In this report we describe significant enhancements to MGD, including two new graphical user interfaces: (i) the Multiple Genome Viewer for exploring the genomes of multiple mouse strains and (ii) the Phenotype/Gene Expression matrix which allows users to compare gene expression and phenotype annotations for mouse genes. Other improvements include improvements to literature curation processes, and the incorporation of TSS annotations from RIKEN’s FANTOM 5 initiative (9).