Survey of Network-Based Approaches to Research of Cardiovascular Diseases

Table 2

Methods that explored topology of biological networks in research of CVDs.

Network	Type of data/interactions in the network	Topological analysis performed on the data	Aims of topological analysis	Reference
Heart failure (HF) network	HF relevant genes, genes differentially expressed in HF and dilated cardiomyopathy (DCM), and PPI data	Connectivity of nodes	Relationship between gene connectivity and gene coexpression levels and their biological functions	[54, 56]
Network of atherosclerosis	Literature associations and gene expression data	Network modules identified based on closeness centrality	GO enrichment of network modules	[57]
Network of ischemic dilated cardiomyopathy (ICM)	Genes differentially expressed in ICM, cardiac myocytes proteins, and PPI data	Number of edges between network clusters	Correlation between number of edges between network clusters and differential gene expression patterns	[60]
Cardiovascular disease “functional linkage network” (CFN)	CVD proteins and PPI data	Degree distribution, betweenness centrality, and modularity measure	Associating functional modules (highly connected subgraphs) with diseases	[61]
Congenital heart disease (CHD) network	Known CHD genes, genes differentially expressed in CHD, and PPI data	Subnetworks based on shortest paths and current flow (network was modelled as an electrical circuit)	Functional subnetwork analysis in search of key pathways of CHD	[62]
Networks for analysis of cardiac development, hypertrophy, and failure	Gene coexpression data	Network modules based on hierarchical clustering and shared network neighbours	Identifying common modules in networks of different types of myocardial tissue	[63]
Human PPI network	PPI data	Node degree, neighbourhood enrichment, betweenness centrality, clustering coefficient, and shortest path length	Inferring coronary artery disease genes based on topological information	[65]
Human PPI network	PPI data	Clustering nodes based on graphlet degree vector similarity	Inferring new CVD genes based on clusters' enrichment in CVD genes	[66]