Table 2

Comparison of the performances by different machine learning algorithms

Number of peaks

Number of peaks with ERE motif

Ratio of peaks with ERE motif match


MACS p = 1E-10

1,286

941

0.73

MACS p = 1E-8

1,966

1,416

0.72

MACS p = 1E-5

4,678

3,077

0.66


k-means (city block)


Cluster 1

26,211

11,943

0.46

Cluster 2

12,113

3,245

0.27


supervised-NB(th = 0.8,1:2)


Positively labeled

11,835

8,196

0.69

Negatively labeled

26,489

6,992

0.26


supervised-SVM(kernel = polynomal,1:2)


Positively labeled

14,915

8,425

0.56

Negatively labeled

23,409

6,763

0.29


supervised-RF(th = 0.7,1:2)


Positively labeled

10,428

6,514

0.62

Negatively labeled

27,896

8,674

0.31


semi-supervised-NB(th = 0.8,1:2, I = 75)


Positively labeled

12,597

8,458

0.67

Negatively labeled

25,727

6,730

0.26


Osmanbeyoglu et al. BMC Genomics 2012 13(Suppl 1):S1   doi:10.1186/1471-2164-13-S1-S1

Open Data