Epigenetic researchers now have a tailored tool to identify differentially expressed miRNA markers on microarrays. NCode™ Profiler software is an advanced experimental design and analysis solution designed for two-dye expression profiling microarray experiments. The software eliminates inherent challenges with miRNA array design and data analysis.

NCode Profiler Software
Figure 1. Experimental Design Module in NCode™ Profiler Software

Experimental Design

NCode™ Profiler software enables simple design of array templates using Loop Design and Dye Swap normalization methods applied to your experimental criteria for tissue samples, species, and controls. The array templates support sample-to-sample comparison within the experiment. They are designed with statistical considerations to reduce or eliminate any general miRNA effect, array effect, dye effect, overall tissue effect, array-miRNA interaction and dye-miRNA interaction from the data.

Data Analysis

Once an experiment has been conducted, the raw data can be imported and analyzed using the statistical methods design into the array. For each tissue on the array, pair wise differential expression is determined and the test statistics, fold change and p-value are generated. Additionally, the ranking of each miRNA marker, with respect to the other markers, within the tissue is given.

Using NCode™ Profiler software, you can expect

  • Simplified experimental design steps
  • Confidence when interpreting results using proven statistical analysis using dye swap or loop design normalization models
  • Enhanced rankings of miRNA markers for selected tissues
  • Easy export of normalized data to visualization software for clustering (tree) and heat map analysis.

Software Details:

  • Software version: 2.0
  • Last software release date: September 20, 2007
  • Cost: Freeware
  • License: See End User License Agreement (EULA)
  • System requirements:
    • Microsoft Windows XP SP2 or Vista
    • CPU with 800 MHz of faster
    • 256 MB of RAM
    • At least 10 MB for storing result files
    • Microsoft .NET Framework 2.0 Redistributable Package - free software available from Microsoft
    • Microsoft Excel (recommended) for viewing results. Output files are tab delimited and can be viewed using statistical or spreadsheet software.
    • Cluster and TreeView (recommended) for analyzing and visualizing the results of complex microarray experiments. Available for download at http://rana.lbl.gov/EisenSoftware.htm. Please note the licensing agreement particularly the differences between academic/non-profit users and commercial users.

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Share your thoughts on NCode™ Profiler v. 2.0

Tell us how we can improve upon version 2.0 and what additional features you would like to see available. Email us at episcientist@invitrogen.com and provide your comments.

Want to learn more about data normalization methods in the miRNA profiling workflow? Visit the Epigenetics Learning Center.