The mouse Gene Expression Database (GXD): 2017 update

Abstract

The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. Through curation of the scientific literature and by collaborations with large-scale expression projects, GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches. At present, GXD includes over 1.5 million expression results and more than 300 000 images, all annotated with detailed and standardized metadata. Since our last report in 2014, we have added a large amount of data, we have enhanced data and database infrastructure, and we have implemented many new search and display features. Interface enhancements include: a new Mouse Developmental Anatomy Browser; interactive tissue-by-developmental stage and tissue-by-gene matrix views; capabilities to filter and sort expression data summaries; a batch search utility; gene-based expression overviews; and links to expression data from other species.

Figure 1.

The Assay Details Page—annotated expression data are displayed with citation information, gene, and experimental information, such as the assay type, probe visualization method and link to probe specifics. The results section of the page includes the level and pattern of expression in anatomical structures (annotated using the Mouse Developmental Anatomy Ontology). Image panes accompany the result annotations when available. The pane can be viewed in the context of the full figure by clicking on the image or the link in the result table. Specimen information includes the age, genetic background and specimen preparation methods. Further details can be viewed by expanding the ‘more’ toggle (boxed region indicated by red circle & arrow). If the specimen is from a mutant mouse, the official allele name is shown with links to all the information for that allele in MGI, including all the other expression data for this specific mouse mutant.

Figure 2.

The Mouse Developmental Anatomy Browser—divided into three sections, the Anatomy Search, the Anatomical Term Detail and the Anatomical Tree View, the user can quickly find terms and explore the mouse anatomy ontology. As indicated in the Term Detail section, individual structures can have multiple parents; ‘branchial arch endoderm’ has Parent Terms ‘embryo endoderm’ and ‘branchial arch’). The EMAPA anatomy ontology terms are represented in the time-independent ‘abstract’ version (as evidenced by the ‘Present at’ range of Theiler stages). Individual Theiler stages can be selected to view an anatomical term in the context of a time-dependent hierarchy (boxed region, blue arrow). In the Anatomical Tree View the chosen term is highlighted and toggles allow the user to explore up and down the tree. A link to the expression results summaries for the selected anatomical structure is provided (red arrow).

Figure 3.

Interactive matrix views—the Tissue-by-Stage (left) and the Tissue-by-Gene (right) matrices are interactive overviews of expression data that can be expanded along the tissue axis (see red arrow) to view more detailed anatomical structures and associated expression data. The Legend, accessed using the top left button, explains the colors and symbols. Clicking an individual cell in either matrix view opens a summary window of the data represented in that cell (shown in the Tissue-by-Gene Matrix by the white arrow). To filter, select individual rows and columns (indicated by the checkmarks and highlighting on the Tissue-by-Stage Matrix) and use the Filter button located at the top left.

Figure 4.

GXD expression data summaries—six views (indicated by red arrow) are available for expression search results: Genes, Assays, Assay Results, Images (shown; tab indicated by blue box), Tissue x Stage Matrix and Tissue × Gene Matrix. Refinements to the data set can be made using the filters (red box), including Anatomical System, Assay Type, Detected? (yes or no), Theiler Stage and Wild type? (or mutant). When applied, these filters (as well as row/column filters on the matrix views) are propagated to all of the data summaries. Sort options are available for many of the columns in the summaries. The red circle indicates the new Specimen Type sort available on the image summary, where images can be sorted into whole mount or section, etc. The Genes Summary and the Assay Results Summary have download or export options for further analysis of the expression data. The data summaries shown here have resulted from the query: ‘Which genes located in the genomic region chr6:86000000-142000000 are expressed in the germ layer at E7-8.5 of mouse development?’, thus illustrating the use case of a candidate gene search.

Figure 5.

The expression section of the MGI gene detail page—the grid of anatomical terms gives a high-level overview of the expression data for the gene. This figure shows the overview for the gene Gbx2. Blue cells indicate that expression was detected in wild type. Gray triangles indicate either absence of expression in wild-type or expression data from mutant specimens. Click in an individual cell in the grid to view the Tissue-by-Stage Matrix for an individual high-level anatomical structure. Click on the matrix icon to view the Tissue-by-Stage Matrix for all high-level anatomical structures. Links to other summaries, such as Images or Assay Results are also included. Links to expression data for the gene at external resources are also available. These include links to other mouse (Allen Institute, GENSAT, GEO, Expression Atlas) and vertebrate (GEISHA, Xenbase, ZFIN) databases.

Figure 6.

A unified database interface—GXD provides numerous entry points to mouse developmental expression data, such as via the Gene Expression Data Query Forms, the Mouse Developmental Anatomy Browser or the MGI Gene Detail Page. All these entry points lead to the same multi-tabbed summaries. Users are provided with the ability to filter, sort and interactively refine the data, download data for further analysis, and view the details and images from many different perspectives.