This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 28 focal events and 10 clinical features across 163 patients, 31 significant findings detected with Q value < 0.25.
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amp_7q22.1 cnv correlated to 'NEOPLASM.DISEASESTAGE'.
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amp_17q25.2 cnv correlated to 'PATHOLOGY.M.STAGE'.
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del_1p36.31 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
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del_3p22.1 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
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del_4q34.3 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
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del_5p14.2 cnv correlated to 'Time to Death' and 'PATHOLOGY.T.STAGE'.
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del_5q35.2 cnv correlated to 'PATHOLOGY.T.STAGE'.
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del_6q21 cnv correlated to 'PATHOLOGY.T.STAGE'.
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del_6q22.31 cnv correlated to 'PATHOLOGY.T.STAGE'.
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del_9p21.3 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
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del_11q22.3 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
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del_11q24.2 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
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del_15q15.2 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
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del_16q24.1 cnv correlated to 'Time to Death'.
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del_xp11.22 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
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del_xq28 cnv correlated to 'Time to Death'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 28 focal events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 31 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 | YEAROFTOBACCOSMOKINGONSET | ||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | t-test | t-test | |
del 1p36 31 | 35 (21%) | 128 |
0.000879 (0.177) |
0.475 (1.00) |
1.99e-05 (0.00448) |
2.41e-05 (0.0054) |
0.013 (1.00) |
0.135 (1.00) |
0.0361 (1.00) |
0.301 (1.00) |
0.453 (1.00) |
|
del 9p21 3 | 24 (15%) | 139 |
5.18e-05 (0.0115) |
0.272 (1.00) |
3.19e-07 (7.34e-05) |
2.02e-06 (0.000461) |
0.00914 (1.00) |
0.00761 (1.00) |
0.00288 (0.576) |
0.314 (1.00) |
||
del 11q22 3 | 17 (10%) | 146 |
0.000127 (0.0279) |
0.114 (1.00) |
0.000152 (0.0329) |
0.000633 (0.13) |
0.0444 (1.00) |
0.0974 (1.00) |
0.401 (1.00) |
0.792 (1.00) |
||
del 11q24 2 | 17 (10%) | 146 |
3.61e-05 (0.00806) |
0.0593 (1.00) |
0.000152 (0.0329) |
0.000633 (0.13) |
0.0776 (1.00) |
0.0974 (1.00) |
0.589 (1.00) |
0.792 (1.00) |
||
del 15q15 2 | 21 (13%) | 142 |
2.86e-07 (6.61e-05) |
0.0511 (1.00) |
0.000171 (0.0368) |
0.000141 (0.0308) |
0.0057 (1.00) |
0.0523 (1.00) |
0.204 (1.00) |
0.348 (1.00) |
||
del xp11 22 | 18 (11%) | 145 |
0.000314 (0.0662) |
