Table 4. Genes with CNAs showing significant association with tumors arising in specific colon sites by χ2 test.
| GENE SYMBOL | p-value | Anatomic Site | ||||||
|---|---|---|---|---|---|---|---|---|
| Ascending colon (n = 7) |
Cecum (n = 6) |
Descending colon (n = 7) |
Hepatic Flexure (n = 8) |
Splenic Flexure (n = 5) | Transverse colon (n = 4) |
|||
|
Genes with CN LOSS |
MBD1 | 0.0005 | Obs* = 0 Exp**= 0.75 (10.7%) |
Obs = 0 Exp = 0.64 (10.7%) |
Obs = 6 (85.7%) Exp = 0.75 (10.7%) |
Obs = 1 (12.5%) Exp = 0.86 (10.7%) |
Obs = 3 (60%) Exp = 0.54 (10.7%) |
Obs = 0 Exp = 0.43 (10.7%) |
| PDGFB | 0.0008 | Obs = 0 Exp = 0.56 (8%) |
Obs = 0 Exp = 0.48 (8%) |
Obs = 0 Exp = 0.56 (8%) |
Obs = 0 Exp = 0.64 (8%) |
Obs = 3 (60%) Exp = 0.4 (8%) |
Obs = 0 Exp = 0.32 (8%) |
|
| DCC | 0.002 | Obs = 1 (14.28%) Exp = 2.45 (35%) |
Obs = 1 (16.66%) Exp = 2.1 (35%) |
Obs = 6 (85.71%) Exp = 2.45 (35%) |
Obs = 1 (12.5%) Exp = 2.81 (35%) |
Obs = 4 (80%) Exp = 1.75 (35%) |
Obs = 0 Exp = 1.4 (35%) |
|
| WRN | 0.007 | Obs = 0 Exp = 0.94 (13%) |
Obs = 0 Exp = 0.81 (13%) |
Obs = 4 (57.14%) Exp = 0.94 (13%) |
Obs = 0 Exp = 1.08 (13%) |
Obs = 0 Exp = 0.67 (13%) |
Obs = 1 (25%) Exp = 0.54 (13%) |
|
| NOTCH2 | 0.007 | Obs = 0 Exp = 0.75 (11%) |
Obs = 1 (16.66%) Exp = 0.64 (11%) |
Obs = 0 Exp = 0.75 (11%) |
Obs = 0 Exp = 0.86 (11%) |
Obs = 3 (60%) Exp = 0.64 (11%) |
Obs = 0 Exp = 0.43 (11%) |
|
| SMAD4 | 0.01 | Obs = 0 Exp = 0.56 (8%) |
Obs = 0 Exp = 0.48 (8%) |
Obs = 3 (42.85%) Exp = 0.56 (8%) |
Obs = 0 Exp = 0.64 (8%) |
Obs = 0 Exp = 0.4 (8%) |
Obs = 0 Exp = 0.32 (8%) |
|
| RNF213 | 0.03 | Obs = 1 (14.28%) Exp = 1.7 (24%) |
Obs = 0 Exp = 1.45 (24%) |
Obs = 5 (71.42) Exp = 1.7 (24%) |
Obs = 2 (25%) Exp = 1.94 (24%) |
Obs = 0 Exp = 1.21 (24%) |
Obs = 1 (25%) Exp = 0.97 (24%) |
|
| APC | 0.03 | Obs = 0 Exp = 0.94 (13 %) |
Obs = 0 Exp = 0.81 (13 %) |
Obs = 3 (42.85%) Exp = 0.94 (13 %) |
Obs = 0 Exp = 1.08 (13 %) |
Obs = 2 (40%) Exp = 0.67 (13 %) |
Obs = 0 Exp = 0.54 (13 %) |
|
| PIK3R1 | 0.03 | Obs = 0 Exp = 0.94 (13%) |
Obs = 0 Exp = 0.81 (13 %) |
Obs = 3 (42.85%) Exp = 0.94 (13 %) |
Obs = 0 Exp = 1.08 (13 %) |
Obs = 2 (40%) Exp = 0.67 (13 %) |
Obs = 0 Exp = 0.54 (13 %) |
|
| RET | 0.04 | Obs = 0 Exp = 1.13 (16%) |
Obs = 0 Exp = 0.97 (16%) |
Obs = 2 (28.57%) Exp = 1.13 (16%) |
Obs = 1 (12.5%) Exp = 1.29 (16%) |
Obs = 3 (60%) Exp = 0.81 (16%) |
Obs = 0 Exp = 0.64 (16%) |
|
| PKHD1 | 0.04 | Obs = 0 Exp = 1.13 (16%) |
Obs = 0 Exp = 0.97 (16%) |
Obs = 2 (28.57%) Exp = 1.13 (16%) |
Obs = 1 (12.5%) Exp = 1.29 (16%) |
Obs = 3 (60%) Exp = 0.81 (16%) |
Obs = 0 Exp = 0.64 (16%) |
|
| Genes with CN GAIN | RB1 | 0.01 | Obs = 0 Exp = 0.56 (8%) |
Obs = 0 Exp = 0.48 (8%) |
Obs = 3 (42.85%) Exp = 0.56 (8%) |
Obs = 0 Exp = 0.64 (8%) |
Obs = 0 Exp = 0.4 (8%) |
Obs = 0 Exp = 0.32 (8%) |
| BCL2L1 | 0.01 | Obs = 0 Exp = 0.37 (5%) |
Obs = 0 Exp = 0.32 (5%) |
Obs = 0 Exp = 0.37 (5%) |
Obs = 0 Exp = 0.43 (5%) |
Obs = 2 (40%) Exp = 0.27 (5%) |
Obs = 0 Exp = 0.21 (5%) |
|
| UBR5 | 0.02 | Obs = 0 Exp = 2.45 (35%) |
Obs = 0 Exp = 2.1 (5%) |
Obs = 4 (57.14%) Exp = 2.45 (5%) |
Obs = 3 (37.5%) Exp = 2.81 (5%) |
Obs = 4 (80%) Exp = 1.75 (5%) |
Obs = 2 (50%) Exp = 1.4 (5%) |
|
*Obs: Observed CC patients showing CNAs.
**Exp: Expected CC patients showing CNAs.