Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors

Table 4 Hypermethylated CpG island location relative to blocks

Cancer type	CGIs in testable area (n)	Testable CGIs significantly (q <0.05; deltaM >0.1) hypermethylated (%)	CGIs in blocks (n)	Hypermethylated CGIs in blocks (%)	Odds ratio of CGI being in block and hypermethylated	Pvalue (Chi-squared test)
Breast	24,206	11	316	20	2.5	<0.0001
Colon	19,827	19	3,769	30	4.1	<0.0001
Lung	22,661	8	1,310	12	2	<0.0001

The `CGIs in testable area (n)' column shows the number of CpGs that are included in the analysis for that tissue. Note that CpGs that were inside region that were borderline from being called blocks are not included (see Methods for details). The next column shows the percentage of these CpG that were statistically significantly hypermethylated. The fourth column shows the number of the CGIs that were inside hypomethylated blocks. The next column shows the % that were hypermethylated among the CGIs that were in blocks (fourth column). The odds ratio and P value shown in the final two columns are based on the two by two table represented in each row: each CGI can be either hypermehtylated or not and inside a block or not.

ISSN: 1756-994X