0.333 (1.00) |
0.000432 (0.089) |
0.000217 (0.0463) |
0.0836 (1.00) |
0.696 (1.00) |
0.00486 (0.942) |
0.467 (1.00) |
||
del 3p22 1 | 15 (9%) | 148 |
0.0198 (1.00) |
0.149 (1.00) |
6.41e-06 (0.00145) |
5.12e-05 (0.0114) |
0.361 (1.00) |
0.114 (1.00) |
0.386 (1.00) |
0.754 (1.00) |
0.453 (1.00) |
|
del 4q34 3 | 18 (11%) | 145 |
0.0288 (1.00) |
0.18 (1.00) |
0.00108 (0.217) |
0.000411 (0.0852) |
0.0698 (1.00) |
0.23 (1.00) |
0.00486 (0.942) |
0.754 (1.00) |
||
del 5p14 2 | 10 (6%) | 153 |
6.3e-05 (0.0139) |
0.185 (1.00) |
0.0109 (1.00) |
0.000382 (0.0799) |
0.0122 (1.00) |
0.359 (1.00) |
0.0673 (1.00) |
0.104 (1.00) |
||
amp 7q22 1 | 97 (60%) | 66 |
0.049 (1.00) |
0.518 (1.00) |
0.000276 (0.0584) |
0.00432 (0.851) |
0.54 (1.00) |
0.314 (1.00) |
0.166 (1.00) |
0.159 (1.00) |
0.354 (1.00) |
0.837 (1.00) |
amp 17q25 2 | 120 (74%) | 43 |
0.871 (1.00) |
0.239 (1.00) |
0.296 (1.00) |
0.395 (1.00) |
0.891 (1.00) |
0.000359 (0.0753) |
0.0319 (1.00) |
0.667 (1.00) |
||
del 5q35 2 | 10 (6%) | 153 |
0.00872 (1.00) |
0.0436 (1.00) |
0.00438 (0.859) |
0.000382 (0.0799) |
0.0903 (1.00) |
0.434 (1.00) |
0.0673 (1.00) |
|||
del 6q21 | 16 (10%) | 147 |
0.206 (1.00) |
0.902 (1.00) |
0.0157 (1.00) |
0.000811 (0.165) |
0.169 (1.00) |
0.445 (1.00) |
0.00717 (1.00) |
0.459 (1.00) |
0.315 (1.00) |
|
del 6q22 31 | 17 (10%) | 146 |
0.0437 (1.00) |
0.857 (1.00) |
0.00578 (1.00) |
0.000217 (0.0463) |
0.139 (1.00) |
0.304 (1.00) |
0.0105 (1.00) |
0.459 (1.00) |
0.315 (1.00) |
|
del 16q24 1 | 7 (4%) | 156 |
1.82e-06 (0.000417) |
0.57 (1.00) |
0.0363 (1.00) |
0.269 (1.00) |
0.192 (1.00) |
0.216 (1.00) |
0.199 (1.00) |
|||
del xq28 | 17 (10%) | 146 |
5.1e-06 (0.00116) |
0.113 (1.00) |
0.00351 (0.699) |
0.0134 (1.00) |
0.0836 (1.00) |
0.632 (1.00) |
0.0105 (1.00) |
0.469 (1.00) |
||
amp 2p23 2 | 32 (20%) | 131 |
0.262 (1.00) |
0.356 (1.00) |
0.46 (1.00) |
0.873 (1.00) |
0.408 (1.00) |
0.0307 (1.00) |
0.196 (1.00) |
0.537 (1.00) |
0.331 (1.00) |
0.477 (1.00) |
amp 2q32 1 | 39 (24%) | 124 |
0.461 (1.00) |
0.856 (1.00) |
0.0642 (1.00) |
0.172 (1.00) |
0.72 (1.00) |
0.0174 (1.00) |
0.424 (1.00) |
0.531 (1.00) |
||
amp 3q22 3 | 56 (34%) | 107 |
0.373 (1.00) |
0.478 (1.00) |
0.295 (1.00) |
0.0523 (1.00) |
1 (1.00) |
0.533 (1.00) |
0.591 (1.00) |
0.126 (1.00) |
0.354 (1.00) |
|
amp 19p13 2 | 19 (12%) | 144 |
0.543 (1.00) |
0.0568 (1.00) |
0.889 (1.00) |
0.0541 (1.00) |
0.521 (1.00) |
0.903 (1.00) |
0.595 (1.00) |
0.268 (1.00) |
||
del 2q37 3 | 8 (5%) | 155 |
0.681 (1.00) |
0.151 (1.00) |
0.018 (1.00) |
0.00691 (1.00) |
0.534 (1.00) |
0.0538 (1.00) |
||||
del 5q15 | 11 (7%) | 152 |
0.00642 (1.00) |
0.0301 (1.00) |
0.0357 (1.00) |
0.00535 (1.00) |
0.0903 (1.00) |
0.389 (1.00) |
0.0886 (1.00) |
|||
del 10p11 21 | 11 (7%) | 152 |
0.822 (1.00) |
0.823 (1.00) |
0.006 (1.00) |
0.0109 (1.00) |
0.0556 (1.00) |
0.52 (1.00) |
0.0886 (1.00) |
0.792 (1.00) |
||
del 14q11 2 | 34 (21%) | 129 |
0.00577 (1.00) |
0.68 (1.00) |
0.00494 (0.949) |
0.00745 (1.00) |
0.118 (1.00) |
0.17 (1.00) |
0.141 (1.00) |
0.448 (1.00) |
||
del 14q32 2 | 34 (21%) | 129 |
0.00427 (0.845) |
0.639 (1.00) |
0.00494 (0.949) |
0.00745 (1.00) |
0.0476 (1.00) |
0.183 (1.00) |
0.141 (1.00) |
