Ensembl 2020

Abstract

The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation and comparative genomics across the vertebrate subphylum and key model organisms. The Ensembl annotation pipeline is capable of integrating experimental and reference data from multiple providers into a single integrated resource. Here, we present 94 newly annotated and re-annotated genomes, bringing the total number of genomes offered by Ensembl to 227. This represents the single largest expansion of the resource since its inception. We also detail our continued efforts to improve human annotation, developments in our epigenome analysis and display, a new tool for imputing causal genes from genome-wide association studies and visualisation of variation within a 3D protein model. Finally, we present information on our new website. Both software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license) and data updates made available four times a year.

Figure 1.

The new epigenome track selection interface, providing a way to find experimental evidence of interest based on cell/tissue and experiment type and to turn those tracks of evidence on in the genome browser. (A) Experiments are grouped by their target of interest i.e. histone modifications (e.g. H3K27ac), open chromatin (e.g. DNaseI hypersensitivity) or transcription factors (e.g. CTCF). Cells and tissues of interest can be selected by clicking on the Cell/Tissue tab. This interface has filtered available tracks by six cells/tissues and two histone modifications. (B) A matrix view of all available tracks of evidence based on the previously selected cells/tissues and experiments. Tracks of evidence, peaks and signals, can be turned on and off based on the cell/tissue (rows), experiment (columns) or individual cells.

Figure 2.

The PDB model 5XRG (linked to ENSP00000221804) is displayed using LiteMol as a Richardson diagram in the central panel. rs1425150829 has been flagged in red at position 128 (ARG) occupying the end of a β strand and shows proximity to a ligand in the 3D structure, suggesting possible disruption. Additional annotation such as exons, protein domains and other variants can be turned on and off by clicking on the associated eye icon on the right hand-side of the visualization.