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Table 1 Link-specific ChIP evaluation bootstrap results

From: Identifying targets of multiple co-regulating transcription factors from expression time-series by Bayesian model comparison

Predicting regulation by single TFs

Top 50

Top 100

Top 200

 

P32

P2

ML

Inf

 

P32

P2

ML

Inf

 

P32

P2

ML

Inf

P32

  

***

*

P32

  

**

**

P32

  

**

**

P2

  

***

**

P2

+

 

***

***

P2

  

***

**

ML

    

ML

    

ML

    

Inf

    

Inf

    

Inf

    

Top 400

Top 800

Top 1600

 

P32

P2

ML

Inf

 

P32

P2

ML

Inf

 

P32

P2

ML

Inf

P32

  

*

***

P32

  

+

***

P32

  

*

***

P2

  

**

***

P2

  

*

***

P2

  

*

***

ML

   

*

ML

   

***

ML

   

***

Inf

    

Inf

    

Inf

    
 

Top 3200

 
      

P32

P2

ML

Inf

     
     

P32

 

***

***

***

     
     

P2

  

*

***

     
     

ML

   

***

     
     

Inf

         

Predicting regulation by TF pairs

Top 50

Top 100

Top 200

 

P32

P4

ML

Inf

 

P32

P4

ML

Inf

 

P32

P4

ML

Inf

P32

  

**

+

P32

  

*

.

P32

  

+

*

P4

  

**

+

P4

  

*

+

P4

  

+

*

ML

    

ML

    

ML

    

Inf

  

.

 

Inf

    

Inf

    

Top 400

Top 800

Top 1600

 

P32

P4

ML

Inf

 

P32

P4

ML

Inf

 

P32

P4

ML

Inf

P32

  

*

**

P32

  

+

***

P32

   

**

P4

  

+

**

P4

  

*

***

P4

**

 

*

***

ML

    

ML

   

.

ML

   

+

Inf

    

Inf

    

Inf

    
 

Top 3200

 
      

P32

P4

ML

Inf

     
     

P32

   

*

     
     

P4

***

 

**

***

     
     

ML

*

  

***

     
     

Inf

         
  1. The results of 100,000-fold bootstrap resampling of the data set of observed genes to assess significance of differences in ranking method performance. The methods studied are: P32 = Posterior-32 method, P2 = Posterior-2 method, P4 = Posterior-4 method, ML = ML Baseline method, Inf = Inferelator. For each pair of methods, the marks in the tables show how often the method on the corresponding row dominated the one on the corresponding column. The marks are interpreted as follows: ‘.’: >80% dominance, ‘+’: >90% dominance, ‘*’: > 95% dominance, ‘**’: >99% dominance, ‘***’: >99.9% dominance, ‘-’: comparison not applicable.