0.448 (1.00) |
0.413 (1.00) |
0.00474 (0.925) |
del 19p13 3 | 16 (10%) | 147 |
0.0285 (1.00) |
0.946 (1.00) |
0.00802 (1.00) |
0.00614 (1.00) |
0.209 (1.00) |
0.412 (1.00) |
0.568 (1.00) |
0.268 (1.00) |
||
del 19q13 42 | 15 (9%) | 148 |
0.179 (1.00) |
0.792 (1.00) |
0.0167 (1.00) |
0.0135 (1.00) |
0.651 (1.00) |
0.512 (1.00) |
0.386 (1.00) |
0.754 (1.00) |
||
del 21q22 3 | 31 (19%) | 132 |
0.577 (1.00) |
0.661 (1.00) |
0.0139 (1.00) |
0.00747 (1.00) |
0.872 (1.00) |
0.143 (1.00) |
0.129 (1.00) |
0.711 (1.00) |
0.332 (1.00) |
P value = 0.000276 (Fisher's exact test), Q value = 0.058
Table S1. Gene #4: 'amp_7q22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 95 | 11 | 37 | 10 |
AMP PEAK 4(7Q22.1) MUTATED | 67 | 4 | 12 | 6 |
AMP PEAK 4(7Q22.1) WILD-TYPE | 28 | 7 | 25 | 4 |
Figure S1. Get High-res Image Gene #4: 'amp_7q22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D4V3.png)
P value = 0.000359 (Fisher's exact test), Q value = 0.075
Table S2. Gene #5: 'amp_17q25.2' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 62 | 6 | 82 |
AMP PEAK 5(17Q25.2) MUTATED | 35 | 4 | 70 |
AMP PEAK 5(17Q25.2) WILD-TYPE | 27 | 2 | 12 |
Figure S2. Get High-res Image Gene #5: 'amp_17q25.2' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'
![](D5V6.png)
P value = 0.000879 (logrank test), Q value = 0.18
Table S3. Gene #7: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 150 | 17 | 0.0 - 194.8 (14.0) |
DEL PEAK 1(1P36.31) MUTATED | 35 | 7 | 0.1 - 123.6 (7.7) |
DEL PEAK 1(1P36.31) WILD-TYPE | 115 | 10 | 0.0 - 194.8 (16.6) |
Figure S3. Get High-res Image Gene #7: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'
![](D7V1.png)
P value = 1.99e-05 (Fisher's exact test), Q value = 0.0045
Table S4. Gene #7: 'del_1p36.31' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 95 | 11 | 37 | 10 |
DEL PEAK 1(1P36.31) MUTATED | 9 | 3 | 17 | 4 |
DEL PEAK 1(1P36.31) WILD-TYPE | 86 | 8 | 20 | 6 |
Figure S4. Get High-res Image Gene #7: 'del_1p36.31' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D7V3.png)
P value = 2.41e-05 (Fisher's exact test), Q value = 0.0054
Table S5. Gene #7: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 102 | 17 | 44 |
DEL PEAK 1(1P36.31) MUTATED | 11 | 4 | 20 |
DEL PEAK 1(1P36.31) WILD-TYPE | 91 | 13 | 24 |
Figure S5. Get High-res Image Gene #7: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D7V4.png)
P value = 6.41e-06 (Fisher's exact test), Q value = 0.0014
Table S6. Gene #9: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 95 | 11 | 37 | 10 |
DEL PEAK 3(3P22.1) MUTATED | 1 | 1 | 10 | 3 |
DEL PEAK 3(3P22.1) WILD-TYPE | 94 | 10 | 27 | 7 |
Figure S6. Get High-res Image Gene #9: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D9V3.png)
P value = 5.12e-05 (Fisher's exact test), Q value = 0.011
Table S7. Gene #9: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 102 | 17 | 44 |
DEL PEAK 3(3P22.1) MUTATED | 2 | 2 | 11 |
DEL PEAK 3(3P22.1) WILD-TYPE | 100 | 15 | 33 |
Figure S7. Get High-res Image Gene #9: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D9V4.png)
P value = 0.00108 (Fisher's exact test), Q value = 0.22
Table S8. Gene #10: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 95 | 11 | 37 | 10 |
