Investigation of DNA damage response and apoptotic gene methylation pattern in sporadic breast tumors using high throughput quantitative DNA methylation analysis technology

Pal, Ranjana; Srivastava, Niloo; Chopra, Rupali; Gochhait, Sailesh; Gupta, Pawan; Prakash, Neeraj; Agarwal, Gaurav; Bamezai, Rameshwar NK

doi:10.1186/1476-4598-9-303

Molecular Cancer

Table 1 Wilcoxon signed rank test showing methylation status between breast tumor and adjacent normal tissue

From: Investigation of DNA damage response and apoptotic gene methylation pattern in sporadic breast tumors using high throughput quantitative DNA methylation analysis technology

SR. NO.	GENE CpG SITE; N = 81 NOR - TUM PAIRS	P^a	P^b	METHYLATION STATUS	LOCATION
1	DR4 18.19 (-35,-39)	0.010	0.041	Hypomethylation	Promoter
2	DR4 20.21 (-89,-93)	0.007	0.033	Hypomethylation	Promoter
3	DR4 23 (-111)	0.009	0.041	Hypomethylation	Promoter
4	DR4 24 (-137)	0.018	0.069	Hypomethylation	Promoter
5	DR5 11 (-149)	0.006	0.031	Hypermethylation	Promoter
6	DR5 27 (-363)	0.040	0.149	Hypermethylation	Promoter
7	DR5 28.29 (-374,-376)	0.0003	0.003	Hypermethylation	Promoter
8	DCR1 4.5.6 (-17,-12,-7)	0.0002	0.002	Hypermethylation	Promoter
9	DCR1 11 (+100)	0.0004	0.003	Hypermethylation	5'UTR
10	DCR1 12 (+110)	0.0003	0.002	Hypermethylation	5'UTR
11	DCR1 13.14.15 (+134,+139,+143)	0.0002	0.001	Hypermethylation	5'UTR
12	DCR1 16 (+154)	0.001	0.008	Hypermethylation	5'UTR
13	DCR1 17 (+166)	0.000008	0.0001	Hypermethylation	5'UTR
14	DCR1 18.19.20 (+183,+186,+189)	0.000001	0.00002	Hypermethylation	5'UTR
15	DCR1 22.23.24 (+231,+234,+237)	0.0001	0.001	Hypermethylation	Ex1 coding
16	DCR1 25.26.27 (+243,+246,+248)	0.0003	0.002	Hypermethylation	Ex1 coding
17	DCR1 32.33 (+306,+309)	0.00002	0.0002	Hypermethylation	Int 1-2
18	DCR1 34 (+327)	0.009	0.041	Hypermethylation	Int 1-2
19	DCR2 1 (+169)	0.0000007	0.00001	Hypermethylation	Ex1 coding
20	DCR2 2 (+166)	0.0000006	0.00001	Hypermethylation	Ex1 coding
21	DCR2 7.8 (+122,+118)	0.0000000007	0.00000005	Hypermethylation	Ex1 coding
22	DCR2 12.13 (+44,+38)	0.0000000003	0.00000004	Hypermethylation	5'UTR
23	DCR2 16 (+11)	0.0000001	0.000003	Hypermethylation	5'UTR
24	DCR2 17.18 (-14,-24)	0.0000002	0.000006	Hypermethylation	Promoter
25	DCR2 19 (-37)	0.0000003	0.000007	Hypermethylation	Promoter
26	DCR2 20 (-48)	0.000000002	0.00000006	Hypermethylation	Promoter
27	DCR2 24 (-178)	0.0000000008	0.00000004	Hypermethylation	Promoter
28	CASP8 2.3 (+532,+537)	0.000009	0.0001	Hypermethylation	Int 1-2
29	CASP8 6 (+635)	0.048	0.176	Hypomethylation	Int 1-3
30	FLIP 18.19.20.21 (+319,+326,+328,+332)	0.001	0.008	Hypomethylation	Int 1-4
31	CYCS 17.18 (+59,+62)	0.001	0.008	Hypermethylation	5'UTR
32	CYCS 19.20.21 (+89,+93,+99)	0.003	0.016	Hypermethylation	5'UTR
33	TP53 6 (-16)	0.017	0.067	Hypermethylation	Promoter
34	BRCA1 16 (-251)	0.005	0.025	Hypermethylation	Promoter
35	BRCA1 17 (-234)	0.016	0.065	Hypermethylation	Promoter
36	BRCA2 32.33 (-6,-8)	0.008	0.038	Hypermethylation	Promoter
37	RNF8 9.10.11.12 (-69,-67,-63,-58)	0.0001	0.001	Hypomethylation	Promoter
38	H2AX 3 (-326)	0.002	0.013	Hypermethylation	Promoter

CpG site positions are mentioned with respect to the transcription start site. P^a value for Wilcoxon signed-rank test between breast tumor and adjacent normal tissue. P^b value for Wilcoxon signed-rank test between breast tumor and adjacent normal tissue after Benjamini Hochberg correction - significant values shown in bold.

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ISSN: 1476-4598

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