Table 1: Gene regulation network and modulator identification methods.

AlgorithmFeaturesReferences

ARACNEInteraction network constructed via mutual information (MI).[14, 42]
Network profilerA varying-coefficient structural equation model (SEM) to represent the modulator-dependent conditional independence between genes.[47]
MINDyGene-pair interaction dependency on modulator candidates by using the conditional mutual information (CMI).[44]
MimosaSearch for modulator by partition samples with a Gaussian mixture model.[45]
GEMA probabilistic method for detecting modulators of TFs that affect the expression of target gene by using a priori knowledge and gene expression profiles.[46]
MuTaMeBased on the hypothesis that shared MREs can regulate mRNAs by competing for microRNAs binding.[21]
HermesExtension of MINDy to include microRNAs as candidate modulators by using CMI and MI from expression profiles of genes and miRNAs of the same samples.[20]
ER   
modulator
Analyzes the interaction between TF and target gene conditioned on a group of specific modulator genes via a multiple linear regression.[48]