DEL PEAK 4(4Q34.3) MUTATED | 4 | 2 | 10 | 2 |
DEL PEAK 4(4Q34.3) WILD-TYPE | 91 | 9 | 27 | 8 |
Figure S8. Get High-res Image Gene #10: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D10V3.png)
P value = 0.000411 (Fisher's exact test), Q value = 0.085
Table S9. Gene #10: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 102 | 17 | 44 |
DEL PEAK 4(4Q34.3) MUTATED | 4 | 3 | 11 |
DEL PEAK 4(4Q34.3) WILD-TYPE | 98 | 14 | 33 |
Figure S9. Get High-res Image Gene #10: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D10V4.png)
P value = 6.3e-05 (logrank test), Q value = 0.014
Table S10. Gene #11: 'del_5p14.2' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 150 | 17 | 0.0 - 194.8 (14.0) |
DEL PEAK 5(5P14.2) MUTATED | 9 | 4 | 0.1 - 63.7 (6.6) |
DEL PEAK 5(5P14.2) WILD-TYPE | 141 | 13 | 0.0 - 194.8 (14.4) |
Figure S10. Get High-res Image Gene #11: 'del_5p14.2' versus Clinical Feature #1: 'Time to Death'
![](D11V1.png)
P value = 0.000382 (Fisher's exact test), Q value = 0.08
Table S11. Gene #11: 'del_5p14.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 102 | 17 | 44 |
DEL PEAK 5(5P14.2) MUTATED | 1 | 1 | 8 |
DEL PEAK 5(5P14.2) WILD-TYPE | 101 | 16 | 36 |
Figure S11. Get High-res Image Gene #11: 'del_5p14.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D11V4.png)
P value = 0.000382 (Fisher's exact test), Q value = 0.08
Table S12. Gene #13: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 102 | 17 | 44 |
DEL PEAK 7(5Q35.2) MUTATED | 1 | 1 | 8 |
DEL PEAK 7(5Q35.2) WILD-TYPE | 101 | 16 | 36 |
Figure S12. Get High-res Image Gene #13: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D13V4.png)
P value = 0.000811 (Fisher's exact test), Q value = 0.16
Table S13. Gene #14: 'del_6q21' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 102 | 17 | 44 |
DEL PEAK 8(6Q21) MUTATED | 5 | 0 | 11 |
DEL PEAK 8(6Q21) WILD-TYPE | 97 | 17 | 33 |
Figure S13. Get High-res Image Gene #14: 'del_6q21' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D14V4.png)
P value = 0.000217 (Fisher's exact test), Q value = 0.046
Table S14. Gene #15: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 102 | 17 | 44 |
DEL PEAK 9(6Q22.31) MUTATED | 5 | 0 | 12 |
DEL PEAK 9(6Q22.31) WILD-TYPE | 97 | 17 | 32 |
Figure S14. Get High-res Image Gene #15: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D15V4.png)
P value = 5.18e-05 (logrank test), Q value = 0.011
Table S15. Gene #16: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 150 | 17 | 0.0 - 194.8 (14.0) |
DEL PEAK 10(9P21.3) MUTATED | 22 | 7 | 0.1 - 93.3 (10.5) |
DEL PEAK 10(9P21.3) WILD-TYPE | 128 | 10 | 0.0 - 194.8 (14.9) |
Figure S15. Get High-res Image Gene #16: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'
![](D16V1.png)
P value = 3.19e-07 (Fisher's exact test), Q value = 7.3e-05
Table S16. Gene #16: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 95 | 11 | 37 | 10 |
DEL PEAK 10(9P21.3) MUTATED | 4 | 0 | 12 | 6 |
DEL PEAK 10(9P21.3) WILD-TYPE | 91 | 11 | 25 | 4 |
Figure S16. Get High-res Image Gene #16: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D16V3.png)
P value = 2.02e-06 (Fisher's exact test), Q value = 0.00046
