Table 1. Differentially hypermethylated genes between chromophobe RCC and renal oncocytoma samples.
| Gene Symbol | Cancer | Target ID | Relation to Gene | CpG region | Meth in Onco (B value > 0.5) | Meth in Chromo (B value > 0.5) | Normal Kidney | Corrected P Value | Chr |
|---|---|---|---|---|---|---|---|---|---|
| ALCAM |
Oc |
cg05645404 |
Body |
N_Shore |
12/21 (57.1%) |
0/20 (0.0%) |
0/4 |
4.20E-05 |
3 |
| TFAP2B |
Ch |
cg05437823 |
3′UTR |
Island |
0/21 (0.0%) |
8/20 (40.0%) |
0/4 |
0.0019 |
6 |
| TRPC4AP; TRPC4AP |
Oc |
cg01154966 |
TSS1500; TSS1500 |
Island |
7/21 (33.3%) |
0/20 (0.0%) |
0/4 |
0.0034 |
20 |
| HOXA9 |
Ch |
cg03217995 |
Body |
N_Shore |
0/21 (0.0%) |
8/20 (40.0%) |
0/4 |
0.0036 |
7 |
| DBC1 |
Ch |
cg03625109 |
TSS1500 |
Island |
0/21 (0.0%) |
7/20 (35.0%) |
0/4 |
0.0038 |
9 |
| CACNG7 |
Ch |
cg21477176 |
3′UTR |
S_Shore |
1/21 (4.8%) |
6/20 (30.%) |
0/4 |
0.0043 |
19 |
| NKX6–2 |
Ch |
cg11174855 |
3′UTR |
Island |
1/21 (4.8%) |
7/20 (35.0%) |
0/4 |
0.0043 |
10 |
| NPHP4 |
Ch |
cg20383686 |
TSS200 |
Island |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0048 |
1 |
| AMH |
Ch |
cg05345154 |
Body |
Island |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0065 |
19 |
| DPP4 |
Ch |
cg19350270 |
Body |
N_Shore |
0/21 (0.0%) |
7/20 (35.0%) |
0/4 |
0.0066 |
2 |
| SOX2OT |
Ch |
cg24513480 |
Body |
N_Shelf |
1/21 (4.8%) |
8/20 (40.0%) |
0/4 |
0.0072 |
3 |
| EN2 |
Ch |
cg12034383 |
TSS1500 |
Island |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0073 |
7 |
| SPG20; SPG20; SPG20; SPG20 |
Ch |
cg10558887 |
5′UTR; 5′UTR; 5′UTR; 5′UTR |
N_Shore |
0/21 (0.0%) |
7/20 (35.0%) |
0/4 |
0.0075 |
13 |
| RALYL; RALYL; RALYL; RALYL; RALYL |
Ch |
cg22403811 |
5′UTR; TSS1500; 5′UTR; 5′UTR; 1stExon |
N_Shore |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0096 |
8 |
| JSRP1 |
Ch |
cg04887494 |
Body |
Island |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0098 |
19 |
| PAX3; PAX3; PAX3; PAX3; PAX3; PAX3; PAX3; PAX3; CCDC140 |
Ch |
cg13767755 |
Body; Body; Body; Body; Body; Body; Body; Body; TSS200 |
N_Shore |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0184 |
2 |
| PITX1 |
Ch |
cg00396667 |
3′UTR |
Island |
1/21 (4.8%) |
6/20 (30.%) |
0/4 |
0.0188 |
5 |
| SH3PXD2A |
Ch |
cg18735015 |
Body |
Island |
1/21 (4.8%) |
6/20 (30.%) |
0/4 |
0.0213 |
10 |
| SIX2 |
Ch |
cg24887265 |
Body |
N_Shore |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0219 |
2 |
| TOX2; TOX2; TOX2 |
Ch |
cg10900455 |
5′UTR; Body; 5′UTR |
Island |
1/21 (4.8%) |
6/20 (30.%) |
0/4 |
0.0224 |
20 |
| HAPLN1 |
Ch |
cg12199221 |
TSS200 |
N_Shore |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0226 |
5 |
| IRX6 |
Ch |
cg01064265 |
Body |
Island |
1/21 (4.8%) |
7/20 (35.0%) |
0/4 |
0.0230 |
16 |
| NKAPL |
Ch |
cg17384889 |
TSS200 |
Island |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0236 |
6 |
| LBX1 |
Ch |
cg03053579 |
Body |
Island |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0237 |
10 |
| BAG2 |
Ch |
cg10230427 |
Body |
S_Shore |
1/21 (4.8%) |
7/20 (35.0%) |
0/4 |
0.0242 |
6 |
| MKX |
Ch |
cg26298409 |
Body |
Island |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0262 |
10 |
| SLITRK1 |
Ch |
cg16727923 |
1stExon |
Island |
1/21 (4.8%) |
7/20 (35.0%) |
0/4 |
0.0376 |
13 |
| BAG2 |
Ch |
cg27164797 |
Body |
S_Shore |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0401 |
6 |
| KRT27 |
Ch |
cg02399249 |
Body |
Island |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0421 |
17 |
| HHEX | Ch | cg09721427 | TSS1500 | Island | 0/21 (0.0%) | 6/20 (30.%) | 0/4 | 0.0476 | 10 |
Oc, renal oncocytoma; Ch, chromophobe RCC; Chr, chromosome.