Ensembl 2017

Abstract

Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a selection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license.

Figure 1.

Regulation view. For each human gene, Regulation view displays correlation statistics (eQTLs) between genetic variation and tissue-specific expression. For BRCA2, data from the GTEx Project are available as Manhattan plots for over 40 tissues, including the four tissues displayed: Artery Coronary, Breast Mammary Tissue, Skin Sun Exposed Lower Leg, and Whole Blood.

Figure 2.

Mouse strains in Ensembl. (A). The Mouse Strain landing page (http://www.ensembl.org/Mus_musculus/Info/Strains) lists available assemblies in Ensembl, and includes links to more information about each strain. Mouse strains BALB/cJ, CBA/J, and DBA/2J are among those now available. (B) GeneTree view showing sequence conservation for Nnt between the mouse strains and the reference mouse and rat. The alignment shows extra sequence in the rat and DBA/2J genes that are not represented in the other mouse annotation. Each gene can be clicked for more information and to navigate to the Gene view. (C). Gene view for Nnt in mouse DBA/2J. The longest annotated protein is 1158 amino acids in length, whereas the longest annotated protein in the reference mouse (GRCm38) is only 835 amino acids in length.