.

Evsikov AV, Dolan ME, Genrich MP et al. (2009) MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biology 10: R84.

Gkoutos GV, Green ECJ, Mallon A‐M et al. (2004) Using ontologies to describe mouse phenotypes. Genome Biology 6: R8.

Goecks J, Nekrutenko A, Taylor J et al. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology 11: R86.

Green ECJ, Gkoutos GV, Lad H et al. (2005) EMPReSS: European Mouse Phenotyping Resource for Standardised Screens. Bioinformatics 21: 2930–2931.

Haider S, Ballester B, Smedley D et al. (2009) BioMart Central Portal – unified access to biological data. Nucleic Acids Research 37: (W23–W27.

Hancock JM and Dobbie M (in press) Phenomics of the laboratory mouse. In: Hancock JM (ed.) Phenomics. Enfield, NH: Science Publishers/CRC Press.

Hancock JM, Mallon AM, Beck T et al. (2009) Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease. Mammalian Genome 20: 457–461.

Heintz N (2004) Gene expression nervous system atlas (GENSAT). Nature Neuroscience 7: 483.

Hoehndorf R, Schofield PN and Gkoutos GV (2011) PhenomeNET: a whole‐phenome approach to disease gene discovery. Nucleic Acids Research 39: e119.

Karasavvas K, Wolstencroft K, Mina E et al. (2012) Opening new gateways to workflows for life scientists. Studies in Health Technology and Informatics 175: 131–141.

Keane TM, Goodstadt L, Danecek P et al. (2011) Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477: 289–94.

Maddatu TP, Grubb SC, Bult CJ et al. (2012) Mouse phenome database (MPD). Nucleic Acids Research 40: D887–94.

Magdaleno S, Jensen P, Brumwell CL et al. (2006) BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. PLoS Biology 4: e86.

Morgan H, Beck T, Blake A et al. (2010) EuroPhenome: a repository for high‐throughput mouse phenotyping data. Nucleic Acids Research 38: D577–85.

Nadeau J H, Forejt J, Takada T et al. (2012) Chromosome substitution strains: gene discovery, functional analysis, and systems studies. Mammalian Genome 23: 693–705.

Oinn T, Addis M, Ferris J et al. (2004) Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 20: 3045–3054.

Paigen K and Eppig JT (2000) A mouse phenome project. Mammalian Genome 11: 715– 7.

Parkinson H, Sarkans U, Kolesnikov N et al. (2011) ArrayExpress update – an archive of microarray and high‐throughput sequencing‐based functional genomics experiment. Nucleic Acids Research 39(Database Issue): D1002–D1004.

Ringwald M, Wu C and Su AI (2012) BioGPS and GXD: mouse gene expression data‐the benefits and challenges of data integration. Mammalian Genome 23: 550–8.

Rosenthal N and Brown S (2007) The mouse ascending: perspectives for human‐disease models. Nature Cell Biology 9: 993–9.

Schofield PN, Gkoutos GV, Gruenberger M et al. (2010) Phenotype ontologies for mouse and man; bridging the semantic gap. Disease Models and Mechanisms 3: 281–289.

Siddiqui AS, Khattra J, Delaney AD et al. (2005) A mouse atlas of gene expression: large‐scale digital gene‐expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proceedings of the National Academy of Sciences of the USA 102: 18485–90.

Singer JB, Hill AE, Burrage LC et al. (2004) Genetic dissection of complex traits with chromosome substitution strains of mice. Science 304: 445–448.

Skarnes WC, Rosen B, West AP et al. (2011) A conditional knockout resource for the genome‐wide study of mouse gene function. Nature 474: 337–42.

Smedley D, Haider S, Ballester B et al. (2009) BioMart‐biological queries made easy. BMC Genomics 10: 22.

Smith CL and Eppig JT (2012) The mammalian phenotype ontology as a unifying standard for experimental and high‐throughput phenotyping data. Mammalian Genome 23: 653–68.

Smith RN, Aleksic J, Butano D et al. (2012) InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics 28: 3163–3165.

Sunkin SM, Ng L, Lau C et al. (2013) Allen Brain Atlas: an integrated spatio‐temporal portal for exploring the central nervous system. Nucleic Acids Research 41(Database Issue): D996–D1008.

Svenson KL, Gatti DM, Valdar W et al. (2012) High‐resolution genetic mapping using the mouse diversity outbred population. Genetics 190: 437–447.

Threadgill DW, Hunter KW and Williams RW (2002) Genetic dissection of complex and quantitative traits: from fantasy to reality via a community effort. Mammalian Genome 13: 175–178.

Waterston RH, Lindblad‐Toh K, Birney E et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520–62.

Yaylaoglu MB, Titmus A, Visel A et al. (2005) Comprehensive expression atlas of fibroblast growth factors and their receptors generated by a novel robotic in situ hybridization platform. Developmental Dynamics 234: 371–386.

Yokoyama S, Ito Y, Ueno‐Kudoh H et al. (2009) A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. Developmental Cell 17: 836–848.

Further Reading

Gates H, Mallon AM, Brown SD et al. (2010) High‐throughput mouse phenotyping. Methods 53: 394–404.

Geffers L, Herrmann B and Eichele G (2012) Web‐based digital gene expression atlases for the mouse. Mammalian Genome 23: 525–538.

Hancock JM and Mallon A‐M (2007) Phenobabelomics‐mouse phenotype data resources. Briefings in Functional Genomics and Proteomics 6: 292–301.

Mammalian Genome (2012) Special Issue: Mouse Genomic Programs and Resources, Vol. 23 (Issue 9–10). ISSN: 0938‐8990 (Print) 1432‐1777 (Online).

Schofield PN, Bubela T, Weaver T et al. (2009) Post‐publication sharing of data and tools. Nature 461: 171–173.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Hancock, John M(Sep 2013) Mouse Genetic and Phenotypic Resources as Tools for Human Genetics. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0025011]