Table 1.

A taxonomy for biological network analysis study

Dimension	Type	Description	Examples
Network Types	Gene interaction networks	Networks represent the interactions at the gene level	S. cerevisiae (Tong et al., 2004 ; van Noort et al., 2004; Luscombe et al., 2004) Mammalian (Shaw, 2003) P53 (Hallinan 2004)
	Protein interaction networks	Networks represent the protein interaction relationship	S. cerevisiae (Jeong et al., 2001; Wuchty et al., 2003; Yook et al., 2004)
	Metabolic networks	Networks represent the relationship of the substrates in the same metabolic pathway	E. coli (Fell and Wagner, 2000; Wagner & Fell, 2001) 43 organisms (Jeong et al., 2000; Ravasz et al., 2002) 65 organisms (Ma & Zeng, 2003)
	Signal transduction networks	Networks represent the for interactions between genes, proteins, and other cellular signaling molecules.	S. cerevisiae (Luscombe et al., 2004) E. coli (Shen-Orr et al., 2002) Cancer protein (Jonsson, 2006)
Data Sources	Experimental data	Relations or correlations derived from the experimental data	Two-hybrid (Jeong et al., 2001; Yook et al., 2004) Microarray (Shaw, 2003; Tong et al., 2004; Luscombe et al., 2004; Carter et al., 2004; Noort et al., 2004)
	Manually compiled ontology or knowledge base	Interactions curated by experts based on prior knowledge	GO (Tari 2005) Manually compiled (Shen-Orr et al., 2002; Hallinan, 2004; Fell and Wagner, 2000; Wagner & Fell, 2001) Knowledge base (Ma and Zeng 2003; Wuchty et al., 2003; Yook et al., 2004)
	Literature-based data	Relations parsed using NLP tools or co-occurrence tools	Genes parsed from abstracts searched from PubMed by some keywords (Chen and Sharp 2004)
Research Focus	Topological characteristics	Topological measures and models	Small-world (Fell and Wagner 2000; Tari 2005) Scale-free (Jeong et al., 2001; Yook et al., 2004; Wagner and Fell, 2001; Shaw, 2003; Tari 2005) Hierarchical structure ( Ravasz et al., 2002;) Giant strong component (Ma and Zeng, 2003)
	Local structures	Special local structures and clusters	Network motif (Luscombe et al., 2004; Wuchty et al., 2003; Shen-Orr et al., 2002) High tendency to cluster (Tong et al., 2004; Carter et al., 2004)
	Topology-function relationship	Correlation between topological characteristics and biological functions	High degree node -> essential (Jeong et al., 2000) Correlation between network structure and protein function and location (Yook et al., 2004) Small world -> central metabolites (Ma and Zeng, 2003) Small world -> gene evolution (Noort et al., 2004) Clusters -> gene pathway (Hallinan, 2004)