What is ExPCRt?

Quantitative, real-time PCR experiments have become the preferred method for quickly and cheaply quantifying gene expression in a typical molecular biology laboratory setting. There is a need to quickly and accurately normalize and evaluate the data generated from qPCR experiments. Comparing quantitative data in graphical form is a powerful way to uncover trends in gene expression studies. This package aims to ease the process of evaluating and making these comparisons by automatically normalizing, evaluating and graphing qPCR results across multiple experiments.

ExPCRt was written for automated analysis and graphing of qPCR data obtained from real-time, quantitative PCR experiments.  The tool was written using Microsoft’s C# .NET programming language.  This language was chosen because of its ability to integrate with the Microsoft Excel programming interface through the Microsoft.Office.Interop.Excel module.  Using this module, the software reads in a formatted list of qPCR measurements.

Output is made to the Excel sheet.  Three separate workbooks are created.  The first has the genes output in target-sample order.  This creates a graph showing with conditions grouped by sample on the x-axis.  This grouping clearly shows the effect of each condition on the targets.  Also, the control levels are all easy to see.  The second graph outputs genes in sample-target order, creating a grouping of targets on the x-axis.  This grouping facilitates viewing the effect on each target across samples.

The graphs are automated using the excel Graph object component of the Excel module.  All properties and labels of the graph are modifiable through code with this object.  Additionally, using this object keeps the graphs modifiable using a normal version of excel so that end-users can use the excel graph capabilities that they are comfortable with to manipulate the final outputs.