CPχ²: Comparative chi-square analysis of interactions

Overview

Comparative Chi-Square Analysis (CPχ²) identifies conserved and differential interactions in two networks sharing the same set of nodes.  The analysis is accomplished through computing chi-square statistics of heterogeneity and homogeneity of interactions across conditions (Song et al., 2014). 

 

The input is two trajectory collection files observed for each network.  Continuous values must be quantized first into discrete ones to use this analysis, for example, by R package Ckmeans.1d.dp.  The output is two networks in which interactions towards each node are declared conserved, absolutely differential, or relatively differential, across the two conditions.

 

Download the program

The CPχ² binary executable files by clicking on the following links:

Windows 7	openSUSE Linux	MacOS X
CPX2.exe	CPX2-linux	CPX2-mac

 

Documentation

·      CPχ² User Guide (CPX2_User_Guide.pdf) defines the command line arguments and an example to use the program. 

·      Trajectory Collection File Format (TrajCollFile.pdf) defines the input file format required by CPχ².

 

Example

Input files:

Click to download 1.trj and 2.trj, two trajectory collection files (TCFs).

 

Run CPχ²

To run the program under Linux, type the following command in your terminal in the directory/folder where you have downloaded the executable and the input files: 

./CPX2-linux -M comparison -k 2 -1 1.trj -2 2.trj -G summary.txt -D summary.dot -w INDEP_SUP -Y BY_EACH_COND

 

Output:

You should be able to see a result file (summary.txt), a graph file of interactions in the Graphviz DOT format (summary.dot), and the screen output.  They are explained in CPχ² User Guide. 

 

How to cite CPχ²

Song, M., Zhang, Y., Katzaroff, A. J., Edgar, B. A., Buttitta, L. (2014) Hunting complex differential gene interaction patterns across molecular contexts. Nucleic Acids Research. doi: 10.1093/nar/gku086