Searching the Mouse Genome Informatics (MGI) Resources for Information on Mouse Biology from Genotype to Phenotype

David R. Shaw1

1 MGI User Support, The Jackson Laboratory, Bar Harbor, Maine
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.7
DOI:  10.1002/cpbi.18
Online Posting Date:  December, 2016
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Abstract

The Mouse Genome Informatics (MGI) resource provides the research community with access to information on the genetics, genomics, and biology of the laboratory mouse. Core data in MGI include gene characterization and function, phenotype and disease model descriptions, DNA and protein sequence data, gene expression data, vertebrate homologies, SNPs, mapping data, and links to other bioinformatics databases. Semantic integration is supported through the use of standardized nomenclature, and through the use of controlled vocabularies such as the mouse Anatomical Dictionary, the Mammalian Phenotype Ontology, and the Gene Ontologies. MGI extracts and organizes data from primary literature. MGI data are shared with and widely displayed from other bioinformatics resources. The database is updated weekly with curated annotations, and regularly adds new datasets and features. This unit provides a guide to using the MGI bioinformatics resource. © 2016 by John Wiley & Sons, Inc.

Keywords: mouse; genome; genes; phenotypes; expression; alleles; function

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Introduction to the MGI Home Page and Quick Search for Gene Information
  • Alternate Protocol 1: Using the Gene Expression Data Search Form to Search for Gene Expression Data by Tissue and Assay Type
  • Alternate Protocol 2: Using the Vocabulary Browsers
  • Alternate Protocol 3: Phenotype Search
  • Alternate Protocol 4: Mouse Models of Human Diseases
  • Alternate Protocol 5: Batch Searches
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

  Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel‐Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., and Sherlock, G. 2000. Gene Ontology: Tool for the unification of biology. Nat. Genet. 25:25‐29.
  Bard, J.B.L., Kaufman, M.H., Dubreuil, C., Brune, R.M., Burger, A., Baldock, R.A., and Davidson, D.R. 1998. An internet‐accessible database of mouse developmental anatomy based on a systematic nomenclature. Mech. Dev. 74:111‐120.
  Drabkin, H.J., Blake, J.A., and the Mouse Genome Informatics Database. 2012. Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database. Database (Oxford). Oct 29; 2012:bas045.
  Eppig, J.T., Blake, J.A., Bult, C.J., Kadin, J.A., Richardson, J.E., and the Mouse Genome Database Group. 2015a. The Mouse Genome Database (MGD): Facilitating mouse as a model for human biology and disease. Nucleic Acids Res. 43:D726‐36.
  Eppig, J.T., Motenko, H., Richardson, J.E., Richards‐Smith, B., and Smith, C.L. 2015b. The International Mouse Strain Resource (IMSR): Cataloging worldwide mouse and ES cell line resources. Mamm. Genome 26:448‐455.
  Motenko, H., Neuhauser, S.B., O'Keefe, M., and Richardson, J.E. 2015. MouseMine: A new data warehouse for MGI. Mamm. Genome 26:325‐330.
  Smith, C.L., Eppig, J.T. 2012. The Mammalian Phenotype Ontology as a unifying standard for experimental and high‐throughput phenotyping data. Mamm. Genome. 23:653‐668.
  Smith, C.M., Finger, J.H., Kadin, J.A., Richardson, J.E., and Ringwald, M. 2014. The gene expression database for mouse development (GXD): Putting developmental expression information at your fingertips. Dev. Dyn. 243:1176‐1186.
Key Reference
  Eppig et al., 2015. See above.
  Nucleic Acids Research's annual Database Issue offers an overview of MGI.
Internet Resources
  http://www.informatics.jax.org/downloads/reports/index.html
  Weekly data reports such as those associating gene symbols with MGI Accessions IDs, map positions, and GenBank Accession IDs are available by FTP from this site.
  http://www.informatics.jax.org/batch
  This Batch Query tool that allows you to retrieve data about many genes in MGI all at once. You can paste or upload a file containing a column of gene symbols or IDs into the batch query tool. You can also specify the output you want in the results, such as nomenclature, genome location, gene ontology, or mammalian phenotype data.
  http://www.informatics.jax.org/mgihome/homepages/help.shtml#UserDocs
  MGI resources are thoroughly documented on this page.
  http://www.informatics.jax.org/submit.shtml
  MGI accepts electronic data submissions of any type of data that MGI maintains. Information on submitting data is available on this Web page.
  http://www.informatics.jax.org/resources.shtml#books
  An electronic version of the book Biology of the Laboratory Mouse, by the staff of The Jackson Laboratory, edited by Earl L. Green, is available online, along with versions of these out‐of‐print books: The Anatomy of the Laboratory Mouse by Margaret J. Cook, Mouse Genetics by Lee Silver, The Coat Colors of Mice by Willys K. Silvers, and Origins of Inbred Mice, edited by Herbert C. Morse III. The books are thoroughly indexed and linked to Gene Detail pages at MGI, as well as to references at MGI and PubMed. Links to all five books can be found on this page.
  http://www.informatics.jax.org/mgihome/lists/lists.shtml
  MGI maintains and moderates an e‐mail bulletin board, mgi‐list, for the mouse genetics research community. A Web interface to the list archives is available on this page.
  http://www.findmice.org/index.jsp
  The International Mouse Strain Resource (IMSR) is a searchable online database of mouse strains and stocks available worldwide from several providers.
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