Table 2. Differentially hypomethylated genes between chromophobe RCC and renal oncocytoma samples.
| Gene Symbol | Cancer | Target ID | Relation to Gene | CpG region | Meth in Onco (B value < 0.25) | Meth in Chromo (B value < 0.5) | Normal Kidney | Corrected P Value | Chr |
|---|---|---|---|---|---|---|---|---|---|
| ITGB5 |
Oc |
cg00171092 |
Body |
Open Sea |
7/21 (33.3%) |
0/20 (0.0%) |
0/4 |
2.73629E-08 |
3 |
| GTF2IRD1; GTF2IRD1 |
Ch |
cg20448594 |
Body; Body |
Open Sea |
0/21 (0.0%) |
7/20 (35.0%) |
0/4 |
2.9116E-08 |
7 |
| PABPC4L |
Ch |
cg15867829 |
3′UTR |
Open Sea |
0/21 (0.0%) |
9//20 (45.0%) |
0/4 |
1.19954E-07 |
4 |
| PRKCE |
Ch |
cg04035064 |
Body |
Open Sea |
0/21 (0.0%) |
7/20 (35.0%) |
0/4 |
2.96639E-07 |
2 |
| CTDSPL; CTDSPL |
Oc |
cg15428496 |
Body; Body |
Open Sea |
7/21 (33.3%) |
0/20 (0.0%) |
0/4 |
3.0075E-07 |
3 |
| PLCL1 |
Oc |
cg02833180 |
Body |
Open Sea |
10/21 (47.6%) |
0/20 (0.0%) |
0/4 |
3.16345E-07 |
2 |
| CD44; CD44; CD44; CD44; CD44 |
Ch |
cg25096745 |
Body; Body; Body; Body; Body |
Open Sea |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
3.33221E-07 |
11 |
| TSPAN5 |
Oc |
cg03234557 |
Body |
Open Sea |
9/21 (42.8%) |
0/20 (0.0%) |
0/4 |
8.95274E-07 |
4 |
| SCG3; SCG3 |
Ch |
cg08884979 |
3′UTR; 3′UTR |
Open Sea |
0/21 (0.0%) |
11/20 (55.0%) |
0/4 |
4.80724E-06 |
15 |
| CSRP2BP; CSRP2BP |
Ch |
cg14329508 |
3′UTR; Body |
Open Sea |
0/21 (0.0%) |
7/20 (35.0%) |
0/4 |
1.54058E-05 |
20 |
| MIR141 |
Ch |
cg19794481 |
TSS200 |
Open Sea |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
1.58595E-05 |
12 |
| SLC44A3; SLC44A3 |
Ch |
cg22608160 |
Body; Body |
Open Sea |
0/21 (0.0%) |
7/20 (35.0%) |
0/4 |
3.38953E-05 |
1 |
| MICAL2 |
Oc |
cg00286773 |
Body |
Open Sea |
7/21 (33.3%) |
0/20 (0.0%) |
0/4 |
3.57384E-05 |
11 |
| PHTF2; PHTF2 |
Ch |
cg27457191 |
5′UTR; 5′UTR |
S.Shore |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
4.13981E-05 |
7 |
| RORA |
Ch |
cg03952578 |
Body |
Open Sea |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
4.68702E-05 |
15 |
| ARID1B; ARID1B; ARID1B |
Ch |
cg04924555 |
Body; Body; Body |
Open Sea |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
5.74559E-05 |
6 |
| LRIG1 |
Ch |
cg11198596 |
Body |
N.Shelf |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
5.78502E-05 |
3 |
| COL18A1; COL18A1; COL18A1 |
Ch |
cg25049844 |
3′UTR; 3′UTR; 3′UTR |
S.Shore |
0/21 (0.0%) |
7/20 (35.0%) |
0/4 |
9.73444E-05 |
21 |
| ITPRIP |
Ch |
cg16301004 |
5′UTR |
Open Sea |
0/21 (0.0%) |
7/20 (35.0%) |
0/4 |
9.8974E-05 |
10 |
| RAB3B |
Ch |
cg00714309 |
Body |
Open Sea |
0/21 (0.0%) |
8/20 (40.0%) |
0/4 |
0.0001 |
1 |
| MIR141 |
Ch |
cg02624246 |
