Regulatory Network Analyzer
RNA has as entry an interaction network represented by a file of .txt format. That file has to be a matrix of size n x n, where n is the number of genes/nodes, and has the notation as follows:
The first row is the names of the genes separated by comma (,);
1: when the gene j is activated by the gene i; 0: when there is no interaction between gene i and gene j; -1: when the gene j is inhibited by gene i;
The numbers are also separated by comma (,).
Here goes an example of matrix of the yeast cell-cycle network:
Cln3,MBF,SBF,Cln12,Cdh1,Swi5,Cdc20,Clb56,Sic1,Clb12,Mcm1 -1,0,0,0,0,0,0,0,0,0,0 1,0,0,0,0,0,0,0,0,-1,0 1,0,0,0,0,0,0,0,0,-1,0 0,0,1,-1,0,0,0,0,0,0,0 0,0,0,-1,0,0,1,-1,0,-1,0 0,0,0,0,0,-1,1,0,0,-1,1 0,0,0,0,0,0,-1,0,0,1,1 0,1,0,0,0,0,-1,0,-1,0,0 0,0,0,-1,0,1,1,-1,0,-1,0 0,0,0,0,-1,0,-1,1,-1,0,1 0,0,0,0,0,0,0,1,0,1,-1
Then the visualization of that matrix is generated as a network in cytoscape.
Besides that visualization we also generate the states transition network, that has the 2^n nodes, so is possible that cytoscape will crash for regulatory networks with more than 20 nodes (2^20), the layout of the network also affects the performance, by default the layout selected is Grid Layout. Each basin of attraction of the network has a different color.
And the app computes some informations from the states transition network like the entropy and the derrida coefficient. These informations is shown in the results panel.
The app is avaliable for download in the Cytoscape App Store - http://apps.cytoscape.org/apps/rna.