Brain Lower Grade Glioma: Correlation between copy number variation genes (focal) and selected clinical features
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 43 arm-level results and 7 clinical features across 207 patients, 14 significant findings detected with Q value < 0.25.

- Amp Peak 1(1q32.1) cnv correlated to 'AGE'.

- Amp Peak 3(7p11.2) cnv correlated to 'AGE'.

- Amp Peak 4(7q32.3) cnv correlated to 'AGE'.

- Amp Peak 11(12q14.1) cnv correlated to 'Time to Death'.

- Amp Peak 13(19q13.2) cnv correlated to 'Time to Death' and 'AGE'.

- Del Peak 1(1p36.31) cnv correlated to 'HISTOLOGICAL.TYPE'.

- Del Peak 2(1p32.3) cnv correlated to 'HISTOLOGICAL.TYPE' and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 13(9p21.3) cnv correlated to 'Time to Death', 'AGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 14(10q26.2) cnv correlated to 'Time to Death'.

- Del Peak 25(19q13.42) cnv correlated to 'HISTOLOGICAL.TYPE'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 43 arm-level results and 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 14 significant findings detected.

|  | Clinical Features | Time to Death | AGE | GENDER | KARNOFSKY PERFORMANCE SCORE | HISTOLOGICAL TYPE | HISTOLOGICCLASSIFICATION | RADIATIONS RADIATION REGIMENINDICATION
| nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test
Del Peak 13(9p21 3) | 74 (36%) | 133 | 3.01e-05 (0.0089) | 0.000488 (0.141) | 1 (1.00) | 0.367 (1.00) | 0.0451 (1.00) | 0.00123 (0.35) | 0.000267 (0.0774)
Amp Peak 13(19q13 2) | 15 (7%) | 192 | 6.78e-05 (0.02) | 0.00011 (0.0322) | 0.792 (1.00) | 0.508 (1.00) | 0.396 (1.00) | 0.423 (1.00) | 0.593 (1.00)
Del Peak 2(1p32 3) | 74 (36%) | 133 | 0.139 (1.00) | 0.0029 (0.807) | 0.771 (1.00) | 0.952 (1.00) | 7.56e-15 (2.27e-12) | 0.146 (1.00) | 0.000489 (0.141)
Amp Peak 1(1q32 1) | 23 (11%) | 184 | 0.0615 (1.00) | 0.000116 (0.0338) | 0.378 (1.00) | 0.0855 (1.00) | 0.182 (1.00) | 0.00378 (1.00) | 0.377 (1.00)
Amp Peak 3(7p11 2) | 53 (26%) | 154 | 0.00366 (1.00) | 0.000626 (0.18) | 0.109 (1.00) | 0.604 (1.00) | 0.0547 (1.00) | 0.00387 (1.00) | 0.34 (1.00)
Amp Peak 4(7q32 3) | 73 (35%) | 134 | 0.247 (1.00) | 8.46e-05 (0.0249) | 0.0283 (1.00) | 0.844 (1.00) | 0.384 (1.00) | 0.559 (1.00) | 0.0416 (1.00)
Amp Peak 11(12q14 1) | 13 (6%) | 194 | 1.49e-05 (0.00442) | 0.0516 (1.00) | 0.564 (1.00) | 0.466 (1.00) | 0.117 (1.00) | 0.39 (1.00) | 0.568 (1.00)
Del Peak 1(1p36 31) | 80 (39%) | 127 | 0.93 (1.00) | 0.00114 (0.325) | 0.474 (1.00) | 0.85 (1.00) | 7.71e-13 (2.31e-10) | 0.478 (1.00) | 0.00432 (1.00)
