Gene trees and homologues, Demo

Demo: gene trees and homology predictions

Fungal Compara

Gene trees

Let’s look at the homologues of Saccharomyces cerevisiae R64-1-1 TAZ1 (gene stable ID: YPR140W). This gene is involved in stress response and conserved across different taxonomic domains. Search for the gene and go to the Gene tab.

Click on Fungal Compara: Gene tree. This will display the current gene in the context of a phylogenetic tree used to determine orthologues and paralogues.

Funnels indicate collapsed nodes. Click on a node (coloured triangle) to open a menu. We can then see what type of node this is, some statistics and options to expand or export the sub-tree.

There are some quick filtering options below the image, where you can add paralogues, and quickly expand or collapse nodes.

You can download the tree in a variety of formats. From the pop-up above you can click to export the sub-tree (everything to the right of the node). Alternatively, click on the Export icon in the bar at the top of the image to get a pop-up where you can choose your format. You can preview this file before you download.

Homologues

We can look at homologues in the Orthologues and Paralogues pages, which can be accessed from the left-hand menu. If there are no orthologues or paralogues, then the name will be greyed out. Click on Fungal Compara: Orthologues to see the orthologues available. In the first table, you will find a summary of orthologues by taxonomic group:

In the second table, you will find orthologue details per species:

Scroll to the bottom of the page to see a list of the species that do not have any orthologues with TAZ1 in S. cerevisiae… there are a lot!

Pan-taxonomic Compara

S. cerevisiae is part of Pan-compara, which compares a subset of fungal species with species from other taxa, such as plants, bacteria and vertebrates. Click on Pan-taxonomic Compara: Orthologues. Let’s see if there are any orthologues of TAZ1 in plants. Click the Show details box for Plants.