Database: hg19    Primary Table: cpgIslandExt    Row Count: 28,691
Format description: Describes the CpG Islands (includes observed/expected ratio)

field	example	SQL type	info	description
bin	585	smallint(6)	range	Indexing field to speed chromosome range queries.
chrom	chr1	varchar(255)	values	Reference sequence chromosome or scaffold
chromStart	28735	int(10) unsigned	range	Start position in chromosome
chromEnd	29810	int(10) unsigned	range	End position in chromosome
name	CpG: 116	varchar(255)	values	CpG Island
length	1075	int(10) unsigned	range	Island Length
cpgNum	116	int(10) unsigned	range	Number of CpGs in island
gcNum	787	int(10) unsigned	range	Number of C and G in island
perCpg	21.6	float	range	Percentage of island that is CpG
perGc	73.2	float	range	Percentage of island that is C or G
obsExp	0.83	float	range	Ratio of observed(cpgNum) to expected(numC*numG/length) CpG in island

bin	chrom	chromStart	chromEnd	name	length	cpgNum	gcNum	perCpg	perGc	obsExp
585	chr1	28735	29810	CpG: 116	1075	116	787	21.6	73.2	0.83
586	chr1	135124	135563	CpG: 30	439	30	295	13.7	67.2	0.64
587	chr1	327790	328229	CpG: 29	439	29	295	13.2	67.2	0.62
588	chr1	437151	438164	CpG: 84	1013	84	734	16.6	72.5	0.64
588	chr1	449273	450544	CpG: 99	1271	99	777	15.6	61.1	0.84
589	chr1	533219	534114	CpG: 94	895	94	570	21	63.7	1.04
589	chr1	544738	546649	CpG: 171	1911	171	1405	17.9	73.5	0.67
590	chr1	713984	714547	CpG: 60	563	60	385	21.3	68.4	0.92
590	chr1	762416	763445	CpG: 115	1029	115	673	22.4	65.4	1.07
591	chr1	788863	789211	CpG: 28	348	28	192	16.1	55.2	1.06

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Description

CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near transcription start sites, and may be associated with promoter regions. Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole.

Methods

CpG islands were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. Each segment was then evaluated for the following criteria:

• GC content of 50% or greater
• length greater than 200 bp
• ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the basis of the number of Gs and Cs in the segment

The CpG count is the number of CG dinucleotides in the island. The Percentage CpG is the ratio of CpG nucleotide bases (twice the CpG count) to the length. The ratio of observed to expected CpG is calculated according to the formula cited in Gardiner-Garden et al. (1987) in the References section below:

    Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)

where N = length of sequence.

Credits

This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).

References

Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J. Mol. Biol. 1987 Jul 20;196(2):261-82.