Table 4.

Representative tools for deriving sample-specific networks. Links to code/tools are provided in Supplementary Table 4.

Tool	Input data	Algorithmic approach	Example application	Reference
SSN	Expression data	Network perturbation	Construction of multicellular gene network to investigating the prognostic role of macrophage–tumor cell interactions in tumor progression in gliomas[156]	[152]
P-SSN	Expression data	Network perturbation	Identify individual-specific driver genes in cancer patients using the TCGA dataset[153]	[153]
LIONESS	Expression data	Network perturbation	Infer sample-specific GRNs from 29 healthy human tissue types to study sex differences in gene expression and regulatory networks[157]	[154]
EGRET	Snapshot expression data; multi-omics data	Message passing	Construction of genotype-specific GRNs in GM12878 and K562 cell lines; construction of patient-specific networks in Crohn’s disease and coronary artery disease[155]	[155]