Table 1.

Features of pathway-based and network-assisted analysis approaches

Feature	Pathway-based analysis	Network-assisted analysis
Gene set annotation	Pathways or gene sets from knowledgebase	A reference network
Gene set component genes	Fixed	Dynamic
Search for sub-pathways/subnetworks	No	Yes
Available for topological characteristics	No	Yes
Assess combined association signals	Yes	Available but not required
Function	Focus on one specific function	No particular function boundaries
Correlation amongst genes (or molecules)	Not always available, e.g., GO does not have interactions amongst genes (or molecules)	Available
Hypothesis testing	Q1 vs. Q2*, pre-defined pathways	Multiple and dynamic

^*Details of Q1 and Q2 are provided in Figure 3 and the main text.