Have you dreamed of looking at genomic pathway data, with experimental information aligned with known pathway details, and wandering easily from one pathway node to another as you consider the implication of increased/decreased gene expression, or potential copy number variations? Easily hopping to related pathways to keep looking? Yeah–me too, for years . If this is something that you think might help your work–have a look at the tools from the Caleydo team.
Last month I got a newsletter from the the team. But due to the holidays and some deadlines I hadn’t had time to look into it. When I went back last week to have a look at some of their new features, I found myself just as impressed as when I looked at their software years ago.
Back then, I loved the idea of having the different views combined for the pathways and the expression levels. And now there are even more ways to do this, and the tools are even cooler.
Here I’ll focus on their “Entourage” and “enRoute” visualization strategies for the pathway data. They are different but related. With these tools you can wander through the KEGG pathway maps. With Entourage–you can have one of the maps in the main area loaded up as the “focus” pathway–but off to the side you can chose to explore other related pathways (context), or jump to ones with specific genes. You can take “portals” to other pathways in such a slick way it’s just amazing.
To get a sense of these features, first take a look at their video for Entourage.
Next, here is their YouTube of the enRoute components. You can again load up a KEGG pathway, or something from Wikipathways, Nearby you can visualize expression levels or copy number status.
I liked the visualizations from Caleydo before, and these additional pieces on that Caleydo framework are even better now. Have a look and kick the tires. There’s more than I covered here, or appears in the videos. So read the papers, check out their site, and download the software. I think there’s a lot of utility here.
Main Caleydo with the software tools: http://www.caleydo.org
Entourage specific page: http://www.icg.tugraz.at/project/caleydo/projects-1/entourage
enRoute specific page: http://www.icg.tugraz.at/project/caleydo/projects-1/enroute
Caleydo help: http://help.caleydo.org/
Lex A., Partl C., Kalkofen D., Streit M., Gratzl S., Wassermann A.M., Schmalstieg D. & Pfister H. (2013). IEEE Transactions on Visualization and Computer Graphics, 19 (12) 2536-2545. DOI: 10.1109/TVCG.2013.154
Partl C., Lex A., Streit M., Kalkofen D., Kashofer K. & Schmalstieg D. (2013). enRoute: dynamic path extraction from biological pathway maps for exploring heterogeneous experimental datasets, BMC Bioinformatics, 14 (Suppl 19) S3. DOI: 10.1186/1471-2105-14-S19-S3