Overview of Ensembl beta

1. Navigate to “beta.ensembl.org”.

2. You have different buttons (Apps) available on the launch bar at the top.

The first app “Species Selector” can be used to add as many species as you want. Your species will then be available across all apps.

3. The next button is for “Genome Browser”.

You can use this app to look at genes & transcripts in their genetic context and download this data. It can be opened from the launch bar at the top of every page.

4. Then we have “Entity viewer”.

Use this app to get gene & transcript information. Entity viewer pages will give information on your gene of interest and as always you can download this data in different formats.

5. The “Blast” app can be used to compare DNA or protein sequences across species.
You can add up to 30 sequences and up to 25 species at a time to view significant sequence matches across species.

6. Click on the “Question mark” to see Ensembl beta help and documentation pages.

7. We will click on “Species selector” to find and select Human and find more information about this species.

8. We have some popular vertebrate and non-vertebrate species shown on this page.

9. Type “Human” in “Find a species” text box.

10. Click “Find”.

11. We will select “Human” reference (Assembly: GRCh38p14).

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13. Click “Add” to add “Human” to your selected species list.

14. Click “HumanGRCh38.p14” to find more information about this assembly.

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16. We’re going to look at the human BRCA2 gene to find out information about it and its transcript.

Click on “Find a gene”.

17. You can select “Only species in list” if you want your results for BRCA2 to be specific to the species you have selected (Human in the case of this demo) or across all species in Ensembl beta.

18. Enter “BRCA2” and click “Go”.

19. You can now view the human “BRCA (ENSG00000139618.18) in the Genome browser or the Entity viewer.

Let’s start with the Genome browser.

20. The genome browser view shows the human BRCA2 gene in the genomic location context. The genomic features (e.g. BRCA2) within this location are represented on horizontal tracks across the genome.

Click on “+15” to view all transcripts associated with the BRCA2 gene.

21. The MANE Select transcript “ENST00000380152.8” is shown at the top of the view by default.

The MANE Select set consists of one transcript at each protein-coding locus across the human genome that is representative of biology at that locus.

22. Click “Download” to export the data from this view.

23. From these options, you can export genomic and protein sequences for the gene and associated transcripts.

24. Click on “>” and then “…” icon on the right-hand side to find out more information about BRCA2 and its transcripts.

25. Click on “Sequence” and then “Download” to view and export the sequence of your interest.

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28. Click this icon.

29. Let’s now explore the Entity viewer. This app allows you to view detailed information about annotation features: genes, transcripts and proteins.

30. This view gives us detailed information on the BRCA2 transcripts, associated exons and translation.

31. Click on “Gene function” to explore interactions, functional annotations and external references for the BRCA2 gene.

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33. Click on “Gene relationships” to view comparative genomics information related to the human BRCA2 gene.

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