Table S17. Gene #16: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 102 | 17 | 44 |
DEL PEAK 10(9P21.3) MUTATED | 5 | 2 | 17 |
DEL PEAK 10(9P21.3) WILD-TYPE | 97 | 15 | 27 |
Figure S17. Get High-res Image Gene #16: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D16V4.png)
P value = 0.000127 (logrank test), Q value = 0.028
Table S18. Gene #18: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 150 | 17 | 0.0 - 194.8 (14.0) |
DEL PEAK 12(11Q22.3) MUTATED | 16 | 5 | 0.1 - 123.6 (8.3) |
DEL PEAK 12(11Q22.3) WILD-TYPE | 134 | 12 | 0.0 - 194.8 (14.6) |
Figure S18. Get High-res Image Gene #18: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'
![](D18V1.png)
P value = 0.000152 (Fisher's exact test), Q value = 0.033
Table S19. Gene #18: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 95 | 11 | 37 | 10 |
DEL PEAK 12(11Q22.3) MUTATED | 3 | 2 | 8 | 4 |
DEL PEAK 12(11Q22.3) WILD-TYPE | 92 | 9 | 29 | 6 |
Figure S19. Get High-res Image Gene #18: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D18V3.png)
P value = 0.000633 (Fisher's exact test), Q value = 0.13
Table S20. Gene #18: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 102 | 17 | 44 |
DEL PEAK 12(11Q22.3) MUTATED | 4 | 2 | 11 |
DEL PEAK 12(11Q22.3) WILD-TYPE | 98 | 15 | 33 |
Figure S20. Get High-res Image Gene #18: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D18V4.png)
P value = 3.61e-05 (logrank test), Q value = 0.0081
Table S21. Gene #19: 'del_11q24.2' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 150 | 17 | 0.0 - 194.8 (14.0) |
DEL PEAK 13(11Q24.2) MUTATED | 16 | 6 | 0.1 - 123.6 (9.9) |
DEL PEAK 13(11Q24.2) WILD-TYPE | 134 | 11 | 0.0 - 194.8 (14.5) |
Figure S21. Get High-res Image Gene #19: 'del_11q24.2' versus Clinical Feature #1: 'Time to Death'
![](D19V1.png)
P value = 0.000152 (Fisher's exact test), Q value = 0.033
Table S22. Gene #19: 'del_11q24.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 95 | 11 | 37 | 10 |
DEL PEAK 13(11Q24.2) MUTATED | 3 | 2 | 8 | 4 |
DEL PEAK 13(11Q24.2) WILD-TYPE | 92 | 9 | 29 | 6 |
Figure S22. Get High-res Image Gene #19: 'del_11q24.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D19V3.png)
P value = 0.000633 (Fisher's exact test), Q value = 0.13
Table S23. Gene #19: 'del_11q24.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 102 | 17 | 44 |
DEL PEAK 13(11Q24.2) MUTATED | 4 | 2 | 11 |
DEL PEAK 13(11Q24.2) WILD-TYPE | 98 | 15 | 33 |
Figure S23. Get High-res Image Gene #19: 'del_11q24.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D19V4.png)
P value = 2.86e-07 (logrank test), Q value = 6.6e-05
Table S24. Gene #22: 'del_15q15.2' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 150 | 17 | 0.0 - 194.8 (14.0) |
DEL PEAK 16(15Q15.2) MUTATED | 20 | 7 | 0.1 - 194.8 (8.2) |
DEL PEAK 16(15Q15.2) WILD-TYPE | 130 | 10 | 0.0 - 129.9 (14.6) |
Figure S24. Get High-res Image Gene #22: 'del_15q15.2' versus Clinical Feature #1: 'Time to Death'
![](D22V1.png)
P value = 0.000171 (Fisher's exact test), Q value = 0.037
Table S25. Gene #22: 'del_15q15.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 95 | 11 | 37 | 10 |
DEL PEAK 16(15Q15.2) MUTATED | 5 | 1 | 9 | 5 |
