# GNC: Gene Network Coherence with direct and indirect relationships
GNC is a Cytoscape app designed to analyze gene networks coherence using direct and indirect relationships.
## Using GNC
First you need to install the app throug the app manager. If everything goes well, you will get a new item in the `Apps` menu called `GNC`.
GNC consider your current selected network as the network to analyzed so you need to have a network or a network view open in Cytoscape.
Open GNC from the `Apps` menu and you'll be presented the configuration dialog. Select one of the preloaded databases or load your own custom biological databases which must be a “.txt” file formatted as:
Node1,Node2
Node1,Node3
...
Node1,Node N
...
Node N, Node M
Sit back and be patient. Although this program is optimized, usually it takes a long time, specially if you use files bigger than 1 MB.
Make sure to give enough memory to the Java Virtual Machine (at least 2048MB).
## Reference
Gómez-Vela, Francisco, José Antonio Lagares, and Norberto Díaz-Díaz. "Gene network coherence based on prior knowledge using direct and indirect relationships." Computational biology and chemistry 56 (2015): 142-151.
Copyright © 2016 Universidad Pablo de Olavide, Spain.
