This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 29 focal events and 11 clinical features across 505 patients, 20 significant findings detected with Q value < 0.25.
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amp_3q26.32 cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'PATHOLOGY.M.STAGE'.
-
del_3p25.3 cnv correlated to 'RACE'.
-
del_3p11.2 cnv correlated to 'GENDER'.
-
del_3q11.2 cnv correlated to 'GENDER'.
-
del_4q34.3 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
-
del_9p23 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
-
del_9p21.3 cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.M.STAGE', and 'GENDER'.
-
del_10q23.31 cnv correlated to 'PATHOLOGY.T.STAGE'.
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del_13q13.3 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
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del_14q31.1 cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'PATHOLOGY.N.STAGE'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 29 focal events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 20 significant findings detected.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
NUMBERPACKYEARSSMOKED | RACE | ETHNICITY | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
del 9p21 3 | 154 (30%) | 351 |
0.068 (1.00) |
0.0388 (1.00) |
1e-05 (0.00296) |
1e-05 (0.00296) |
0.0293 (1.00) |
5e-05 (0.0143) |
0.000554 (0.155) |
0.824 (1.00) |
0.0678 (1.00) |
1 (1.00) |
|
amp 3q26 32 | 86 (17%) | 419 |
0.141 (1.00) |
0.979 (1.00) |
0.00017 (0.0483) |
0.00043 (0.12) |
0.0582 (1.00) |
0.00082 (0.228) |
0.711 (1.00) |
0.465 (1.00) |
0.392 (1.00) |
1 (1.00) |
|
del 14q31 1 | 221 (44%) | 284 |
0.0624 (1.00) |
0.0751 (1.00) |
3e-05 (0.00867) |
0.00025 (0.0705) |
0.000115 (0.0326) |
0.00229 (0.623) |
0.222 (1.00) |
0.126 (1.00) |
0.465 (1.00) |
0.0795 (1.00) |
0.833 (1.00) |
del 4q34 3 | 78 (15%) | 427 |
0.562 (1.00) |
0.559 (1.00) |
1e-05 (0.00296) |
1e-05 (0.00296) |
0.726 (1.00) |
0.0394 (1.00) |
0.44 (1.00) |
0.542 (1.00) |
0.291 (1.00) |
0.571 (1.00) |
|
del 9p23 | 146 (29%) | 359 |
0.16 (1.00) |
0.0212 (1.00) |
1e-05 (0.00296) |
3e-05 (0.00867) |
0.0997 (1.00) |
0.00091 (0.252) |
0.00144 (0.398) |
0.824 (1.00) |
0.234 (1.00) |
0.817 (1.00) |
|
del 13q13 3 | 79 (16%) | 426 |
0.00573 (1.00) |
0.732 (1.00) |
0.00011 (0.0315) |
1e-05 (0.00296) |
0.2 (1.00) |
0.0917 (1.00) |
0.898 (1.00) |
0.752 (1.00) |
0.149 (1.00) |
0.557 (1.00) |
|
del 3p25 3 | 445 (88%) | 60 |
0.226 (1.00) |
0.382 (1.00) |
0.062 (1.00) |
0.00185 (0.509) |
1 (1.00) |
0.885 (1.00) |
0.568 (1.00) |
0.202 (1.00) |
0.00022 (0.0623) |
0.753 (1.00) |
|
del 3p11 2 | 237 (47%) | 268 |
0.218 (1.00) |
0.113 (1.00) |
0.655 (1.00) |
0.605 (1.00) |
1 (1.00) |
0.129 (1.00) |
1.12e-05 (0.00326) |
0.788 (1.00) |
1 (1.00) |
0.623 (1.00) |
0.833 (1.00) |
del 3q11 2 | 156 (31%) | 349 |
0.196 (1.00) |
0.0352 (1.00) |
0.475 (1.00) |
0.0954 (1.00) |
0.598 (1.00) |
0.243 (1.00) |
3.68e-07 (0.000109) |
0.409 (1.00) |
1 (1.00) |
0.262 (1.00) |
0.245 (1.00) |
del 10q23 31 | 94 (19%) | 411 |
0.155 (1.00) |
0.579 (1.00) |
0.0135 (1.00) |
0.00035 (0.0983) |
1 (1.00) |
0.28 (1.00) |
0.0559 (1.00) |
0.678 (1.00) |
0.363 (1.00) |
0.408 (1.00) |
|
amp 1q24 1 | 61 (12%) | 444 |
0.199 (1.00) |
0.0976 (1.00) |
0.282 (1.00) |
0.196 (1.00) |
0.0815 (1.00) |
0.267 (1.00) |
0.775 (1.00) |
0.7 (1.00) |
0.916 (1.00) |
0.508 (1.00) |
|
amp 1q32 1 | 61 (12%) | 444 |
0.22 (1.00) |
0.0267 (1.00) |
0.193 (1.00) |
0.17 (1.00) |
0.712 (1.00) |
0.417 (1.00) |
0.775 (1.00) |
0.7 (1.00) |
0.916 (1.00) |
