CSC8312 -- Bioinformatics Theory and Applications

ENSEMBL

Next we are going to examine a tool for investigating genes and their DNA in their genomic context. This tool is called ENSEMBL.

Someway down the page is a database cross-reference to ENSMUSG00000027168. For some reason, it's not hyperlinked, so google for it.

The link that you want looks like this:

http://www.ensembl.org/Mus_musculus/geneview?gene=ENSMUSG00000027168

You should notice that this URL is of a regular form. It has four items:

• the location of ENSEMBL
• the species we are interested in
• that we want to see a geneview (more on this later).
• and that the gene is ENSMUSG00000027168

So, if you know the name of the ENSEMBL gene, then it's easy to write a tool to go to the ENSEMBL report ¹. In programming terms, these form of URL forms a public API; this form of API is called a REST API.

GeneView

You should now be looking at a tremendously complicated looking web page, something like this.

Fortunately, GeneView is mostly a set of duplicated sections which is why it's so long. In recognition of this, you can shrink or grow most of the sections. Most of the sections are transcripts.

Why are there multiple transcripts for a single gene?

Expand the "Transcripts" section

You should be able to see a large number of different transcripts in the table. You should also get a graphic showing the exonic structure of the PAX6 gene, and how these exons are used to make up the different transcripts. Most of these are clickable; you can use them to navigate around.

1. So why did SRS not hyperlink it? Well, I don't know.