Del Peak 14(10q26 2) | 65 (31%) | 142 | 0.000151 (0.0439) | 0.0104 (1.00) | 0.0717 (1.00) | 0.33 (1.00) | 0.0167 (1.00) | 0.0511 (1.00) | 0.765 (1.00)
Del Peak 25(19q13 42) | 111 (54%) | 96 | 0.0266 (1.00) | 0.629 (1.00) | 0.888 (1.00) | 0.566 (1.00) | 9.51e-08 (2.83e-05) | 0.675 (1.00) | 0.889 (1.00)
Amp Peak 2(4q12) | 10 (5%) | 197 | 0.953 (1.00) | 0.606 (1.00) | 0.748 (1.00) | 0.325 (1.00) | 0.0461 (1.00) | 0.00216 (0.609) | 0.748 (1.00)
Amp Peak 5(8q24 21) | 42 (20%) | 165 | 0.903 (1.00) | 0.56 (1.00) | 0.0837 (1.00) | 0.332 (1.00) | 0.011 (1.00) | 0.301 (1.00) | 0.119 (1.00)
Amp Peak 6(10p15 1) | 33 (16%) | 174 | 0.739 (1.00) | 0.00528 (1.00) | 0.127 (1.00) | 0.636 (1.00) | 0.00415 (1.00) | 0.26 (1.00) | 0.255 (1.00)
Amp Peak 7(10q11 21) | 4 (2%) | 203 | 0.782 (1.00) | 0.692 (1.00) | 0.636 (1.00) |  | 0.0125 (1.00) | 0.127 (1.00) | 1 (1.00)
Amp Peak 8(11q23 3) | 35 (17%) | 172 | 0.605 (1.00) | 0.0473 (1.00) | 0.349 (1.00) | 0.568 (1.00) | 0.35 (1.00) | 0.577 (1.00) | 0.266 (1.00)
Amp Peak 9(12p13 32) | 32 (15%) | 175 | 0.899 (1.00) | 0.0809 (1.00) | 0.176 (1.00) | 0.47 (1.00) | 0.486 (1.00) | 0.849 (1.00) | 0.848 (1.00)
Amp Peak 10(12p11 22) | 19 (9%) | 188 | 0.906 (1.00) | 0.193 (1.00) | 0.0521 (1.00) | 0.448 (1.00) | 0.297 (1.00) | 1 (1.00) | 0.631 (1.00)
Amp Peak 12(19p13 3) | 48 (23%) | 159 | 0.828 (1.00) | 0.0993 (1.00) | 0.869 (1.00) | 0.338 (1.00) | 0.0146 (1.00) | 1 (1.00) | 0.744 (1.00)
Amp Peak 14(Xp22 33) | 14 (7%) | 193 | 0.579 (1.00) | 0.877 (1.00) | 1 (1.00) | 0.611 (1.00) | 0.00384 (1.00) | 0.267 (1.00) | 0.407 (1.00)
Amp Peak 15(Xq11 2) | 29 (14%) | 178 | 0.666 (1.00) | 0.451 (1.00) | 0.163 (1.00) | 0.687 (1.00) | 0.00489 (1.00) | 0.685 (1.00) | 0.424 (1.00)
Del Peak 3(1q43) | 12 (6%) | 195 | 0.942 (1.00) | 0.546 (1.00) | 0.369 (1.00) | 0.244 (1.00) | 0.491 (1.00) | 0.757 (1.00) | 0.768 (1.00)
Del Peak 4(2q37 3) | 31 (15%) | 176 | 0.818 (1.00) | 0.0889 (1.00) | 1 (1.00) | 0.542 (1.00) | 0.114 (1.00) | 1 (1.00) | 0.242 (1.00)
Del Peak 5(3p21 1) | 19 (9%) | 188 | 0.288 (1.00) | 0.0149 (1.00) | 0.634 (1.00) | 0.674 (1.00) | 0.362 (1.00) | 0.328 (1.00) | 0.147 (1.00)
Del Peak 6(3q29) | 20 (10%) | 187 | 0.381 (1.00) | 0.655 (1.00) | 0.1 (1.00) | 0.0446 (1.00) | 0.159 (1.00) | 0.644 (1.00) | 0.481 (1.00)
Del Peak 7(4q33) | 60 (29%) | 147 | 0.614 (1.00) | 0.813 (1.00) | 0.164 (1.00) | 0.532 (1.00) | 0.133 (1.00) | 0.759 (1.00) | 0.284 (1.00)
