BioMed Research International / 2009 / Article / Tab 1

Review Article

Computational Challenges in miRNA Target Predictions: To Be or Not to Be a True Target?

Table 1

Common softwares for “–omics” data analysis allowing in-depth analysis of high-throughput data.

Method nameReferenceBrief descriptionComputer platformWeb interfaceAvailabilityURL

BabelomicsAl-Shahrour et al. 2006Web-based tools for genomic data analysis. Gene annotations include predicted microRNAAny platform, web browseryesFree accesshttp://www.babelomics.org/
M@iaLe Bechec et al. 2008Modular tools for genomic data analysis. Gene annotations include predicted microRNALinux, MacOs, Windows. PHP language, Apache web server and MySQL database requirednoOpen-sourcehttp://maia.genouest.org/
TIGR Multiexperiment Viewer (MeV)Integrated environment for -omics data analysis. Gene annotations include predicted microRNAWindows, MacOs; Java required.noFree executablehttp://www.tm4.org/mev.html
BRB-ArrayTools Tools for -omics data analysis. The working environment is Microsoft Excel, an R engine is providing to Excel through and add-in module. Gene annotations include predicted microRNAWindows. Java, Excel and R language requirednoFree executablehttp://linus.nci.nih.gov/~brb/download.html
GeneSpring GXIntegrated environment for -omics data analysis. Gene annotations include predicted microRNAWindows, Java requirednoCommercial from Agilent Technologies, free trialhttp://www.silicongenetics.com/
Ingenuity Pathway AnalysisIntegrated environment for -omics data analysis. Gene annotations include predicted microRNA. Functional annotation and analysis of biological networks.Windows, Java requirednoCommercial from Ingenuity Systems Inc., free trialhttp://www.ingenuity.com/index.html
R BionconductorA common open source environment for -omics data analysis and statistics. It includes tools for microRNA analysis and annotation.Linux, MacOs, Windows.noOpen Sourcehttp://www.bioconductor.org/