CSC8312 -- Bioinformatics Theory and Applications

Chromosome View

Let's move to the equivalent section of the human genome.

Open the orthologue section. Find the human equivalent gene. Click on this.

What's an othologue? What's a paralogue? You've seen two. How many species are available in ENSEMBL?

Let's move into "Chromosome View" which shows the gene in it's genomic context.

Click on location in "Genomic Location".

The URL should look something similar to this:

http://www.ensembl.org/Homo_sapiens/geneview?panel_transcript=on;db=core;gene=ENSG00000007372

Again, this is a REST style URL. You could automate access to this page. This page is also complex looking, but it's possible to work through it.

First, we have the chromosome displaying the chromosomal location of the gene. Next down is the overview. This shows the main features — contigs, markers, genes as predicted by several methods. Finally, the detailed view which has more still; in this case, ESTs, BLAST results, conservation.

Don't worry too much if the large amount of terminology. You may not have done all of these in lectures yet. When you get to them in the lectures, you will have seen them before!

Let's try one feature on the detailed view.

Click on the comparative menu item Select "Mouse Blastz" Click on "close menu" at the bottom of the menu (ENSEMBL uses fairly old web technology now, so this is a little clunky). You should see a Mmus blastz track has appeared. Click on this near the start of the PAX6 gene. This should transport you back to the mouse ENSEMBL.