SpotXplore
SpotXplore is a plug-in for Cytoscape which enhances the visual analysis of gene expression obtained by, e.g., microarrays or the newer RNA-seq techniques in various ways. It enables visualization of multiple conditions or time series by glyphs that encode both expression value and statistical confidence. This visual mapping was introduced in GENeVis, which we have developed as a stand-alone application. SpotXplore can also detect subnetworks of interest based on the expression data, and it provides visualization techniques to explore these subnetworks.
SpotXplore features:
- runs as plug-in for Cytoscape
- improved visualization of time points or multiple conditions
- active subnetwork (hotspot) detection and visualization
Publication
M. A. Westenberg, J. B. T. M. Roerdink, O. P. Kuipers, S. A. F. T. van Hijum. SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks. Bioinformatics, 26(22):2922-2923, 2010.
Download and installation
- Download and install Cytoscape [Cytoscape web site].
- Download SpotXplore archive (version 2010/08/04) [zip]. Install by unpacking the archive in the Cytoscape plugins folder. There is only a single Java jar file contained in the archive. Note: some browsers already unpack the archive, but do not rename the resulting file. If the plugin does not show up in Cytoscape's menu, try to rename SpotXplore.zip to SpotXplore.jar, and restart Cytoscape.
- Download an example data set [Cytoscape session file]. Details about the data set are in de user manual.
- Download the user manual [pdf].
Quick start: Run Cytoscape, load the session bsubtsession.cys, and invoke SpotXplore from the Plugins menu.
Time series visualization
Hotspot detection and visualization
SpotXplore supports a number of ways to find or define hotspots of gene expression:
- GiGA: automatic detection by graph-based iterative group analysis, see Breitling et al. (2004).
- Luscombe: trace-back algorithm by Luscombe et al. (2004) to identify subnetworks that are active.
- Manual: converts a selection set in Cytoscape to a hotspot. It is possible to construct multiple hotspots per time point or condition.
[Play an animation of the time series].
The short 'movie of life' makes apparent that the impact of the ccpA mutation dynamically develops and intensifies during growth of B. subtilis cells. At the last time point, one hotspot is detected which overlaps almost completely with the SigB regulon. This regulon is involved in the response to harmful environmental conditions, such as heat, osmotic, acid, or alkaline shock. This hotspot is interesting, since it explicitly reveals that the SigB regulon is recruited stronger during the late growth stages of the wild-type strain than the ccpA deletion strain. Additional data might be required to provide a biological explanation for this effect.