The goal of this renewal application is the continued development and maintenance of the Gene Expression Database (GXD). GXD is a community resource for capturing and integrating experimental data on gene expression during development of the laboratory mouse. By integrating primary data from diverse assay types and providing appropriate user tools, GXD allows the scientific community to examine patterns of gene expression, elucidate biologically important molecular networks, and explore the genetic programs that underlie normal development, and dysregulations of development leading to cancer and to other diseases. As data accumulate, GXD provides increasingly complete and refined information. Data integration is fundamental to GXD's design. A comprehensive anatomical hierarchy provides a common standard for describing the time and location of expression. Integration with the Mouse Genome Database (MGD) provides standardized gene nomenclature and detailed phenotype descriptions, while enabling comparisons of genetic and functional information. Comprehensive cross-references with such databases as GenBank and SWISS-PROT help to place GXD data in the larger biological and analytical context. Finally, digitized images of the original experimental data and pervasive notes complement GXD records and help the user to comprehend the data.
The specific aims of this proposal are to: 1. Populate GXD with gene expression data and promote GXD use in the scientific community. Expression data will be acquired via electronic submissions from laboratories and via annotation of the literature by GXD editorial staff. Data accuracy will be reviewed at several levels. User support will be provided to help users with electronic submissions and database querying, and to develop user documentation and training. 2. Continue to develop GXD infrastructure to enhance its value as a community resource. GXD must deal with large volumes of complex expression data, and must accommodate new types of expression data, as methodologies change. 3. Develop advanced query and display tools for GXD. We will develop and improve interfaces to GXD to search, sort, and present information concisely and clearly.
| Ringwald, Martin; Eppig, Janan T (2011) Mouse mutants and phenotypes: accessing information for the study of mammalian gene function. Methods 53:405-10 |
| Finger, Jacqueline H; Smith, Constance M; Hayamizu, Terry F et al. (2011) The mouse Gene Expression Database (GXD): 2011 update. Nucleic Acids Res 39:D835-41 |
| Reference Genome Group of the Gene Ontology Consortium (2009) The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol 5:e1000431 |
| Shaw, David R (2009) Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotype. Curr Protoc Bioinformatics Chapter 1:Unit1.7 |
| Smith, Constance M; Finger, Jacqueline H; Hayamizu, Terry F et al. (2007) The mouse Gene Expression Database (GXD): 2007 update. Nucleic Acids Res 35:D618-23 |
| Blake, Judith A; Bult, Carol J (2006) Beyond the data deluge: data integration and bio-ontologies. J Biomed Inform 39:314-20 |
| Bult, C J (2006) From information to understanding: the role of model organism databases in comparative and functional genomics. Anim Genet 37 Suppl 1:28-40 |
| Dolan, Mary E; Ni, Li; Camon, Evelyn et al. (2005) A procedure for assessing GO annotation consistency. Bioinformatics 21 Suppl 1:i136-43 |
| Hayamizu, Terry F; Mangan, Mary; Corradi, John P et al. (2005) The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biol 6:R29 |
| Hill, David P; Begley, Dale A; Finger, Jacqueline H et al. (2004) The mouse Gene Expression Database (GXD): updates and enhancements. Nucleic Acids Res 32:D568-71 |
Showing the most recent 10 out of 24 publications
