Friday, February 8, 2013

v14: alternative gene models viewing and selection

The version 14 of WashU Genome Browser provides a very useful feature related to handeling of alternative gene models. Please see below for details.

To get the source code of this version use the links below:

Alternative gene models

Alternative gene model is prevalent phenomena in higher organisms. This screen shot shows multiple gene models of the human TP53 gene, as provided by two tracks:

Now if you use "Relocation" function of the Browser to relocate to TP53 gene, you have the option to choose which exact gene model you want to relocate to.

To see this, go to the Browser and show human genome, and click the blue button on the top of the page in the middle to show relocation options (if you're running Gene Set View, please quit to go to genome view to see this button):

In the second text box enter "tp53" then hit "Enter" or press :

A long list of TP53 gene models are shown. Click on one to select as destination for relocation. You can notice following points that aim to help you better visualize the differences between models:

  1. structure of each model is plotted;
  2. the widths of the graphs are proportional to the bp length of each model;
  3. the models are aligned to indicate their relative position on the genome. In this case all of the TP53 gene models are from an interval (7565096-7590868) in chromosome 17.

Such handy function is also made into Gene Set View function as well. After you submit a set of genes, the gene list is displayed in the control panel with a green button for everybody:

Click the  ⇄  shows the list of gene models belonging to the queried gene in same fashion:

By selecting a model that entry in the gene set will be updated to the coordinate of your choice.

Bug fix and minor improvements
In the Gene Set View panel, the Choosing flank size options is back for gene set editing. We're still working to bring back the KEGG pathway query function.

An error associated with Zebrafish chromosome representation was fixed. This problem caused no chromosomes to be displayed in the relocation panel.