Table 1

Types of networks and characteristics
Network type Used here Examples Variable Ease of estimation Utility for modeling Adjacencies Used in GO
types discussed enrichment
this article analysis
GRN Reduce Direct Time Nonlin. Sign
Correlation network Yes WGCNA [5] Numeric Easy Yes Yes No Maybe No Yes unsignedA Yes
signedA Yes
TOM Yes
Polynomial or Yes WGCNA [5] Numeric Moderate Yes Yes No Maybe Yes No polyR2 No
Spline regression splineR2 No
network
Mutual information network Yes ARACNE Discretized Moderate Yes Not clear No Maybe Yes No ASU No
[9], RELNET numeric, AUV1 No
[6,28], CLR categorical AUV2 Yes
[26], MRNET ARACNE Yes
[27], MIC [35] ARACNE0.2 Yes
ARACNE0.5 Yes
CLR Yes
MRNET Yes
RELNET Yes
MIC Yes
Boolean network No Boolean network [71] Dichoto-mized numeric Moderate Yes Not clear Yes Yes NA NA No No
Probabilistic network No Bayesian network [72,73] Any Hard Yes Not clear Yes Yes Yes Yes No No

For each network method, the table reports what kinds of biological insights can be gained and what kind of data can be analyzed. Column “GRN” indicates whether the network has been (or can be) used for studying gene regulatory networks. Column “Reduce” indicates whether the method has been used for reducing high dimensional data (e.g. via modules and their representatives). Column “Direct” indicates whether the the network can encode directional information. Column “time” indicates whether the network method is suited for studying time series data. Column “Nonlin. ” indicates whether the network can capture non-linear relationships between pairs of variables (represented as nodes). Column “Sign” indicates whether the network adjacency provides information on the sign of the relationship between two variables, e.g. a correlation coefficient can take on positive and negative values. The table entry “NA” stands for not applicable. Adjacencies discussed in this article: unsignedA: unsigned bicor; signedA: signed bicor; TOM: TOM transformed signed bicor; ASU: AMI,SymmetricUncertainty; AUV1: AMI,UniversalVersion1; AUV2: AMI,UniversalVersion2; ARACNE: ARACNE, ε = 0 ; ARACNE0.2: ARACNE, ε = 0.2 ; ARACNE0.5: ARACNE, ε = 0.5.

Song et al.

Song et al. BMC Bioinformatics 2012 13:328   doi:10.1186/1471-2105-13-328

Open Data