The mouse Gene Expression Database (GXD): 2017 update

The Gene Expression Database (GXD) provides the scientific community with an extensive and easily searchable database of gene expression information about the mouse. Its primary emphasis is on developmental studies. By integrating different types of expression data, GXD aims to provide comprehensive information about expression patterns of transcripts and proteins in wild-type and mutant mice. Integration with the other Mouse Genome Informatics (MGI) databases places the gene expression information in the context of genetic, sequence, functional and phenotypic information, enabling valuable insights into the molecular biology that underlies developmental and disease processes. In recent years the utility of GXD has been greatly enhanced by a large increase in data content, obtained from the literature and provided by researchers doing large-scale in situ and cDNA screens. In addition, we have continued to refine our query and display features to make it easier for users to interrogate the data. GXD is available through the MGI web site at or directly at .

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

[2]  EMAGE: a spatial database of gene expression patterns during mouse embryo development , 2005, Nucleic Acids Res..

[3]  R D Klausner,et al.  The mammalian gene collection. , 1999, Science.

[4]  J T Eppig,et al.  A database for mouse development. , 1994, Science.

[5]  Jamie A Davies,et al.  GUDMAP: the genitourinary developmental molecular anatomy project. , 2008, Journal of the American Society of Nephrology : JASN.

[6]  Robert D. Finn,et al.  InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..

[7]  Judith A. Blake,et al.  The Mouse Genome Database (MGD): updates and enhancements , 2005, Nucleic Acids Res..

[8]  D. Geschwind.  GENSAT: a genomic resource for neuroscience research , 2004, The Lancet Neurology.

[9]  Peter J. Tonellato,et al.  The Rat Genome Database (RGD): developments towards a phenome database , 2004, Nucleic Acids Res..

[10]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

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

[12]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt): an expanding universe of protein information , 2005, Nucleic Acids Res..

[13]  Dennis B. Troup,et al.  NCBI GEO: mining millions of expression profiles—database and tools , 2004, Nucleic Acids Res..

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

[15]  J. Eppig,et al.  Gene expression database for the laboratory mouse , 1999, Nature Genetics.

[16]  Ryan D. Morin,et al.  The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). , 2004, Genome research.

[17]  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.

[18]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2004, Nucleic Acids Res..

[19]  Cathy H. Wu,et al.  InterPro, progress and status in 2005 , 2004, Nucleic Acids Res..

[20]  Jay H. Konieczka,et al.  GEISHA: an in situ hybridization gene expression resource for the chicken embryo , 2007, Cytogenetic and Genome Research.

[21]  Janan T. Eppig,et al.  GXD: a Gene Expression Database for the laboratory mouse: current status and recent enhancements , 2000, Nucleic Acids Res..

[22]  Janan T. Eppig,et al.  GXD: a gene expression database for the laboratory mouse. The Gene Expression Database Group , 1999, Nucleic Acids Res..

[23]  Jian Hu,et al.  The ARKdb: genome databases for farmed and other animals , 2001, Nucleic Acids Res..

[24]  Gavin Sherlock,et al.  The Stanford Microarray Database accommodates additional microarray platforms and data formats , 2004, Nucleic Acids Res..

[25]  Andreas Prlic,et al.  Ensembl 2006 , 2005, Nucleic Acids Res..

[26]  T. Wolfsberg,et al.  Using the NCBI Map Viewer to Browse Genomic Sequence Data , 2006, Current protocols in bioinformatics.

[27]  Allan R. Jones,et al.  Genome-wide atlas of gene expression in the adult mouse brain , 2007, Nature.

[28]  P. Silver,et al.  A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain , 2005, BMC Developmental Biology.

[29]  Gregor Eichele,et al.  Human chromosome 21 gene expression atlas in the mouse , 2002, Nature.

[30]  Carol J Bult,et al.  MouseCyc: a curated biochemical pathways database for the laboratory mouse , 2009, Genome Biology.

[31]  Wolfgang Wurst,et al.  A Mouse for All Reasons , 2007, Cell.

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

[33]  Mary E. Mangan,et al.  The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data , 2005, Genome Biology.

[34]  Petr Divina,et al.  The Mouse SAGE Site: database of public mouse SAGE libraries , 2004, Nucleic Acids Res..

[35]  John Quackenbush,et al.  The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes , 2004, Nucleic Acids Res..

[36]  R. Drysdale.  FlyBase : a database for the Drosophila research community. , 2008, Methods in molecular biology.

[37]  Ibrahim Emam,et al.  ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression , 2008, Nucleic Acids Res..

[38]  Tatiana A. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2004, Nucleic Acids Res..

[39]  S. Batalov,et al.  A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[40]  N. Heintz.  Gene Expression Nervous System Atlas (GENSAT) , 2004, Nature Neuroscience.

[41]  Kenneth H Buetow,et al.  An anatomy of normal and malignant gene expression , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[42]  Alan F. Scott,et al.  McKusick's Online Mendelian Inheritance in Man (OMIM®) , 2008, Nucleic Acids Res..

[43]  Martin Ringwald,et al.  Connecting sequence and biology in the laboratory mouse. , 2003, Genome research.

[44]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[45]  Sergio Contrino,et al.  ArrayExpress—a public repository for microarray gene expression data at the EBI , 2004, Nucleic Acids Res..

[46]  Janet Kelso,et al.  Assembly, verification, and initial annotation of the NIA mouse 7.4K cDNA clone set. , 2002, Genome research.

[47]  The HSA21 expression map initiative.  A gene expression map of human chromosome 21 orthologues in the mouse , 2002 .

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

[49]  Janan T. Eppig,et al.  Mouse Tumor Biology Database (MTB): status update and future directions , 2006, Nucleic Acids Res..

[50]  Judith A Blake,et al.  Mouse Genome Database , 2000, Mammalian Genome.

[51]  Gene Ontology Consortium,et al.  The Gene Ontology (GO) project in 2006 , 2005, Nucleic Acids Res..

[52]  Yang Liu,et al.  Mouse Brain Organization Revealed Through Direct Genome-Scale TF Expression Analysis , 2004, Science.

[53]  Dennis B. Troup,et al.  NCBI GEO: archive for high-throughput functional genomic data , 2008, Nucleic Acids Res..

[54]  Dale A. Begley,et al.  Electronic tools to manage gene expression data , 2002 .

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

[56]  L. Ohno-Machado,et al.  Genomic Analysis of Mouse Retinal Development , 2004, PLoS biology.

[57]  T. Curran,et al.  BGEM: An In Situ Hybridization Database of Gene Expression in the Embryonic and Adult Mouse Nervous System , 2006, PLoS biology.

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

[59]  J. Blake,et al.  The mouse genome database: a resource for today and tomorrow. , 2000, Lab animal.

[60]  Judith A. Blake,et al.  The mouse Gene Expression Database (GXD): updates and enhancements , 2004, Nucleic Acids Res..

[61]  Dawood B. Dudekula,et al.  Verification and initial annotation of the NIA mouse 15K cDNA clone set , 2001, Nature Genetics.

[62]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[63]  E. Birney,et al.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs , 2002, Nature.