EMAGE mouse embryo spatial gene expression database: 2010 update

EMAGE (http://www.emouseatlas.org/emage) is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Here, we describe recent enhancements to EMAGE including: the release of a completely re-designed website, which offers integration of many different search functions in HTML web pages, improved user feedback and the ability to find similar expression patterns at the click of a button; back-end refactoring from an object oriented to relational architecture, allowing associated SQL access; and the provision of further access by standard formatted URLs and a Java API. We have also increased data coverage by sourcing from a greater selection of journals and developed automated methods for spatial data annotation that are being applied to spatially incorporate the genome-wide (∼19 000 gene) ‘EURExpress’ dataset into EMAGE.

[1]  James G. R. Gilbert,et al.  The vertebrate genome annotation (Vega) database , 2004, Nucleic Acids Res..

[2]  Richard Baldock,et al.  Computational genetics: Bioinformatics beyond sequence: mapping gene function in the embryo , 2001, Nature Reviews Genetics.

[3]  Judith A. Blake,et al.  The Mouse Genome Database (MGD): mouse biology and model systems , 2007, Nucleic Acids Res..

[4]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[5]  Janan T. Eppig,et al.  The mouse Gene Expression Database (GXD): 2017 update , 2016, Nucleic Acids Res..

[6]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2006, Nucleic Acids Research.

[7]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[8]  Andrew M. Jenkinson,et al.  Ensembl 2009 , 2008, Nucleic Acids Res..

[9]  Thorsten Henrich,et al.  Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE) , 2008, Nature Biotechnology.

[10]  The UniProt Consortium,et al.  The Universal Protein Resource (UniProt) 2009 , 2008, Nucleic Acids Res..

[11]  J. Bard,et al.  An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature , 1998, Mechanisms of Development.

[12]  Paula Murphy,et al.  Integrating technologies for comparing 3D gene expression domains in the developing chick limb , 2008, Developmental biology.

[13]  Damian Smedley,et al.  BioMart – biological queries made easy , 2009, BMC Genomics.

[14]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[15]  Janet Rossant,et al.  Microarray analysis of Foxa2 mutant mouse embryos reveals novel gene expression and inductive roles for the gastrula organizer and its derivatives , 2008, BMC Genomics.

[16]  Janan T. Eppig,et al.  The Mouse Gene Expression Database (GXD) , 2001, Nucleic Acids Res..

[17]  T. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2010, Nucleic Acids Res..

[18]  Gregor Eichele,et al.  GenePaint.org: an atlas of gene expression patterns in the mouse embryo , 2004, Nucleic Acids Res..

[19]  Nicholas Burton,et al.  EMAGE: a spatial database of gene expression patterns during mouse embryo development , 2005, Nucleic Acids Res..

[20]  J. Vane,et al.  Optical Projection Tomography as a Tool for 3D Microscopy and Gene Expression Studies , 2002 .

[21]  Paul Smith,et al.  EMAGE—Edinburgh Mouse Atlas of Gene Expression: 2008 update , 2007, Nucleic Acids Res..

[22]  Midori A. Harris,et al.  The Gene Ontology project , 2005 .

[23]  Giorgio Valle,et al.  The Gene Ontology project in 2008 , 2007, Nucleic Acids Res..