Tip of the Week: Caleydo for gene expression and pathway visualization
Recently while watching the #bioinformatics tag on Twitter I saw Khader Shameer mention Caleydo. I was instantly hooked at the very clever visualization strategy that they are using to provide more surface area for examining the data you are interested in viewing. Their specific topics are pathways and gene expression, but it got me thinking about various data types that I would like to see connected in this way.
To skip right over to Caleydo and start trying it out, go here: http://www.caleydo.org/
Caleydo delivers a 3D representation of the expression and pathway data. The main user interface has an area that is a box. They call it a bucket, but in my head buckets are round, so I think of this as a box. On the floor of the box you have a graphic. But because you also have 4 interior surfaces of the box you have 4 more places to display and link the data. You can have a heat map microarray representation on one side, and various pathways associated with the genes in that microarray on the other sides.
There’s a short systems biology Application Note in Bioinformatics that describes the framework and gives an overview of the tool. But there’s also a more detailed paper over at their publication site that will get you started (that 2010 paper for the Visualization conference in Taipei).
My computer is a bit underpowered, but I was able to load their webstart version and begin to look around. They provide some sample data you can select and examine. For the movie this week, though, I was unable to load that and run the recording software at the same time. So mostly it’s an introduction to the concept and the site. You’ll have to go over and load it up yourself to try it out. If the webstart version doesn’t work for you, there are a couple of other download options for different platforms.
The Caleydo team has also done a YouTube overview of the features that you can examine.
So try out this visualization strategy and see what you think. I really like the concept.
Streit, M., Lex, A., Kalkusch, M., Zatloukal, K., & Schmalstieg, D. (2009). Caleydo: connecting pathways and gene expression Bioinformatics, 25 (20), 2760-2761 DOI: 10.1093/bioinformatics/btp432