An effective way to access the expression information for a single gene is to look up the ‘Expression’ section on the corresponding gene detail page (). Gene detail pages can be easily found via the ‘Quick Search’ tool placed at the top of all MGI pages. Because these pages are a central hub within MGI, we have improved the layout of the expression section, implemented a new images summary (see below), and added new gene-specific links to external expression resources, including the Allen Brain Atlas (18
), GENSAT (17
), GEO (33
) and ArrayExpress (34
). Future work will include the implementation of links to model organisms from other species that hold developmental expression data, such as ZFIN (35
), GEISHA (36
), Xenbase (37
) and Flybase (38
Figure 2. Expression data summaries. Gene detail pages in MGI feature an ‘Expression’ section that summarizes the GXD data available for the gene from a variety of perspectives: literature content, assays, results, tissues, images, developmental (more ...)
The query forms available from the GXD homepage, as well as from the MGI search menu, provide more direct and more powerful means to access expression data. The ‘Gene Expression Data Query Form’ includes search fields that allow users to specify genes, tissue, developmental stage and expression assay type, as well as genome coordinates and gene ontology (GO) terms. Users can search for instances where expression was detected or not detected, as well as for expression data in specific mutants. Thus, this form enables both simple and very complex queries. The ‘Expanded Expression Data Query Form’ allows users to find genes that are expressed in one set of tissues and/or developmental stages, but not in others. The ‘Mouse Anatomical Dictionary Browser’ lets users search or browse for specific anatomical structures and the expression data associated with them. The ‘EMAGE Anatomical Section Browser’ uses the Edinburgh Mouse Atlas as a starting point for identifying anatomical structures and expression data associated with them in GXD and EMAGE.
Searches from the query form as well as the links from the expression section on the gene detail page lead to data summaries listing all assays/results that match the user’s criteria. We have improved the layout of these summaries. They now feature clear ‘data’ links that take the user to the detailed entries, as well as camera icons that indicate if the detailed entries contain links to primary image data ( and ).
Other avenues in MGI can be used to access the expression data as well. We have increased the utility of the Quick Search tool by adding the capability to return expression results if the user enters anatomical terms. We have expanded the Batch Query tool so that it can return GXD expression data for a list of genes or sequence IDs, as well as export expression data as Excel worksheets or tab-delimited text files ().
Figure 3. MGI Batch Query. Batch queries can return GXD expression data for a list of genes or sequence IDs. Affymetrix probe set IDs are also accepted as input. Because MGI maintains up-to-date mappings of microarray probe set-to-gene associations, users can easily (more ...)
In addition to implementing gene specific links to the microarray gene expression data at GEO and ArrayExpress, we have, in collaboration with the Mouse Genome Database (MGD) project, developed new tools that allow researchers to combine microarray expression results with data in MGI. Specifically, we have begun to provide up-to-date mappings between microarray probe sets and genes so that users can query MGI by microarray probe set ID to retrieve the associated gene, or download reports of all probe set-to-gene mappings. We have also enhanced the MGI Batch Query tool so that it accepts sets of microarray probe IDs. Therefore, one can easily extract information about genes for sets of microarray probes, including RNA in situ hybridization, immunohistochemistry and RT–PCR expression data, GO annotations, mouse phenotype data and disease data associated with the orthologous human genes. Query results are available as web page displays and can also be downloaded as tab-delimited text and thus fed into other analysis tools ().
GXD is implemented in the Sybase relational database management system. If a user’s queries are beyond the capabilities of our web-based forms, custom SQLs or direct SQL access can be requested via our user support group. In addition, a number of reports for specific data sets, such as a list of all the genes that have annotated expression data, are produced nightly and are available on the website.