Table 2.

Summary of tools in network construction. The short description and homepages of some tools in the manuscript are summarized

Class	Name	Homepage and description
Data-driven model	ARACNE (39)	■ http://minet.meyerp.com/ ■ Standalone tool available ■ Mutual information based network generation
	WGCNA (36)	■ https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/ ■ R package available ■ Correlation-based network generation
	Cancer Landscapes (45)	■ http://www.cancerlandscapes.org/ ■ Web-based tool ■ Sparse inverse covariance selection-based network generation
	Ultranet (46, 47)	■ www.broadinstitute.org/ultranet ■ Standalone tool available ■ Sparse inverse covariance selection-based network generation
	Banjo (48)	■ https://users.cs.duke.edu/~amink/software/banjo/ ■ Standalone tool available ■ Network generation by using Bayesian networks
	CATNET (50)	■ https://cran.r-project.org/web/packages/catnet/index.html ■ Standalone tool available ■ Bayesian networks
Hybrid model	EDDY (28)	■ http://biocomputing.tgen.org/software/EDDY ■ Standalone tool available ■ Gene sets and Bayesian networks combined
	PATHOME (7)	■ Web version of the algorithm under construction (available on request) ■ KEGG pathways and correlation-based statistic combined
	SPIA (58)	■ http://bioconductor.org/packages/release/bioc/html/SPIA.html ■ R package available ■ KEGG pathways and permutation tests combined