WGCNA theory: Bin Zhang and Steve Horvath (2005) "A General Framework for Weighted Gene Co-Expression Network Analysis”

WGCNA: downloads, slides & tutorials: https://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/  

WebGestalt: http://bioinfo.vanderbilt.edu/webgestalt/   

GeneMania: http://www.genemania.org

 

CytoScape: http://www.cytoscape.org