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Table 2 The number of genome-wide enhancers predicted by different methods and thresholds

From: Enhancer prediction in the human genome by probabilistic modelling of the chromatin feature patterns

  

The threshold of 0.5

The best operating point or the threshold of 0.25 for RFECS

The FPR 1% Threshold

Method

Cell

all

without TSS

threshold

all

without TSS

threshold

all

without TSS

PREPRINT ML

K562

27347

21238

0.51917

26423

20476

0.65472

20531

15531

PREPRINT Bayesian

K562

36079

29747

0.35121

45472

37387

0.63137

29632

24553

RFECS

K562

18956

15786

0.25

44522

35089

   

ChromHMM Weak Enhancer

K562

180471

176912

      

ChromHMM Strong Enhancer

K562

69019

66888

      

PREPRINT ML

GM12878

34448

29189

0.51917

33358

28246

0.65472

26274

22088

PREPRINT Bayesian

GM12878

42480

38048

0.35121

52176

46446

0.63137

35447

31904

RFECS

GM12878

20059

17746

0.25

58560

49699

   

ChromHMM Weak Enhancer

GM12878

178474

175487

      

ChromHMM Strong Enhancer

GM12878

64052

62599

      

The thresholds estimated from the GM12878 test data

        

PREPRINT ML

GM12878

  

0.23675

58053

50012

0.68115

24934

20916

PREPRINT Bayesian

GM12878

  

0.26116

60412

53681

0.81953

25401

23134