Mouse Genome Database (MGD) 2019 - PubMed (original) (raw)

Mouse Genome Database (MGD) 2019

Carol J Bult et al. Nucleic Acids Res. 2019.

Abstract

The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism genetic and genome resource for the laboratory mouse. MGD is the authoritative source for biological reference data sets related to mouse genes, gene functions, phenotypes, and mouse models of human disease. MGD is the primary outlet for official gene, allele and mouse strain nomenclature based on the guidelines set by the International Committee on Standardized Nomenclature for Mice. In this report we describe significant enhancements to MGD, including two new graphical user interfaces: (i) the Multi Genome Viewer for exploring the genomes of multiple mouse strains and (ii) the Phenotype-Gene Expression matrix which was developed in collaboration with the Gene Expression Database (GXD) and allows researchers to compare gene expression and phenotype annotations for mouse genes. Other recent improvements include enhanced efficiency of our literature curation processes and the incorporation of Transcriptional Start Site (TSS) annotations from RIKEN's FANTOM 5 initiative.

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Figures

Figure 1.

Figure 1.

A screenshot of MGD’s Multiple Genome Viewer showing the display of genome annotations across multiple strains of mice. (A) Users may select one or more genomes to be displayed. (B) Equivalent genome features across the strains are highlighted by ‘swim lanes’ when a user clicks on one or more genome features. (C) Genome feature types (protein coding gene, pseudogene, etc.) are indicated by color; classes of genome features can be toggled on and off in the display.

Figure 2.

Figure 2.

Screenshot of the Gene Expression-Phenotype Matrix. The first column (gold highlight) summarizes the wild-type expression pattern of the Pax3 gene. The color of matrix cells in the column indicates the type and number of expression annotations for each tissue; the conventions are defined in the matrix legend (inset). Genotype summary data associated with alleles of Pax3 are displayed in the adjacent columns. The tissues where each mutation/genotype has phenotypic effects are indicated by the presence of colored matrix cells. Cells with an ‘N’ indicate that an expected abnormality was not detected. A red exclamation point indicates the phenotype is affected by changes in mouse strain background. Clicking on blue toggles next to term names expands and collapses the anatomy vocabulary tree. Annotation details are displayed when users click in the cells of the matrix.

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