The Mouse Gene Expression Database (GXD): 2007 Update

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2006 Nov 30

PMID 17130151

Citations 49

Authors

Constance M Smith

Jacqueline H Finger

Terry F Hayamizu

Ingeborg J McCright

Janan T Eppig

James A Kadin

Joel E Richardson

Martin Ringwald

Affiliations

Soon will be listed here.

Abstract

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 http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu.shtml.

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References

Ringwald M, Eppig J, Begley D, Corradi J, McCright I, Hayamizu T . The Mouse Gene Expression Database (GXD). Nucleic Acids Res. 2000; 29(1):98-101. PMC: 29814. DOI: 10.1093/nar/29.1.98. View

Hayamizu T, Mangan M, Corradi J, Kadin J, Ringwald M . The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biol. 2005; 6(3):R29. PMC: 1088948. DOI: 10.1186/gb-2005-6-3-r29. View

Divina P, Forejt J . The Mouse SAGE Site: database of public mouse SAGE libraries. Nucleic Acids Res. 2003; 32(Database issue):D482-3. PMC: 308792. DOI: 10.1093/nar/gkh058. View

Carninci P, Kasukawa T, Katayama S, Gough J, Frith M, Maeda N . The transcriptional landscape of the mammalian genome. Science. 2005; 309(5740):1559-63. DOI: 10.1126/science.1112014. View

Reymond A, Marigo V, Yaylaoglu M, Leoni A, Ucla C, Scamuffa N . Human chromosome 21 gene expression atlas in the mouse. Nature. 2002; 420(6915):582-6. DOI: 10.1038/nature01178. View

de la Cruz N, Bromberg S, Pasko D, Shimoyama M, Twigger S, Chen J . The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Res. 2004; 33(Database issue):D485-91. PMC: 540004. DOI: 10.1093/nar/gki050. View

Ringwald M, Baldock R, Bard J, Kaufman M, Eppig J, Richardson J . A database for mouse development. Science. 1994; 265(5181):2033-4. DOI: 10.1126/science.8091224. View

Gray P, Fu H, Luo P, Zhao Q, Yu J, Ferrari A . Mouse brain organization revealed through direct genome-scale TF expression analysis. Science. 2004; 306(5705):2255-7. DOI: 10.1126/science.1104935. View

Kargul G, Dudekula D, Qian Y, Lim M, Jaradat S, Tanaka T . Verification and initial annotation of the NIA mouse 15K cDNA clone set. Nat Genet. 2001; 28(1):17-8. DOI: 10.1038/ng0501-17. View

10.

Hu J, Mungall C, Law A, Papworth R, Nelson J, Brown A . The ARKdb: genome databases for farmed and other animals. Nucleic Acids Res. 2000; 29(1):106-10. PMC: 29807. DOI: 10.1093/nar/29.1.106. View

11.

Baldarelli R, Hill D, Blake J, Adachi J, Furuno M, Bradt D . Connecting sequence and biology in the laboratory mouse. Genome Res. 2003; 13(6B):1505-19. PMC: 403701. DOI: 10.1101/gr.991003. View

12.

Gitton Y, Dahmane N, Baik S, Ruiz i Altaba A, Neidhardt L, Scholze M . A gene expression map of human chromosome 21 orthologues in the mouse. Nature. 2002; 420(6915):586-90. DOI: 10.1038/nature01270. View

13.

Mulder N, Apweiler R, Attwood T, Bairoch A, Bateman A, Binns D . InterPro, progress and status in 2005. Nucleic Acids Res. 2004; 33(Database issue):D201-5. PMC: 540060. DOI: 10.1093/nar/gki106. View

14.

Maglott D, Ostell J, Pruitt K, Tatusova T . Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 2004; 33(Database issue):D54-8. PMC: 539985. DOI: 10.1093/nar/gki031. View

15.

Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Wheeler D . GenBank. Nucleic Acids Res. 2005; 34(Database issue):D16-20. PMC: 1347519. DOI: 10.1093/nar/gkj157. View

16.

VanBuren V, Piao Y, Dudekula D, Qian Y, Carter M, Martin P . Assembly, verification, and initial annotation of the NIA mouse 7.4K cDNA clone set. Genome Res. 2002; 12(12):1999-2003. PMC: 187561. DOI: 10.1101/gr.633802. View

17.

Strausberg R, Feingold E, Klausner R, Collins F . The mammalian gene collection. Science. 1999; 286(5439):455-7. DOI: 10.1126/science.286.5439.455. View

18.

Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G . Ensembl 2006. Nucleic Acids Res. 2005; 34(Database issue):D556-61. PMC: 1347495. DOI: 10.1093/nar/gkj133. View

19.

Visel A, Thaller C, Eichele G . GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res. 2003; 32(Database issue):D552-6. PMC: 308763. DOI: 10.1093/nar/gkh029. View

20.

Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo W . Genomic analysis of mouse retinal development. PLoS Biol. 2004; 2(9):E247. PMC: 439783. DOI: 10.1371/journal.pbio.0020247. View