Del Peak 8(4q35 2) | 61 (29%) | 146 | 0.56 (1.00) | 0.759 (1.00) | 0.125 (1.00) | 0.663 (1.00) | 0.0924 (1.00) | 0.879 (1.00) | 0.361 (1.00)
Del Peak 9(5q35 2) | 27 (13%) | 180 | 0.0993 (1.00) | 0.34 (1.00) | 0.305 (1.00) | 0.31 (1.00) | 0.11 (1.00) | 0.0119 (1.00) | 0.0376 (1.00)
Del Peak 10(6p24 1) | 17 (8%) | 190 | 0.0458 (1.00) | 0.525 (1.00) | 0.31 (1.00) | 0.698 (1.00) | 0.00129 (0.364) | 0.802 (1.00) | 0.127 (1.00)
Del Peak 11(6q24 3) | 30 (14%) | 177 | 0.0186 (1.00) | 0.482 (1.00) | 0.43 (1.00) | 0.56 (1.00) | 0.0243 (1.00) | 0.425 (1.00) | 0.0026 (0.724)
Del Peak 12(8p23 2) | 10 (5%) | 197 | 0.362 (1.00) | 0.514 (1.00) | 1 (1.00) | 0.249 (1.00) | 0.133 (1.00) | 0.00216 (0.609) | 0.332 (1.00)
Del Peak 15(11p15 5) | 43 (21%) | 164 | 0.381 (1.00) | 0.0493 (1.00) | 0.0598 (1.00) | 0.671 (1.00) | 0.00928 (1.00) | 0.865 (1.00) | 0.304 (1.00)
Del Peak 16(11q25) | 13 (6%) | 194 | 0.0051 (1.00) | 0.944 (1.00) | 0.246 (1.00) | 0.864 (1.00) | 0.623 (1.00) | 0.775 (1.00) | 0.568 (1.00)
Del Peak 17(12q24 11) | 27 (13%) | 180 | 0.861 (1.00) | 0.286 (1.00) | 0.305 (1.00) | 0.34 (1.00) | 0.11 (1.00) | 0.538 (1.00) | 0.681 (1.00)
Del Peak 18(13q14 2) | 62 (30%) | 145 | 0.462 (1.00) | 0.853 (1.00) | 0.648 (1.00) | 0.0725 (1.00) | 0.0745 (1.00) | 0.128 (1.00) | 0.095 (1.00)
Del Peak 19(13q34) | 48 (23%) | 159 | 0.361 (1.00) | 0.528 (1.00) | 0.506 (1.00) | 0.433 (1.00) | 0.551 (1.00) | 0.62 (1.00) | 0.138 (1.00)
Del Peak 20(14q24 3) | 48 (23%) | 159 | 0.000981 (0.28) | 0.184 (1.00) | 0.0455 (1.00) | 0.994 (1.00) | 0.0652 (1.00) | 0.182 (1.00) | 0.411 (1.00)
Del Peak 21(15q21 3) | 26 (13%) | 181 | 0.15 (1.00) | 0.34 (1.00) | 1 (1.00) | 0.212 (1.00) | 0.646 (1.00) | 0.293 (1.00) | 0.681 (1.00)
Del Peak 22(17q25 3) | 11 (5%) | 196 | 0.606 (1.00) | 0.454 (1.00) | 0.761 (1.00) | 0.731 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00)
Del Peak 23(18p11 32) | 29 (14%) | 178 | 0.822 (1.00) | 0.852 (1.00) | 0.225 (1.00) | 0.349 (1.00) | 0.875 (1.00) | 0.841 (1.00) | 0.0439 (1.00)
Del Peak 24(18q23) | 32 (15%) | 175 | 0.722 (1.00) | 0.383 (1.00) | 0.699 (1.00) | 0.843 (1.00) | 0.876 (1.00) | 1 (1.00) | 0.0826 (1.00)
Del Peak 26(22q13 31) | 29 (14%) | 178 | 0.116 (1.00) | 0.281 (1.00) | 0.319 (1.00) | 0.733 (1.00) | 0.0023 (0.644) | 0.044 (1.00) | 1 (1.00)
Del Peak 27(Xp22 31) | 48 (23%) | 159 | 0.54 (1.00) | 0.489 (1.00) | 0.319 (1.00) | 0.675 (1.00) | 0.831 (1.00) | 0.869 (1.00) | 0.411 (1.00)
Del Peak 28(Xq21 1) | 29 (14%) | 178 | 0.582 (1.00) | 0.233 (1.00) | 0.55 (1.00) | 0.957 (1.00) | 0.206 (1.00) | 0.109 (1.00) | 0.844 (1.00)

