BMC Genomic Data

Table 2 Comparison of the number of CpG islands identified in the human genome with different methods (NCBI.36)

From: CpGPAP: CpG island predictor analysis platform

				*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

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