0.184 (1.00) |
|
amp 4q32 1 | 16 (3%) | 489 |
0.0445 (1.00) |
0.298 (1.00) |
0.664 (1.00) |
0.396 (1.00) |
0.571 (1.00) |
0.796 (1.00) |
0.596 (1.00) |
0.0908 (1.00) |
1 (1.00) |
1 (1.00) |
|
amp 5q35 1 | 321 (64%) | 184 |
0.0519 (1.00) |
0.134 (1.00) |
0.676 (1.00) |
0.384 (1.00) |
0.309 (1.00) |
0.444 (1.00) |
0.122 (1.00) |
0.618 (1.00) |
0.174 (1.00) |
0.00826 (1.00) |
0.829 (1.00) |
amp 7q36 3 | 170 (34%) | 335 |
0.397 (1.00) |
0.719 (1.00) |
0.0183 (1.00) |
0.0588 (1.00) |
0.444 (1.00) |
0.00745 (1.00) |
0.0232 (1.00) |
0.151 (1.00) |
0.0859 (1.00) |
0.169 (1.00) |
|
amp 8q24 22 | 77 (15%) | 428 |
0.0638 (1.00) |
0.00767 (1.00) |
0.00337 (0.913) |
0.00216 (0.59) |
0.738 (1.00) |
0.104 (1.00) |
0.121 (1.00) |
0.84 (1.00) |
0.374 (1.00) |
0.223 (1.00) |
|
amp 10p14 | 20 (4%) | 485 |
0.994 (1.00) |
0.0426 (1.00) |
0.403 (1.00) |
0.0323 (1.00) |
0.213 (1.00) |
0.681 (1.00) |
0.812 (1.00) |
0.222 (1.00) |
0.559 (1.00) |
0.605 (1.00) |
|
amp xp22 2 | 30 (6%) | 475 |
0.299 (1.00) |
0.797 (1.00) |
0.0573 (1.00) |
0.105 (1.00) |
1 (1.00) |
0.197 (1.00) |
0.846 (1.00) |
0.976 (1.00) |
0.0444 (1.00) |
0.611 (1.00) |
|
amp xp11 4 | 32 (6%) | 473 |
0.365 (1.00) |
0.954 (1.00) |
0.0447 (1.00) |
0.127 (1.00) |
1 (1.00) |
0.0685 (1.00) |
1 (1.00) |
0.976 (1.00) |
0.0907 (1.00) |
0.629 (1.00) |
|
amp xq11 2 | 28 (6%) | 477 |
0.562 (1.00) |
0.302 (1.00) |
0.429 (1.00) |
0.449 (1.00) |
1 (1.00) |
0.278 (1.00) |
1 (1.00) |
0.976 (1.00) |
0.0976 (1.00) |
0.611 (1.00) |
|
amp xq28 | 35 (7%) | 470 |
0.852 (1.00) |
0.445 (1.00) |
0.556 (1.00) |
0.699 (1.00) |
1 (1.00) |
0.0732 (1.00) |
0.855 (1.00) |
0.976 (1.00) |
1 (1.00) |
0.383 (1.00) |
|
del 1p36 23 | 101 (20%) | 404 |
0.0198 (1.00) |
0.11 (1.00) |
0.369 (1.00) |
0.105 (1.00) |
1 (1.00) |
0.382 (1.00) |
0.132 (1.00) |
0.721 (1.00) |
0.732 (1.00) |
0.197 (1.00) |
|
del 1p31 1 | 75 (15%) | 430 |
0.16 (1.00) |
0.135 (1.00) |
0.659 (1.00) |
0.0399 (1.00) |
0.492 (1.00) |
0.544 (1.00) |
0.0267 (1.00) |
0.721 (1.00) |
0.409 (1.00) |
0.0752 (1.00) |
|
del 1q43 | 40 (8%) | 465 |
0.179 (1.00) |
0.706 (1.00) |
1 (1.00) |
0.162 (1.00) |
1 (1.00) |
0.838 (1.00) |
1 (1.00) |
1 (1.00) |
0.74 (1.00) |
0.479 (1.00) |
|
del 2q37 3 | 50 (10%) | 455 |
0.119 (1.00) |
0.718 (1.00) |
0.496 (1.00) |
0.733 (1.00) |
1 (1.00) |
0.196 (1.00) |
0.163 (1.00) |
0.376 (1.00) |
0.491 (1.00) |
||
del 3p12 3 | 321 (64%) | 184 |
0.36 (1.00) |
0.738 (1.00) |
0.32 (1.00) |
0.0494 (1.00) |
0.617 (1.00) |
0.243 (1.00) |
0.00198 (0.543) |
0.377 (1.00) |
1 (1.00) |
0.169 (1.00) |
0.828 (1.00) |
del 6q26 | 147 (29%) | 358 |
0.654 (1.00) |
0.285 (1.00) |
0.382 (1.00) |
0.636 (1.00) |
0.00882 (1.00) |
0.776 (1.00) |
0.0182 (1.00) |
0.506 (1.00) |
0.0347 (1.00) |
0.196 (1.00) |
0.172 (1.00) |
del 6q26 | 147 (29%) | 358 |
0.385 (1.00) |
0.237 (1.00) |
0.38 (1.00) |
0.635 (1.00) |
0.00882 (1.00) |
0.779 (1.00) |
0.0102 (1.00) |
0.506 (1.00) |
0.0347 (1.00) |
0.196 (1.00) |
0.172 (1.00) |
del 8p23 2 | 151 (30%) | 354 |
0.182 (1.00) |
0.13 (1.00) |
0.122 (1.00) |
0.138 (1.00) |
1 (1.00) |
0.29 (1.00) |
0.31 (1.00) |
0.796 (1.00) |
0.291 (1.00) |
0.253 (1.00) |
0.017 (1.00) |
P value = 0.00017 (Fisher's exact test), Q value = 0.048
Table S1. Gene #3: 'amp_3q26.32' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 244 | 56 | 126 | 79 |
AMP PEAK 3(3Q26.32) MUTATED | 28 | 6 | 27 | 25 |
AMP PEAK 3(3Q26.32) WILD-TYPE | 216 | 50 | 99 | 54 |
Figure S1. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D3V3.png)
P value = 0.00043 (Fisher's exact test), Q value = 0.12
Table S2. Gene #3: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 250 | 67 | 177 | 11 |
