Table 3.

Network-based methods for N-of-1 tumor analyses to identify altered pathways or driver mutations.

Method	Application	Approach	URL	Reference
Ingenuity Pathway Analysis	N-of-1 pathway analysis	Regulatory network inference and scoring from expression data using a curated causal network from the Ingenuity Knowledge Base	http://www.ingenuity.com	[148]
Pathifier	N-of-1 pathway analysis	Inferring pathway dysregulation scores for each tumor sample on the basis of expression data	www.weizmann.ac.il/pathifier/	[149]
FAIME	N-of-1 transcriptomic analysis	Pathway and molecular functional profiles from gene expression	http://www.lussiergroup.org/publications/FAIME/	[144]
N-of-1-pathway	N-of-1 transcriptomic analysis	Pathway and molecular functional profiles from gene expression (paired samples)	http://lussierlab.org/publications/N-of-1-pathways	[145]
MixEnrich	N-of-1 transcriptomic analysis	Detects bidirectionally responsive pathways using mixture models to group genes	http://lussiergroup.org/publications/MixEnrich	[147]
kMEn	N-of-1 transcriptomic analysis	Detects bidirectionally responsive pathways using K-means to group genes (paired samples)	http://www.lussierlab.org/publications/kMEn/	[146]
N-OF-1-PATHWAYS-MD	N-of-1 transcriptomic analysis	Approximates the magnitude of dysregulation of pathways with biological or clinical significance (paired samples)	http://www.lussierlab.net/publications/N-of-1-pathways	[143]
OncoRep	N-of-1 transcriptomic analysis	Derives multiple layers of clinically relevant information from single sample RNA-Seq data	https://bitbucket.org/sulab/oncorep/	[151]
Merid et al.	N-of-1 driver prediction	Co-occurrence of mutations and CNVs in a functional network	http://research.scilifelab.se/andrej_alexeyenko/downloads.html	[154]
DawnRank	N-of-1 driver prediction	Ranks mutated genes for overall impact on differential expression of downstream genes in the molecular interaction network	http://bioen-compbio.bioen.illinois.edu/DawnRank/*	[155]
OncoIMP ACT	N-of-1 driver prediction	Formulates the minimum set cover problem on a bipartite network linking mutated genes to downstream targets identified from network path analysis	https://sourceforge.net/projects/oncoimpact/	[156]
SSN	N-of-1 driver prediction	Sample-specific networks based on expression differences relative to a panel of reference samples	http://sysbio.sibcb.ac.cn/cb/chenlab/software.htm	[157]
SCS	N-of-1 driver prediction	Formulates the minimum set cover problem on a bipartite patient-specific network linking mutated genes to downstream targets identified using control theory	http://sysbio.sibcb.ac.cn/cb/chenlab/software.htm	[158]

^*Link listed in the original publication of the method is not valid.