Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

Abstract

The Mouse Genome Database (MGD: http://www.informatics.jax.org) is the primary community data resource for the laboratory mouse. It provides a highly integrated and highly curated system offering a comprehensive view of current knowledge about mouse genes, genetic markers and genomic features as well as the associations of those features with sequence, phenotypes, functional and comparative information, and their relationships to human diseases. MGD continues to enhance access to these data, to extend the scope of data content and visualizations, and to provide infrastructure and user support that ensures effective and efficient use of MGD in the advancement of scientific knowledge. Here, we report on recent enhancements made to the resource and new features.

Figure 1.

(A) The Human–Mouse: Disease Connection can be used to search for mouse and human genes, phenotypic similarity between patients and mouse models, and human and mouse model disease data. Multiple search parameters may be used individually or in combination, and include gene names or IDs or lists of genes, phenotype and disease names and IDs, or mouse or human genome location. (B) Sample results for the disease search term ‘Hemochromatosis’. The grid view summarizes gene and ortholog information with high level human and mouse phenotype and disease associations. Additional tabs show detailed gene and disease information in tabular format (not shown). Searches may be further refined by use of filters shown at the top of the grid. (C) Detailed phenotype and disease information may be accessed by clicking on the grid squares.

Figure 2.

Screenshots of improved SNP data interfaces in MGD. (A) Gene and region search forms are on different tabs to simplify the search interface. Mouse strains for which data are available are shown in alphabetical order and are selected with checkboxes. (B) Search results can be filtered by SNP functional classes. Columns can be manually re-ordered using ‘drag and drop’.

Figure 3.

Improvements in display of annotations of mouse genes and gene products to the Gene Ontology are here show for the mouse gene Atg5: autophagy related 5. (A) Here the high-level overall summation of annotations for Atg5 are shown across all three aspects of the GO. The blue cells indicated annotations tagging Atg5 as implicated in that component, function or biological process. Clicking on the cell retrieves all the annotations. Clicking on the (red arrow) All GO Annotations (53) brings back the detailed set of annotations (B) with new columns for context and proteoform. Here context from controlled vocabularies for anatomy and cell types as well as the relationship of the gene product to that context are details. A new column for proteoform permits the capture of isoforms participating in the activities and will be populated as these are identified.