AMP PEAK 3(3Q26.32) MUTATED | 29 | 8 | 45 | 4 |
AMP PEAK 3(3Q26.32) WILD-TYPE | 221 | 59 | 132 | 7 |
Figure S2. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D3V4.png)
P value = 0.00082 (Fisher's exact test), Q value = 0.23
Table S3. Gene #3: 'amp_3q26.32' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 417 | 78 | 9 |
AMP PEAK 3(3Q26.32) MUTATED | 59 | 25 | 2 |
AMP PEAK 3(3Q26.32) WILD-TYPE | 358 | 53 | 7 |
Figure S3. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'
![](D3V6.png)
P value = 0.00022 (Fisher's exact test), Q value = 0.062
Table S4. Gene #17: 'del_3p25.3' versus Clinical Feature #10: 'RACE'
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 33 | 457 |
DEL PEAK 5(3P25.3) MUTATED | 6 | 21 | 411 |
DEL PEAK 5(3P25.3) WILD-TYPE | 2 | 12 | 46 |
Figure S4. Get High-res Image Gene #17: 'del_3p25.3' versus Clinical Feature #10: 'RACE'
![](D17V10.png)
P value = 1.12e-05 (Fisher's exact test), Q value = 0.0033
Table S5. Gene #19: 'del_3p11.2' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 178 | 327 |
DEL PEAK 7(3P11.2) MUTATED | 60 | 177 |
DEL PEAK 7(3P11.2) WILD-TYPE | 118 | 150 |
Figure S5. Get High-res Image Gene #19: 'del_3p11.2' versus Clinical Feature #7: 'GENDER'
![](D19V7.png)
P value = 3.68e-07 (Fisher's exact test), Q value = 0.00011
Table S6. Gene #20: 'del_3q11.2' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 178 | 327 |
DEL PEAK 8(3Q11.2) MUTATED | 30 | 126 |
DEL PEAK 8(3Q11.2) WILD-TYPE | 148 | 201 |
Figure S6. Get High-res Image Gene #20: 'del_3q11.2' versus Clinical Feature #7: 'GENDER'
![](D20V7.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.003
Table S7. Gene #21: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 244 | 56 | 126 | 79 |
DEL PEAK 9(4Q34.3) MUTATED | 19 | 7 | 31 | 21 |
DEL PEAK 9(4Q34.3) WILD-TYPE | 225 | 49 | 95 | 58 |
Figure S7. Get High-res Image Gene #21: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D21V3.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.003
Table S8. Gene #21: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 250 | 67 | 177 | 11 |
DEL PEAK 9(4Q34.3) MUTATED | 20 | 9 | 43 | 6 |
DEL PEAK 9(4Q34.3) WILD-TYPE | 230 | 58 | 134 | 5 |
Figure S8. Get High-res Image Gene #21: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D21V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.003
Table S9. Gene #25: 'del_9p23' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 244 | 56 | 126 | 79 |
DEL PEAK 13(9P23) MUTATED | 47 | 12 | 51 | 36 |
DEL PEAK 13(9P23) WILD-TYPE | 197 | 44 | 75 | 43 |
Figure S9. Get High-res Image Gene #25: 'del_9p23' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D25V3.png)
P value = 3e-05 (Fisher's exact test), Q value = 0.0087
Table S10. Gene #25: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 250 | 67 | 177 | 11 |
DEL PEAK 13(9P23) MUTATED | 51 | 16 | 74 | 5 |
DEL PEAK 13(9P23) WILD-TYPE | 199 | 51 | 103 | 6 |
Figure S10. Get High-res Image Gene #25: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D25V4.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.003
Table S11. Gene #26: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 244 | 56 | 126 | 79 |
DEL PEAK 14(9P21.3) MUTATED | 48 | 11 | 55 | 40 |
DEL PEAK 14(9P21.3) WILD-TYPE | 196 | 45 | 71 | 39 |
Figure S11. Get High-res Image Gene #26: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D26V3.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.003
Table S12. Gene #26: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 250 | 67 | 177 | 11 |
