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Table 1 Summaries of the evaluated network inference methods

From: Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size

Category

Methods

Cor-based

MI-based

Ref.

Deal with indirect edges explicitly

RLowPC

Yes

  
 

PC

Yes

 

[2, 45]

 

PCIT

Yes

Yes

[33, 38, 50, 51]

 

MRNET

 

Yes

[29, 33, 39, 50]

 

MRNETB

 

Yes

[27, 29, 33, 50]

 

ARACNE

 

Yes

[28, 33, 50]

Not deal with indirect edges

Cor

Yes

  
 

CLR

 

Yes

[33, 48, 50]

 

Random

   
  1. Nine correlation-based, MI-based and random network inference methods have been compared and evaluated in this study. The methods are classified into two main groups: Deal with indirect edges explicitly and Not deal with indirect edges