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 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 proposal are (1) to continue and expand GXD's curation of expression data and anatomical ontologies, and ensure high-quality data annotation and integration. We will continue to curate data from RNA in situ hybridization, in situ-reporter knock-in, immunohistochemistry, RT-PCR, Northern blot and Western blot experiments, and expand our curation efforts to High-Throughput Sequencing (HTS) expression data. We will continue to enhance the mouse anatomy ontologies. We will (2) maintain the GXD database, and expand and enhance GXD infrastructure to accommodate new types of expression data and to enable new search capabilities. We will develop new data structures that will enhance our anatomical ontologies, enable the analysis of differentiation pathways, and allow the correlation of spatio-temporal (conditional) mutation patterns, expression patterns, and phenotype data. We will implement new links to expression databases from other model organisms to enable a comparative analysis of developmental expression patterns. We will (3) continue to evolve GXD's user interface and develop advanced query and display tools. We will build on our efforts to make GXD more intuitive and interactive. We will implement new search and display capabilities; expand the utilities of our interactive matrix views; and provide increased support for batch queries, iterative queries, enrichment analysis, and export of selected data to external applications. We will continue to improve programmatic access to GXD for computational biologists. We will continue our collaboration with the Edinburgh Mouse Atlas Project to enable 3D graphical storage and display and analysis of in situ expression data. We will (4) provide user support and promote use of GXD by the scientific community. We will continue to provide training and to solicit feedback on how we can improve GXD.
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 |
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| 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 |
| Motenko, H; Neuhauser, S B; O'Keefe, M et al. (2015) MouseMine: a new data warehouse for MGI. Mamm Genome 26:325-30 |
| 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 |
| 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 |
| 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 |
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