DEL PEAK 14(9P21.3) MUTATED | 52 | 15 | 81 | 6 |
DEL PEAK 14(9P21.3) WILD-TYPE | 198 | 52 | 96 | 5 |
Figure S12. Get High-res Image Gene #26: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D26V4.png)
P value = 5e-05 (Fisher's exact test), Q value = 0.014
Table S13. Gene #26: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 417 | 78 | 9 |
DEL PEAK 14(9P21.3) MUTATED | 115 | 39 | 0 |
DEL PEAK 14(9P21.3) WILD-TYPE | 302 | 39 | 9 |
Figure S13. Get High-res Image Gene #26: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'
![](D26V6.png)
P value = 0.000554 (Fisher's exact test), Q value = 0.15
Table S14. Gene #26: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 178 | 327 |
DEL PEAK 14(9P21.3) MUTATED | 37 | 117 |
DEL PEAK 14(9P21.3) WILD-TYPE | 141 | 210 |
Figure S14. Get High-res Image Gene #26: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'
![](D26V7.png)
P value = 0.00035 (Fisher's exact test), Q value = 0.098
Table S15. Gene #27: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 250 | 67 | 177 | 11 |
DEL PEAK 15(10Q23.31) MUTATED | 32 | 12 | 44 | 6 |
DEL PEAK 15(10Q23.31) WILD-TYPE | 218 | 55 | 133 | 5 |
Figure S15. Get High-res Image Gene #27: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D27V4.png)
P value = 0.00011 (Fisher's exact test), Q value = 0.031
Table S16. Gene #28: 'del_13q13.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 244 | 56 | 126 | 79 |
DEL PEAK 16(13Q13.3) MUTATED | 25 | 3 | 31 | 20 |
DEL PEAK 16(13Q13.3) WILD-TYPE | 219 | 53 | 95 | 59 |
Figure S16. Get High-res Image Gene #28: 'del_13q13.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D28V3.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.003
Table S17. Gene #28: 'del_13q13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 250 | 67 | 177 | 11 |
DEL PEAK 16(13Q13.3) MUTATED | 27 | 4 | 42 | 6 |
DEL PEAK 16(13Q13.3) WILD-TYPE | 223 | 63 | 135 | 5 |
Figure S17. Get High-res Image Gene #28: 'del_13q13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D28V4.png)
P value = 3e-05 (Fisher's exact test), Q value = 0.0087
Table S18. Gene #29: 'del_14q31.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 244 | 56 | 126 | 79 |
DEL PEAK 17(14Q31.1) MUTATED | 80 | 27 | 67 | 47 |
DEL PEAK 17(14Q31.1) WILD-TYPE | 164 | 29 | 59 | 32 |
Figure S18. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D29V3.png)
P value = 0.00025 (Fisher's exact test), Q value = 0.07
Table S19. Gene #29: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 250 | 67 | 177 | 11 |
DEL PEAK 17(14Q31.1) MUTATED | 86 | 35 | 96 | 4 |
DEL PEAK 17(14Q31.1) WILD-TYPE | 164 | 32 | 81 | 7 |
Figure S19. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D29V4.png)
P value = 0.000115 (Fisher's exact test), Q value = 0.033
Table S20. Gene #29: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 230 | 18 |
DEL PEAK 17(14Q31.1) MUTATED | 97 | 16 |
DEL PEAK 17(14Q31.1) WILD-TYPE | 133 | 2 |
Figure S20. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'
![](D29V5.png)
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Copy number data file = transformed.cor.cli.txt
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Clinical data file = KIRC-TP.merged_data.txt
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Number of patients = 505
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Number of significantly focal cnvs = 29
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Number of selected clinical features = 11
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Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.