Gene Regulation, Modulation, and Their Applications in Gene Expression Data Analysis

Table 1

Gene regulation network and modulator identification methods.

Algorithm	Features	References
ARACNE	Interaction network constructed via mutual information (MI).	[14, 42]
Network profiler	A varying-coefficient structural equation model (SEM) to represent the modulator-dependent conditional independence between genes.	[47]
MINDy	Gene-pair interaction dependency on modulator candidates by using the conditional mutual information (CMI).	[44]
Mimosa	Search for modulator by partition samples with a Gaussian mixture model.	[45]
GEM	A probabilistic method for detecting modulators of TFs that affect the expression of target gene by using a priori knowledge and gene expression profiles.	[46]
MuTaMe	Based on the hypothesis that shared MREs can regulate mRNAs by competing for microRNAs binding.	[21]
Hermes	Extension 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]
ER𝛼; modulator	Analyzes the interaction between TF and target gene conditioned on a group of specific modulator genes via a multiple linear regression.	[48]