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Table 4 Performance comparison of various methods with Arabidopsis networks of less than 40,000 edges (the numbers before "/") and less than 70,000 edges (the numbers after "/") .

From: Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana

Applied Method

Network Size

Confirmed Edges

Ratio

Pearson Correlation (Cutoff=0.70)

35,253/71,417

25/36

7.09e-4/5.04e-4

Causal Linear Regression Model

30,000/59,557

5/16

1.66e-4/2.68e-4

Graphical Gaussian Model

GeneNet: Static method

30,000/68,624

9/10

3.00e-4/1.46e-4

 

GeneNet: Dynamic Method

30,000/68,658

9/10

3.00e-4/1.45e-4

Meta-analysis (Microarray data partition)

Tissue-wide partition

12,300/59,676

35/57

28.5e-4/9.55e-4

 

Experiment-wide partition

37,850/56,775

14/18

3.96e-4/3.17e-4

 

Development-based partition

37,850/57,339

18/22

4.75e-4/3.84e-4