Thursday, May 15, 2025
5/15/2025
Gene Expression Database for Mouse Development - Abstract – OVERALL COMPONENT 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 biologically complex data, such as RNA in situ hybridization and immunohistochemistry results, and high-throughput expression data from RNA-seq experiments. 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 analyses. 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 annotation of bulk and single-cell RNA-seq data sets. We will enhance the mouse anatomy ontology, and refine our expression annotations by combining anatomy and cell type terms. We will (2) maintain the GXD database and enhance GXD’s infrastructure and data entry interfaces to accommodate large volumes of expression data and to represent new types of data and relationships. We will enhance the database and software infrastructure to accommodate the expected increase in RNA-seq data. We will expand the database to represent anatomical differentiation pathways, as well as expression annotations to cell type terms. We will continue to modernize the editorial interface and expand the interface as needed for the annotation of new data types. We will automate more steps of the literature selection process to increase curation efficiency. We will (3) continue to evolve GXD’s user interface and develop advanced query and display tools. We will develop expression searches that allow the analysis of anatomical differentiation pathways and cell types. We will add support for quantitative expression analyses, comparisons and profiling. We will develop displays that superimpose expression data with molecular pathway and protein interaction data to support the analysis of molecular networks with co- expression information. 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.
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