The development of real-time PCR is a major step forward in gene expression analysis and, in particular, gene expression monitoring. The higher quality of real-time PCR data compared to microarray or Northern blotting provides a basis to classify samples and monitor biochemical/biological processes. However, proper interpretation of experimental results requires stringent analysis of data in many respects including conversion of Ct values, calculation of relative efficiency-based gene expression, identification of optimum reference genes and clustering of similar samples. Until now, only basic software (usually based on spreadsheet-macros) has been available for real-time PCR data analysis. These software packages perform only basic operations and are rather clumsy, resulting in frequent crashes and incorrect performance. For the rapidly growing real-time PCR community, a commercial, robust, flexible and user-friendly analytical software package was called for.
The recently launched DATAN GenEx software package provides both the novice and the advanced user with all the analytical tools needed to properly analyze real-time PCR data. Developed by MultiD (a leading Swedish company focused on multivariate data analysis), in close collaboration with the TATAA Biocenter (a world reputed Swedish company focused on real-time PCR), the DATAN GenEx package offers user-friendly, advanced methods to handle real-time PCR data. The graphics available in GenEx are impressive (although not all options are available to display final results) and there are many options for plotting/presenting data, including very attractive 3-dimensional plots. Of course, advanced use of all the GenEx capabilities requires studying the manual and some knowledge in basic statistics (which is covered by the manual), but most functions are intuitive, making it very easy to get started with GenEx.
The functions available include handling of data files (in a powerful Excel-compatible spreadsheet), Ct to copy number conversion, scaling options and normalization features and advanced methods (including validation of reference genes using GeNorm, classification of samples, analysis of time dependent processes, comparing samples etc.). The multivariate methods include: Principal Component Analysis, Hierarchical Clustering and Self Organizing Maps (Kohonen neural nets).
MultiD claims GenEx will soon be upgraded free of charge with complementary state-of-the art methods available in other packages from MultiD including partial least square analysis, potential curves, K-means, procrustes rotation and trilinear decomposition. I have no doubt that when all these methods are combined in a single package, GenEx will be difficult to beat for more expensive competitors in Bioinformatics and Chemometrics. DATAN GenEx runs under Windows XP without special requirements and the software is readily downloaded from the MuldiD and TATAA Biocenter websites (www.multid.se, www.tataa.com). After a free trial period of 45 days, the full version can be purchased for an excellent introductory price.
Jose Manuel Andrade
Senior Teacher
Dept. Analytical Chemistry
University of A Coruña