You could have a look at the regulatory interaction plugin for PathVisio: http://www.pathvisio.org/wiki/PluginDocumentation (near the bottom). That is a plugin under development though and there is no online documentation yet. If you want to use it please contact the authors, there is at least a thesis about the development.
Whether that is useful to you depends on what you want to do. PathVisio allows you to do pathway analysis on pathways from WikiPathways (and others once you get them in the right format). This plugin allows you to do on the fly extension of a pathway with regulatory information. The miRNAs (or other selected regulatory biomolecules like transcription factors) are shown in a sidepanel once you click a gene of interest. The sidepanel can then also be used to show data for the regulatory molecules themselves.
We expect this to be a useful approach if you want to combine transcriptomics analysis with miRNA analysis. The actual pathway statistics is preformed on the transcriptomics data but the miRNAs influencing the pathway and their analytical values can be observed interactively.
The reason we did it in this way is that miRNA data tends to clutter pathways, so people tend to only add the most important miRNAs to a pathway. The alternative to this approach would be to copy the pathway into Cytoscape (which you could do with the GPML plugin) and then add the miRNA information in Cytoscape (using the new CyTargetLinker plugin see http://apps.cytoscape.org/apps/cytargetlinker and http://code.google.com/p/cytargetlinker/) and show and evaluate miRNA data on top of that. But that also assumes that you already know which pathways you are interested in.
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felciano •
