Tech Development Core

Abstract - TECHNOLOGY DEVELOPMENT COMPONENT The Technology Development Component of the Gene Expression Database project (GXD) delivers to users the integrated expression data generated by Curation and Computation Components, via an intuitive and versatile web navigation paradigm. Users can refine their expression data searches in many ways (by properties of the mouse sample and/or by properties of the gene studied), and the summary of their search results has links to a variety of associated data (images, references, specimens, etc.). GXD provides an integrated combination of expression data from classical expression studies (RNA in situ hybridization and immunohistochemistry assays, northern blot, western blot and RT-PCR experiments) with high throughput RNA-Seq (HT) data, such that a user's search returns data from both classical and HT studies. This is a rare feature among expression resources, and it allows users to seamlessly exchange between these assay types, fostering comparison and confirmation. The Technology Development Component has four major parts (Aims) that can be sub-divided into interface components that deliver the following features: (1) Providing new ways to search and view expression results by mouse developmental anatomy. These include searches for genes expressed in tissues that follow differentiation paths and genes expressed in highly resolved cell types. (2) Adding new search and display functions for quantitative expression analyses, comparisons and profiling. This will give users ready access to gene sets that show altered expression patterns between defined sample states (between wild type and specific mutants, for example). (3) Providing graphical views of complex expression data, such as GXD's tissue x stage and tissue x gene matrices, and interactive RNA-Seq heat maps, to help users interpret expansive, integrated expression results. (4) Expanding the ability to analyze gene expression in the context of important biological concepts, such as gene function, phenotype and disease associations, and biological source parameters (like, tissue, stage and genotype), and adding a critical co-expression perspective to biological pathway and protein-protein interaction data by integrating with GXD data (genes must be co-expressed in the same cell, for their gene products to interact). (5) Enhancing users’ ability to compare expression between mouse and other important developmental species, such as zebra fish, frog and chicken. And lastly, (6) Allowing users to access GXD data for their own lists of genes and to use their GXD search results at other resources. All interface Aims proposed will be developed and administered with a balance of function and performance to ensure a productive GXD user experience.