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Table 3 Overview of methods for the identification of differential correlation/interaction changes in pathways

From: Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods

Principle Method Reference Software
Graph edit distance [106]  
Gene-set co-expression analysis (GSCA) [107] GSCA (http://www.biostat.wisc.edu/kendzior/GSCA/)
Differential co-expression (dCoxS) between gene-sets [108] dCoxS (http://www.snubi.org/publication/dCoxS/index.html)
DiffCoEx [109] R code is provided in the paper
Differential disease network using C3NET [106, 110] c3net (http://cran.r-project.org/web/packages/c3net/index.html)
Disease associated interactions using Synergy network [111] MATLAB code is provided in the paper