State of the Art of Fuzzy Methods for Gene Regulatory Networks Inference

Table 4

Main fuzzy methods in GRN inference.

Dataset	Modeling method	Tool/technique software/database	References
Saccharomyces cerevisiae (yeast)	Fuzzy logic + clustering	Preprocessing algorithm coded in MATLAB	Ram et al. [9]
Saccharomyces cerevisiae (yeast) cell cycle	Fuzzy rules	GeneChip + SAGE	Woolf and Wang [12]
Saccharomyces cerevisiae	Fuzzy logic + clustering	DSOM approach + ART	Ressom et al. [20]
Breast cancer (cancerous cells in human)	AFEGRN	AFEGRN framework	Sehgal et al. [6]
10 different cancer datasets (cancerous cells in human)	Coalesce GRN (CGRN)	Cross platform GRN fusion	Sehgal et al. [21, 22]
Bacterium Escherichia coli	FRBPN	FRBPN technique	Hamed [19]
Saccharomyces cerevisiae	Combined fuzzy clustering and Bayesian networks (FCBN)	Software platform MATLAB and BNT package	Wang et al. [11]
Lac operon in Escherichia coli	Combined ODEs models and FIS	Simulink, fuzzy logic Toolbox and Optimization Toolbox in MATLAB	Muñoz et al. [17]
Arabidopsis thaliana plants, Affymetrix Arabidopsis ATH1 genome with 22K genes	Fuzzy cognitive map (FCM) model + clustering	FCModeler tool	Du et al. [13]
Escherichia coli bacteria SOS DNA consisting of 30 genes	Fuzzy logic + artificial bee colony (ABC)	ABC- and DE-based simulations, on Pentium	Das et al. [15]
Saccharomyces cerevisiae	Fuzzy Petri net (FPN)	FPN graphical tool	Hamed et al. [18]
Saccharomyces cerevisiae	Fuzzy logic based modeling	Fuzzy data mining technique	Ma and Chan [3]
Escherichia coli and Saccharomyces cerevisiae (210 time points in 100-gene networks), 10 DREAM-4 datasets	Fuzzy cognitive maps (FCMs) model and ant colony optimization (ACO)	Simulation using stochastic differential equations, DREAM project	Chen et al. [2]
Saccharomyces cerevisiae microarray time series (three datasets)	Activator-repressor regulatory model, SRS biological model	SRS program, regulatory-fit scoring method	Volkert and Malhis [14]
Saccharomyces cerevisiae genes time series gene expression data (about 800 cell cycle regulated genes)	Fuzzy data mining model	C4.5, SVM, and FID, 10-fold cross validation strategy	Ma and Chan [16]
Yeast cell cycle (cell-synchronized datasets with 14 time points)	Fuzzy logic genetic search algorithm model	KEGG database, k-nearest-neighbor (kNN) algorithm	Brock et al. [4]