Table 2.
Recurrently altered regions in 48 breast cancer specimens
|
RARs |
Chr |
Map position |
Size |
Cytoband |
P- value |
Freq |
Freq |
Freq |
Event* |
Cancer-related genes |
|---|---|---|---|---|---|---|---|---|---|---|
| (Mp) | (Mp) | (Total) | (S-I) | (S-II) | ||||||
| RAR-G1 |
1 |
143,83-144,30 |
0.47 |
q21.1 |
0.04 |
48% |
36% |
51% |
Earlier |
TXNIP |
| RAR-G2 |
1 |
148,12-150,25 |
2.13 |
q21.2-q21.3 |
0.01 |
50% |
36% |
54% |
Earlier |
MCL1, CTSK, ARNT, SETDB1, SELENBP1, S100A10 |
| RAR-G3 |
1 |
150,75-155,11 |
4.36 |
q21.3-q23.1 |
0.04 |
48% |
36% |
51% |
Earlier |
CREB3L4, TPM3, HAX1, IL6R, PYGO2, SHC1, CKS1B, NES, ADAM15, EFNA1, MUC1, YY1AP1, ARHGEF2, RAB25, CCT3, CRABP2, HDGF, PRCC |
| RAR-G4 |
1 |
158,48-159,47 |
0.99 |
q23.2-q23.3 |
0.04 |
48% |
45% |
49% |
Earlier |
F11R, USF1 |
| RAR-G5 |
1 |
226,10-226,90 |
0.80 |
q24.13 |
0.04 |
48% |
45% |
49% |
Earlier |
WNT9A, WNT3A |
| RAR-G6 |
6 |
64,05-64,75 |
0.70 |
q12 |
0.00 |
38% |
45% |
35% |
Earlier |
- |
| RAR-G7 |
8 |
123,47-124,74 |
1.27 |
q24.13 |
0.02 |
50% |
36% |
54% |
Earlier |
FAM83A |
| RAR-G8 |
8 |
126,23-127,30 |
1.07 |
q24.13-q24.21 |
0.02 |
50% |
36% |
54% |
Earlier |
- |
| RAR-G9 |
8 |
140,69-143,86 |
3.17 |
q24.3 |
0.02 |
50% |
36% |
54% |
Earlier |
PTK2, PTP4A3, PSCA, LYNX1 |
| RAR-G10 |
8 |
144,34-146,27 |
1.93 |
q24.3 |
0.02 |
50% |
36% |
54% |
Earlier |
SCRIB, HSF1, SLCA4 |
| RAR-G11 |
16 |
0-3,22 |
3.22 |
p13.3 |
0.05 |
38% |
27% |
41% |
UC |
MPG, AXIN1, RHOT2, STUB1, MSLN, CACNA1H, IGFALS, GFER, TSC2, PDPK1, MMP25 |
| RAR-G12 |
16 |
28,32-31,19 |
2.87 |
p11.2 |
0.05 |
40% |
36% |
41% |
Earlier |
NUPR1, SULT1A2, SULT1A1, MVP, MAPK3, FUS, PYCARD |
| RAR-G13 |
17 |
34,97-35,30 |
0.33 |
q12 |
0.03 |
38% |
36% |
38% |
Earlier |
PPP1R1B, PNMT, PERLD1, ERBB2, GRB7 |
| RAR-G14 |
17 |
70,76-71,21 |
0.45 |
q25.1 |
0.03 |
38% |
9% |
46% |
Later |
GRB2 |
| RAR-G15 |
17 |
76,90-78,77 |
1.87 |
q25.3 |
0.03 |
38% |
9% |
46% |
Later |
HGS, SIRT7, RAC3, FASN, CSNK1D |
| RAR-G16 |
20 |
43,84-44,15 |
0.31 |
q13.12 |
0.00 |
33% |
18% |
38% |
UC |
UBE2C, MMP9 |
| RAR-G17 |
20 |
60,17-61,61 |
1.44 |
q13.33 |
0.04 |
31% |
18% |
35% |
UC |
ADRM1, LAMA5, NTSR1, BIRC7, EEF1A2 |
| RAR-G18 |
20 |
61,67-62,44 |
0.77 |
q13.33 |
0.04 |
31% |
27% |
32% |
UC* |
TNFRSF6B |
| RAR-L1 |
8 |
8,14-14,07 |
5.93 |
p23.1-p22 |
0.00 |
50% |
36% |
54% |
Earlier |
CLDN23, PINX1, GATA4, NEIL2, FDFT1, CTSB, DLC1 |
| RAR-L2 |
8 |
15,66-17,12 |
1.44 |
p22 |
0.02 |
48% |
36% |
51% |
Earlier |
TUSC3, MSR1, FGF20 |
| RAR-L3 |
8 |
24,01-26,72 |
2.71 |
p21.2 |
0.02 |
48% |
36% |
51% |
Earlier |
ADAM28, GNRH1, PPP2R2A, ADRA1A |
| RAR-L4 |
16 |
75,79-80,74 |
4.95 |
q23.1-q23.3 |
0.00 |
33% |
27% |
35% |
UC |
WWOX, DYNLRB2, PLCG2, HSD17B2 |
| RAR-L5 | 17 | 10,54-14,10 | 3.56 | p13.1-p12 | 0.04 | 44% | 27% | 49% | UC | MAP2K4, ELAC2 |
RAR-G: RAR-gain, RAR-L: RAR-loss, Chr: chromosome, Freq: frequency, S-I: stage I, S-II: stage II.
Cancer-related genes: Among all RefSeq genes located in the RARs, the genes which can be searched by the keyword “Cancer/Tumor” from NCBI Gene (http://www.ncbi.nlm.nih.gov/gene) are listed as “cancer-related genes”.
*Earlier: RARs detected commonly in both stage I and II groups, Later: RARs appearing in <10% of stage I samples, but in >40% of stage II samples, UC: unclassified.