Epigenetic Alterations of Chromosome 3 Revealed by NotI-Microarrays in Clear Cell Renal Cell Carcinoma

Table 2

List of chromosome 3 NotI-sites with methylation/deletion frequencies more than 17% in clear cell renal cell carcinoma.

Number	NotI-site*	Gene**	Locus	Methylation/deletion,; frequency %
1	NL1-CJ4R (C)	NKIRAS1/RPL15	3p24.2	57 (13/23)
2	NL6-FJ5R (C)	LRRN1	3p26.2	43 (10/23)
3	NL3-CA11RS	LRRC3B	3p24	43 (10/23)
4	NLJ-003RD	RBSP3 (CTDSPL)	3p21.3	35 (8/23)
5	NL3003R (U)	GORASP1/TTC21A	3p22–p21.33	35 (8/23)
6	NRLA404R (U)	VHL	3p25.3	30 (7/23)
7	NR1-XM13C	IQSEC1	3p25.2	26 (6/23)
8	NL1-BA6R	FOXP1	3p14.1	26 (6/23)
9	NR1-AN24RS	ABHD5/C3orf77	3p21	22 (5/23)
10	NL3A006R (D)	NBEAL2	3p21.31	22 (5/23)
11	NL3A001R (D)	GNAI2	3p21.31	22 (5/23)
12	NR1-NC7RS	PPM1M	3p21.2	22 (5/23)
13	NR1-NJ9R (C)	PRICKLE2	3p14.1	22 (5/23)
14	HSJ4-AB7R (C)	RPL32/IQSEC1	3p25.2	17 (4/23)
15	NL4-DP2RS	FGD5	3p25.1	17 (4/23)
16	NL4-AP18R (C)	PLCL2	3p24.3	17 (4/23)
17	NL4-BC8R (C)	ALDH1L1	3q21.3	17 (4/23)
18	NL1A079R (D)	EPHB1	3q21–q23	17 (4/23)
19	NR1-PD1R	ZIC4	3q24	17 (4/23)

Note: ∗sequences are available at http://www.ncbi.nlm.nih.gov/nuccore/;**slash between gene names indicates that these genes have common NotI-site.