Body |
Open Sea |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0001 |
12 |
| GBE1 |
Ch |
cg05514531 |
Body |
Open Sea |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0002 |
3 |
| SLC27A3 |
Ch |
cg15930240 |
Body |
S.Shore |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0002 |
1 |
| MKLN1; MKLN1 |
Ch |
cg02776119 |
Body; Body |
S.Shelf |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0002 |
7 |
| C14orf169; HEATR4 |
Ch |
cg02935494 |
TSS1500; Body |
N.Shore |
0/21 (0.0%) |
9//20 (45.0%) |
0/4 |
0.0002 |
14 |
| VPS13B; VPS13B |
Ch |
cg18520777 |
Body; Body |
Open Sea |
0/21 (0.0%) |
7/20 (35.0%) |
0/4 |
0.0002 |
8 |
| MYO3B; MYO3B; MYO3B |
Ch |
cg16066505 |
Body; Body; Body |
Open Sea |
0/21 (0.0%) |
8/20 (40.0%) |
0/4 |
0.0002 |
2 |
| DSG1 |
Ch |
cg07703790 |
TSS1500 |
Open Sea |
0/21 (0.0%) |
8/20 (40.0%) |
0/4 |
0.0005 |
18 |
| RNPEP |
Ch |
cg16047663 |
3′UTR |
Open Sea |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0005 |
1 |
| OR2B2 |
Ch |
cg19173375 |
TSS200 |
Open Sea |
0/21 (0.0%) |
8/20 (40.0%) |
0/4 |
0.0006 |
6 |
| NEK11; NEK11; NEK11 |
Ch |
cg06239593 |
Body; Body; Body |
S.Shelf |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0009 |
3 |
| NRP2; NRP2; NRP2; NRP2; NRP2 |
Ch |
cg14157435 |
Body; Body; Body; Body; Body |
Open Sea |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0012 |
2 |
| PLEKHG7; PLEKHG7 |
Ch |
cg05916700 |
1stExon; 5′UTR |
Open Sea |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0021 |
12 |
| CDKAL1 |
Ch |
cg00682125 |
Body |
Open Sea |
0/21 (0.0%) |
7/20 (35.0%) |
0/4 |
0.0031 |
6 |
| HOXC4; HOXC6; HOXC5 |
Ch |
cg18040878 |
TSS1500; TSS1500; TSS1500 |
S.Shore |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0046 |
12 |
| ACTN2 |
Ch |
cg18381395 |
Body |
Open Sea |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0050 |
1 |
| C6orf195 |
Ch |
cg01285783 |
Body |
Open Sea |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0055 |
6 |
| MGRN1; MGRN1; MGRN1; MGRN1 |
Ch |
cg02074956 |
Body; Body; Body; Body |
N.Shore |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0090 |
16 |
| SVIL; SVIL |
Ch |
cg04678141 |
TSS200; 5′UTR |
Open Sea |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0149 |
10 |
| CAST; CAST; CAST; CAST; CAST |
Ch |
cg01741836 |
TSS1500; TSS1500; TSS1500; TSS1500; TSS1500 |
N.Shore |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0169 |
5 |
| NDUFAF1 |
Ch |
cg13897914 |
TSS1500 |
S.Shore |
0/21 (0.0%) |
6/20 (30.%) |
0/4 |
0.0234 |
15 |
| ACCN4; ACCN4 | Ch | cg08614334 | Body; Body | S.Shelf | 0/21 (0.0%) | 6/20 (30.%) | 0/4 | 0.0275 | 2 |
Oc, renal oncocytoma; Ch, chromophobe RCC; Chr, chromosome.