Overview of the Ensembl Genome Browser

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Ensembl

Navigate to "www.ensembl.org".

You can find some of the most popular links on the blue navigation bar at the top of the homepage.

Use the search option on the homepage to look for gene names, IDs, coordinates and more. You can do a species specific search by selecting your genome of interest from the drop-down menu.

Favourite genomes are set to Human, Mouse and Zebrafish by default. You can click on the pencil icon to change these.

You can view all available species by clicking the "View full list of all species" link underneath the coloured search block. You can search for your species of interest (either the common or scientific name) using the search bar at the top right-hand corner of the table. Click on the common name of your species of interest to go to the species information page. We’ll click on "Human".

The page displays a table with all vertebrate assemblies present in www.ensembl.org. You can search for your species of interest (either the common or scientific name) using the search bar at the top right-hand corner of the table.

Click on the common name of your species of interest to go to the species information page. We’ll click on "Human".

Here, you can see links to example features and download flat files. To find out more about the genome assembly and gene build, click on "More information and statistics" under the Genome assembly section.

Let's search for the BRCA2 gene in human. Enter "BRCA2" in the text box and click "Go".

Or Return to the homepage by clicking the "Ensembl logo" at the top left-hand side corner. Click on this search drop-down menu, select "Human", enter "BRCA2" and click "Go".

Click "BRCA2 (Human Gene)" from the search results.

This takes us to the Gene tab. This page gives an overview of the information available at the gene level, and it's composed of three sections. At the top, the page shows the gene ID, its genomic location and its strand information.

The summary provides information on gene biotypes and the annotation method. Then we have the gene diagram which depicts the gene and all its transcripts in the context of the genome.

Click "Show transcript table" to view all transcripts associated with the human BRCA2 gene.

The left-hand side menu allows you to explore gene-based displays.

Click "Phenotypes" to view the list of diseases and phenotypes directly associated with a gene by the Online Mendelian Inheritance in Man (OMIM) compendium, Orphanet, DDG2P and other sources in human.

Click "Pathway" to display the biochemical pathways that the BRCA2 gene is involved in. The data and interface come in directly from Reactome (www.reactome.org).

Ensembl works on a tab system for different types of features, such as genes, transcripts or variants. These appear side-by-side across the blue bar, allowing you to jump back and forth between features of interest. Each tab has its own navigation column down the left-hand side of the page, listing all the things you can see for this feature. To view the BRCA2 gene in the location context, click "Location: 13:32,315,086-32,400,268".

The Region in Detail page is made up of three images; The first image shows the chromosome view.

The second image shows a 1 MB region (the size varies per genome and depends on the gene size and density) around the selected region (BRCA2 in this case). This view allows you to scroll back and forth along the chromosome.

The third image is a detailed, configurable view of the region.

You can add more data to the image by clicking on "Configure this page" on the left-hand side menu. The configurations allow you to add some tracks in different styles; more details are in this FAQ: (http://www.ensembl.org/Help/Faq?id=335).

Click "Export data" to download the data from this page.

You can export the data in various formats such as FASTA, BED, GTF, GFF and many more.

Click on "Share this page" to generate a version specific link.