DEL PEAK 16(15Q15.2) WILD-TYPE | 90 | 10 | 28 | 5 |
Figure S25. Get High-res Image Gene #22: 'del_15q15.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D22V3.png)
P value = 0.000141 (Fisher's exact test), Q value = 0.031
Table S26. Gene #22: 'del_15q15.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 102 | 17 | 44 |
DEL PEAK 16(15Q15.2) MUTATED | 6 | 1 | 14 |
DEL PEAK 16(15Q15.2) WILD-TYPE | 96 | 16 | 30 |
Figure S26. Get High-res Image Gene #22: 'del_15q15.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D22V4.png)
P value = 1.82e-06 (logrank test), Q value = 0.00042
Table S27. Gene #23: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 150 | 17 | 0.0 - 194.8 (14.0) |
DEL PEAK 17(16Q24.1) MUTATED | 6 | 3 | 0.7 - 21.6 (9.5) |
DEL PEAK 17(16Q24.1) WILD-TYPE | 144 | 14 | 0.0 - 194.8 (14.5) |
Figure S27. Get High-res Image Gene #23: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'
![](D23V1.png)
P value = 0.000314 (logrank test), Q value = 0.066
Table S28. Gene #27: 'del_xp11.22' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 150 | 17 | 0.0 - 194.8 (14.0) |
DEL PEAK 21(XP11.22) MUTATED | 17 | 5 | 0.1 - 79.9 (10.1) |
DEL PEAK 21(XP11.22) WILD-TYPE | 133 | 12 | 0.0 - 194.8 (14.4) |
Figure S28. Get High-res Image Gene #27: 'del_xp11.22' versus Clinical Feature #1: 'Time to Death'
![](D27V1.png)
P value = 0.000432 (Fisher's exact test), Q value = 0.089
Table S29. Gene #27: 'del_xp11.22' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 95 | 11 | 37 | 10 |
DEL PEAK 21(XP11.22) MUTATED | 3 | 1 | 10 | 2 |
DEL PEAK 21(XP11.22) WILD-TYPE | 92 | 10 | 27 | 8 |
Figure S29. Get High-res Image Gene #27: 'del_xp11.22' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D27V3.png)
P value = 0.000217 (Fisher's exact test), Q value = 0.046
Table S30. Gene #27: 'del_xp11.22' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 102 | 17 | 44 |
DEL PEAK 21(XP11.22) MUTATED | 4 | 2 | 12 |
DEL PEAK 21(XP11.22) WILD-TYPE | 98 | 15 | 32 |
Figure S30. Get High-res Image Gene #27: 'del_xp11.22' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D27V4.png)
P value = 5.1e-06 (logrank test), Q value = 0.0012
Table S31. Gene #28: 'del_xq28' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 150 | 17 | 0.0 - 194.8 (14.0) |
DEL PEAK 22(XQ28) MUTATED | 16 | 5 | 0.1 - 25.1 (9.9) |
DEL PEAK 22(XQ28) WILD-TYPE | 134 | 12 | 0.0 - 194.8 (14.5) |
Figure S31. Get High-res Image Gene #28: 'del_xq28' versus Clinical Feature #1: 'Time to Death'
![](D28V1.png)
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Copy number data file = transformed.cor.cli.txt
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Clinical data file = KIRP-TP.merged_data.txt
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Number of patients = 163
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Number of significantly focal cnvs = 28
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Number of selected clinical features = 10
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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 continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' 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.