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. 2010 Jan;38(Database issue):D570-6.
doi: 10.1093/nar/gkp799. Epub 2009 Sep 26.

EMMA--mouse mutant resources for the international scientific community

Phil Wilkinson  1 , Jitka Sengerova, Raffaele Matteoni, Chao-Kung Chen, Gaetan Soulat, Abel Ureta-Vidal, Sabine Fessele, Michael Hagn, Marzia Massimi, Karen Pickford, Richard H Butler, Susan Marschall, Ann-Marie Mallon, Amanda Pickard, Marcello Raspa, Ferdinando Scavizzi, Martin Fray, Vanessa Larrigaldie, Johan Leyritz, Ewan Birney, Glauco P Tocchini-Valentini, Steve Brown, Yann Herault, Lluis Montoliu, Martin Hrabé de Angelis, Damian Smedley
Affiliations

EMMA--mouse mutant resources for the international scientific community

Phil Wilkinson et al. Nucleic Acids Res. 2010 Jan.

Abstract

The laboratory mouse is the premier animal model for studying human disease and thousands of mutants have been identified or produced, most recently through gene-specific mutagenesis approaches. High throughput strategies by the International Knockout Mouse Consortium (IKMC) are producing mutants for all protein coding genes. Generating a knock-out line involves huge monetary and time costs so capture of both the data describing each mutant alongside archiving of the line for distribution to future researchers is critical. The European Mouse Mutant Archive (EMMA) is a leading international network infrastructure for archiving and worldwide provision of mouse mutant strains. It operates in collaboration with the other members of the Federation of International Mouse Resources (FIMRe), EMMA being the European component. Additionally EMMA is one of four repositories involved in the IKMC, and therefore the current figure of 1700 archived lines will rise markedly. The EMMA database gathers and curates extensive data on each line and presents it through a user-friendly website. A BioMart interface allows advanced searching including integrated querying with other resources e.g. Ensembl. Other resources are able to display EMMA data by accessing our Distributed Annotation System server. EMMA database access is publicly available at http://www.emmanet.org.

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Figures

Figure 1.
Figure 1.
Browsing and searching for mouse lines in EMMA. Relevant strains can be identified by either (i) typing case-insensitive, full/partial terms in the top text field which searches against the affected gene symbols and name, approved international designated and common strain names, phenotype description and EMMA ID, or (ii) browsing through a complete list of lines or partial lists categorised by the affected gene(s), mutant type (targeted, gene trap, transgenic, induced, chromosomal anomalies or spontaneous), research tool [Cre recombinase expressing strains, lines for tetracycline (Tet)-regulated gene expression systems], strains provided by the Wellcome Trust Knockout Mouse Resource and finally strains produced out of the EUCOMM programme. Results are presented as a table of the EMMA ID, affected gene, common and approved international strain names alongside links to order or register interest in ordering a line when it becomes available. Clicking on any of the common strain names pops up a description of the strain.
Figure 2.
Figure 2.
EMMA strain descriptions. Data presented includes the mutation type, genetic background it is currently maintained on, brief genetic and phenotype descriptions if known, the original producer, literature references, the genotyping protocol needed to confirm the mutation, what material is available along with delivery times and costs and a link for downloading associated MTA documentation, if applicable.
Figure 3.
Figure 3.
The EMMA BioMart interface. This interface allows advanced querying of the EMMA database as well as distributed and integrated querying with the Ensembl resource. In this example EMMA targeted knock-out lines are identified that have affected genes annotated by Ensembl as being located within the first 100 Mbp of chromosome 1 and containing a transmembrane domain in their protein products. The results table is fully configurable from within the interface and here shows the strain name, EMMA ID (hyperlinked back to the strain description at EMMA), gene symbol and phenotype description from the EMMA BioMart and the Ensembl Gene ID, chromosome, start and end from the Ensembl BioMart located at the Wellcome Trust Sanger Institute, Hinxton, UK.
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