The goal of this application is the continued development and maintenance of the Gene Expression Database for Mouse Development (GXD). GXD is a well-established community resource. It integrates different types of expression data, including very complex biological information, such as RNA in situ hybridization and immunohistochemistry results. It places these data in the larger biological context through integration with other Mouse Genome Informatics (MGI) resources and interconnections with many other databases, supporting complex queries that enable thorough biological and computational analysis.
The specific aims of this application are (1) to continue and expand GXD's current data acquisition effort, ensure high-quality data annotation and integration, and maintain GXD database as well as software infrastructure. To do so, data will be continually acquired by curation from the literature, via electronic submissions, and through collaborations with large-scale expression data providers and with other public databases;(2) to enhance GXD infrastructure to accommodate new types of expression data, and to enable important new querying capabilities. To do so, expression data will be accommodated from conditional mutants by enhancing of anatomical ontologies, and by enabling the direct correlation of spatio-temporal (conditional) mutation patterns, expression patterns, as well as phenotype data, and by developing anatomical cross-references to support the comparative analysis of developmental expression patterns, and by devising means for researchers to analyze microarray and HTS expression data in the context of GXD and MGI;(3) to refine GXD's user interface and develop advanced query and display tools. To do so, interfaces to GXD will be improved to search, sort, and present information concisely and clearly by supporting batch queries and iterative queries, and by developing further integration of GXD and EMAGE to enable 3D graphical storage, display, and analysis of in situ expression and anatomy data;and (4) to provide user support, and promote GXD's use and electronic data submissions by the scientific community b y continuing to provide training and by soliciting feedback on how GXD can be improved.
The Gene Expression Database for Mouse Development (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 disregulations of development leading to human birth defects, to cancer and to many other diseases.
|Finger, Jacqueline H; Smith, Constance M; Hayamizu, Terry F et al. (2017) The mouse Gene Expression Database (GXD): 2017 update. Nucleic Acids Res 45:D730-D736|
|Jiang, Xiangying; Ringwald, Martin; Blake, Judith et al. (2017) Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD). Database (Oxford) 2017:|
|Eppig, Janan T; Smith, Cynthia L; Blake, Judith A et al. (2017) Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research. Methods Mol Biol 1488:47-73|
|Eppig, Janan T; Richardson, Joel E; Kadin, James A et al. (2015) Mouse Genome Informatics (MGI): reflecting on 25 years. Mamm Genome 26:272-84|
|Smith, Constance M; Finger, Jacqueline H; Hayamizu, Terry F et al. (2015) GXD: a community resource of mouse Gene Expression Data. Mamm Genome 26:314-24|
|Hayamizu, Terry F; Baldock, Richard A; Ringwald, Martin (2015) Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data. Mamm Genome 26:422-30|
|Motenko, H; Neuhauser, S B; O'Keefe, M et al. (2015) MouseMine: a new data warehouse for MGI. Mamm Genome 26:325-30|
|Finger, Jacqueline H; Smith, Constance M; Hayamizu, Terry F et al. (2015) The mouse gene expression database: New features and how to use them effectively. Genesis 53:510-22|
|Dolan, Mary E; Baldarelli, Richard M; Bello, Susan M et al. (2015) Orthology for comparative genomics in the mouse genome database. Mamm Genome 26:305-13|
|Smith, Constance M; Finger, Jacqueline H; Kadin, James A et al. (2014) The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips. Dev Dyn 243:1176-86|
Showing the most recent 10 out of 18 publications