Last week I talked about some of the terrific visualization tools from the Caleydo team, the ones that are focused on looking at pathway data. There’s another tool that I learned about in their newsletter that offers another type of visualization, which you can also supplement with pathway data. StratomeX offers a look at comparisons within stratified data. For example, you might want to look at some cancer data with certain subsets of patients to evaluate subtypes.
A review paper by Schroeder et al last year examined a number of cancer-related analysis tools and websites. As with any group of tools, some have specific features that are suited for specific tasks. And there may be times you are going to take the data you obtain from one tool and explore it with another. So it’s useful to have a number of these in your back pocket. They described StratomeX this way:
Caleydo StratomeX is especially well suited to exploring relationships between groups of samples (Figure 2). These relationships are visualized as ribbons of varying width drawn between neighboring columns. Wide ribbons encode a high co-occurrence of samples in different groupings, whereas their absence indicates mutual exclusion. This coding provides a straightforward and scalable overview of the consistency of group memberships of tumor samples across different data types.
Of course, the StratomeX team also has publications and presentations that describe the work in more detail. which you can obtain from the introduction page they have provided. That page offers a nice overview level, though, which can help you to begin to assess whether this tool would suit your research goals.
But also have a look at their video, which covers their Data View Integrator, and StratomeX. It’s a really compelling example of glioblastoma subtypes. The gene expression data can be supplemented with other data types–in this case “days to death” curves, and then pathway data can be brought in to provide further insights.
This tool is another winner from the Caleydo team. Usually we highlight web-based tools, but these tools need a little bit more overhead. You have to download and install it. But I think they are really worth it. You should try the Caleydo team’s tools.
StratomeX specific page: http://www.icg.tugraz.at/project/caleydo/projects-1/stratomex
Calyedo main page: http://www.caleydo.org
Lex A., Streit M., Schulz H.J., Partl C., Schmalstieg D., Park P.J. & Gehlenborg N. (2012). StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization, Computer Graphics Forum, 31 (3pt3) 1175-1184. DOI: 10.1111/j.1467-8659.2012.03110.x
Schroeder M.P., Gonzalez-Perez A. & Lopez-Bigas N. (2013). Visualizing multidimensional cancer genomics data, Genome Medicine, 5 (1) 9. DOI: 10.1186/gm413