Genome Browsing and Visualization - Ensembl
The Ensembl Genome Browser provides a portal to sequence data, gene annotations/predictions, and other types of data hosted in the various Ensembl databases. Many consider Ensembl to be the most comprehensive and systematic gene annotation resource in the world. Ensembl supports a large number of species and makes data available through a powerful web portal as well as through direct database downloads and APIs. Their excellent Help & Documentation pages provide instruction on using the website, data access, APIs, and their procedures for gene annotation and prediction. Their outreach team have put together extensive teaching materials that are available for free online. Rather than duplicate effort, we have linked to some of their instructional videos below. We will review these and then perform some simple exercises to familiarize ourselves with the Ensembl Genome browser.
Introduction to genome browsers using Ensembl
The Ensembl Genome Browser: an overview
Data Visualization with Ensembl
An excellent way to explore the data visualization possibilities with Ensembl is to use their Find a Data Display page. This is linked directly from the Ensembl home page (see red box below). From this page, you can you can choose a gene, region or variant and then browse a selection of relevant visualisations.

Navigate to the Find a Data Display page. To illustrate, select ‘Species’ -> ‘Human’, ‘Feature Type’ -> ‘Genes’, and then ‘Identifier’ -> ‘TP53’. You will be presented with a number of possible matches. Select the exact ‘TP53’ match and select ‘Go’. The results page, at time of writing, returned a comprehensive set of 47 views for TP53 (ENSG00000141510) associated with: Sequence & Structure, Expression & Regulation, Transcripts & Proteins, Comparative Genomics, and Variants. We will display just a few examples here and then explore others through exercises.

Select the ‘Splice Variants’ view and scroll down the page a little. You will see a graphical representation (see below) of all known and predicted transcripts for TP53, and how these exons line up with each other and with other features such as protein domains.

Next, examine the ‘Gene Gain/Loss Tree’ for TP53. User your browser back button (or the instructions above) to go back to the data display views for TP53 and then select ‘Gene Gain/Loss Tree’. If this does not work, you can also select ‘Gene Gain/Loss tree’ from the side bar of ‘Gene-based displays’ -> ‘Comparative Genomics’ menu on any gene page.

Ensembl Data Display Exercise
Using your knowledge of tissue-specific expression for a specific species/gene, explore the Gene Expression views in Ensembl. Does the available data confirm your knowledge of these genes. For example, considering human genes, we might investigate: MSLN (Mesothelin) - normally present on the mesothelial cells lining the pleura, peritoneum and pericardium and over-expressed in several cancers. Other interesting human/cancer tissue markers include: KLK3 (PSA), EPCAM, SCGB2A2 (Mammaglobin), CD19, etc. Below you can see an example for PSA.

Ensembl Genomes - Extending Ensembl across the taxonomic space
The EnsemblGenomes site hosts genome-scale data from ~52,000 species, most of which are not available through the core Ensembl. Data are organized into five taxonomic categories: bacteria (n=50364), protists (n=200), fungi (n=1802), plants (n=63), and metazoa (n=74). Each generally provides at least a preliminary genome assembly, gene annotations, and to varying degrees includes: variation data, pan compara data, genome alignments, peptide alignments, and other alignments. If your species is not in Ensembl it is worth checking whether it is available in EnsemblGenomes.