. Author manuscript; available in PMC: 2017 Sep 1.

Published in final edited form as: Mol Cancer Res. 2016 Jun 3;14(9):787–794. doi: 10.1158/1541-7786.MCR-16-0097

Table 1.

Summary of HGSC vs. patient-matched FTE and OSE DNA methylome comparisons

Sample Group Comparison	Differentially Methylated CpG sites (DMC)¹					Differentially Methylated Regions (DMR)²
Sample Group Comparison	All Sites	CpG Islands	CpG Island Shores	HOX Genes	Enhancers	5kb Tiles	CpG Islands	Promoters	Genes
Karpf 450K, HGSC (n=10), Patient-Matched FTE and OSE (n=5)
HGSC vs. FTE	1,017	388	417	222	29	3	32	0	0
HGSC vs. OSE	19,102	3,625	6,096	1,825	530	741	472	223	41
Fold Difference³	18.8 ^(****)⁴	9.3 ^(****)	14.6 ^(****)	8.2 ^(****)	18.3 ^(****)	247 ^(****)	14.8 ^(****)	223 ^(****)	41 ^(****)
Karpf Methyl-seq, HGSC (n=3), Patient-Matched FTE and OSE (n=2)
HGSC vs. FTE	123,586	40,298	50,322	20,850	3,019	2,649	714	530	325
HGSC vs. OSE	161,561	47,816	62,991	23,550	4,061	4,580	1,543	913	510
Fold Difference³	1.3 ^(****)	1.2 ^(****)	1.3 ^(****)	1.1 ^(****)	1.3 ^(****)	1.7 ^(****)	2.2 ^(****)	1.7 ^(****)	1.6 ^(****)
Bowtell 450K, HGSC (n=78), Patient-Matched FTE and OSE (n=5)
HGSC vs. FTE	21,646	3,130	7,209	1,732	455	1,085	460	379	190
HGSC vs. OSE	39,439	5,461	12,158	2,711	991	1,879	882	641	302
Fold Difference³	1.8 ^(****)	1.7 ^(****)	1.7 ^(****)	1.6 ^(****)	2.2 ^(****)	1.7 ^(****)	1.9 ^(****)	1.7 ^(****)	1.6 ^(****)
TCGA 27K, HGSC (n=550), Patient-Matched FTE and OSE (n=5)
HGSC vs. FTE	1,280	134	523	55	9	N/A	N/A	N/A	N/A
HGSC vs. OSE	1,592	180	583	77	8	N/A	N/A	N/A	N/A
Fold Difference³	1.2 ^(****)	1.3 ^(**)	1.1 (ns)	1.4 (ns)	0.9 (ns)	N/A	N/A	N/A	N/A

FDR < 0.05, methylation difference ≥ 25%

FDR < 0.05, mean methylation difference ≥ 25%, ≥ 3 CpGs per region

Increase in HGSC vs. OSE as compared to HGSC vs. FTE

⁴

Chi-square p-value:

^(****)

<0.0001;

^(***)

<0.001,

^(**)

<0.01,

^(*)

<0.05

N/A: Insufficient coverage to conduct DMR measurements

ns: not significant