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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