Table 2

Comparison of the number of CpG islands identified in the human genome with different methods (NCBI.36)

Chromosome 21


CpGPlot

CpGcluster

CpGProD

CpGIS

PSO

CPSO

GA

CGA


Chromosome Length (bp)

46,944,329


Total length of CpG islands

347,334

639,161

1,072,192

1,280,505

1,564,596

1,607,472

1,262,449

1,589,629


Number of islands predicted

973

2,703

1,091

3,704

2,648

2,813

2,513

3,304


Island coverage (%)

0.73

1.36

2.28

2.73

3.3

3.4

2.68

3.39


Island length (bp)


Average

357

237

983

346

591

571

502

482


Minimum

101

8

500

200

202

202

201

201


Maximum

3,047

3,028

6,732

1,948

4,020

4,035

6,126

10,687


GC-content ± SD (%)

62.17 ± 0.07

65.49 ± 0.07

54.49 ± 0.06

57.98 ± 0.04

53.73 ± 0.05

53.72 ± 0.05

54.24 ± 0.05

55.07 ± 0.05


CpG island O/E ratio ± SD

0.84 ± 0.1

0.87 ± 0.3

0.63 ± 0.1

0.68 ± 0.1

0.64 ± 0.08

0.65 ± 0.08

0.68 ± 0.1

0.71 ± 0.1


Chromosome 22


CpGPlot

CpGcluster

CpGProD

CpGIS

PSO

CPSO

GA

CGA


Chromosome Length (bp)

49,691,432


Total length of CpG islands

679,803

522,748

2,067,653

2,842,255

2,802,675

2,907,983

2,251,454

3,085,715


Number of islands predicted

1,642

2,186

1,903

6,875

4,571

4,882

3,902

4,985


Island coverage (%)

1.36

1.05

4.16

5.71

5.64

5.85

4.53

6.20


Island length (bp)


Average

414

239

1,087

413

613

596

577

619


Minimum

200

8

500

200

198

202

201

201


Maximum

7,902

7,774

8,363

3,339

4,076

4,076

5,340

5,905


GC-content ± SD (%)

63.70 ± 0.08

70.23 ± 0.08

55.84 ± 0.07

55.12 ± 0.06

54.50 ± 0.07

54.46 ± 0.07

55.21 ± 0.05

56.15 ± 0.06


CpG island O/E ratio ± SD

0.84 ± 0.1

0.95 ± 0.3

0.62 ± 0.1

0.68 ± 0.1

0.63 ± 0.05

0.63 ± 0.05

0.64 ± 0.1

0.68 ± 0.1


SD: Standard Deviation. Proportion (%) of the chromosome sequence covered by methods

Chuang et al. BMC Genetics 2012 13:13   doi:10.1186/1471-2156-13-13

Open Data