Can anybody tel me how can we do pathway analysis of pathways regulated by miRNA using bioinformatics approach? any idea?
One of the most powerful tool to do so is Ingenuity Pathway Analysis. http://www.ingenuity.com/products/pathways_analysis.html
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.
As Ingenuity Pathway Analysis (IPA) isn't free or open-source I'd reccomend looking at miRpath http://diana.cslab.ece.ntua.gr/pathways/ .
You can you use DIANA-microT, Pictar, or TargetScan 5 to predict the targets of your miRNA of interest in Human or Mouse and it looks for KEGG pathway annotations enriched in the targets.
a new version of mirPath is now available http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=mirpath/index
Be careful with the common pitfalls coming with the straightforward strategies proposed above when applied on microRNAs. Look at this paper for more information: http://nar.oxfordjournals.org/content/early/2015/03/23/nar.gkv249.full
This paper might also help you get some insights http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0040016
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Ingenuity Pathway Analysis is free to try out for a limited period of time. If you already have a dataset ready to analyze you may be able to get quite a bit of valuable results from this free period. The hope is that if you find the tool useful through this free access, you'll consider rolling a license into your budget for future grants to continue to support its development.
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