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Table 1 Performance comparison for three methods

From: A stochastic model for identifying differential gene pair co-expression patterns in prostate cancer progression

Data type

Statistics

Methods

  

SIG method

ECF method

DAGA method

HS vs. HR

Identified pairs

428,582

2,101,425

5,212,394

 

RS

1.49%

100%

91.07%

 

P-value of RS

0.011

1

0.93

 

PS_Avg

1.74

0

0.02

 

P-value of PS_Avg

0.032

1

0.97

 

TFR

1.39%

0.49%

0.26%

 

PES_Avg

3.56

2.56

2.02

cancer vs. healthy

Identified pairs

303,992

14,228,478

32,569,223

 

RS

1.40%

100%

96.21%

 

P-value of RS

0.013

1

0.87

 

PS_Avg

1.65

0

0.01

 

P-value of PS_Avg

0.036

1

0.99

 

TFR

0.92%

0.39%

0.25%

 

PES_Avg

3.32

2.36

1.86

  1. RS: Re-identification Scale, overlap between the pairs identified before and after changing disease progression relation; PS: Progression Score, ratio of the nominal P-value of a pair before changing disease progression relation to that of a pair after changing disease progression relation; TPR: True Positive Rate, the proportion of functionally relevant pairs in all characterized pairs; PES: Pathway Enrichment Score, the degree to which differentially co-expressed gene pairs are overrepresented at a pathway. The 'Avg' refers to the average value for an item.
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BMC Genomics

ISSN: 1471-2164

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