Comparison of co-expression measures: mutual information, correlation, and model based indices

BMC Bioinformatics

Table 1 Types of networks and characteristics

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: A^{MI,SymmetricUncertainty}; AUV1: A^{MI,UniversalVersion 1}; AUV2: A^{MI,UniversalVersion 2}; ARACNE: ARACNE, ε = 0 ; ARACNE0.2: ARACNE, ε = 0. 2 ; ARACNE0.5: ARACNE, ε = 0. 5.

ISSN: 1471-2105