'Amp Peak 1(1q32.1) mutation analysis' versus 'AGE'

P value = 0.000116 (t-test), Q value = 0.034

Table S1. Gene #1: 'Amp Peak 1(1q32.1) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 207 | 43.1 (13.4)
AMP PEAK 1(1Q32.1) MUTATED | 23 | 53.2 (11.4)
AMP PEAK 1(1Q32.1) WILD-TYPE | 184 | 41.8 (13.1)

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q32.1) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 3(7p11.2) mutation analysis' versus 'AGE'

P value = 0.000626 (t-test), Q value = 0.18

Table S2. Gene #3: 'Amp Peak 3(7p11.2) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 207 | 43.1 (13.4)
AMP PEAK 3(7P11.2) MUTATED | 53 | 48.7 (13.4)
AMP PEAK 3(7P11.2) WILD-TYPE | 154 | 41.2 (12.9)

Figure S2. Get High-res Image Gene #3: 'Amp Peak 3(7p11.2) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 4(7q32.3) mutation analysis' versus 'AGE'

P value = 8.46e-05 (t-test), Q value = 0.025

Table S3. Gene #4: 'Amp Peak 4(7q32.3) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 207 | 43.1 (13.4)
AMP PEAK 4(7Q32.3) MUTATED | 73 | 48.1 (13.1)
AMP PEAK 4(7Q32.3) WILD-TYPE | 134 | 40.4 (12.9)

Figure S3. Get High-res Image Gene #4: 'Amp Peak 4(7q32.3) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 11(12q14.1) mutation analysis' versus 'Time to Death'

P value = 1.49e-05 (logrank test), Q value = 0.0044

Table S4. Gene #11: 'Amp Peak 11(12q14.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 206 | 51 | 0.0 - 211.2 (13.4)
AMP PEAK 11(12Q14.1) MUTATED | 13 | 9 | 1.2 - 80.0 (12.4)
AMP PEAK 11(12Q14.1) WILD-TYPE | 193 | 42 | 0.0 - 211.2 (13.4)

Figure S4. Get High-res Image Gene #11: 'Amp Peak 11(12q14.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 13(19q13.2) mutation analysis' versus 'Time to Death'

P value = 6.78e-05 (logrank test), Q value = 0.02

Table S5. Gene #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 206 | 51 | 0.0 - 211.2 (13.4)
AMP PEAK 13(19Q13.2) MUTATED | 15 | 6 | 0.0 - 43.9 (10.6)
AMP PEAK 13(19Q13.2) WILD-TYPE | 191 | 45 | 0.1 - 211.2 (14.3)

Figure S5. Get High-res Image Gene #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 13(19q13.2) mutation analysis' versus 'AGE'

P value = 0.00011 (t-test), Q value = 0.032

Table S6. Gene #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 207 | 43.1 (13.4)
AMP PEAK 13(19Q13.2) MUTATED | 15 | 53.1 (8.0)
AMP PEAK 13(19Q13.2) WILD-TYPE | 192 | 42.3 (13.5)

Figure S6. Get High-res Image Gene #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 1(1p36.31) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.71e-13 (Fisher's exact test), Q value = 2.3e-10

Table S7. Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA
--- | --- | --- | ---
ALL | 63 | 54 | 89
DEL PEAK 1(1P36.31) MUTATED | 9 | 11 | 60
DEL PEAK 1(1P36.31) WILD-TYPE | 54 | 43 | 29

Figure S7. Get High-res Image Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 2(1p32.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.56e-15 (Fisher's exact test), Q value = 2.3e-12

Table S8. Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA
--- | --- | --- | ---
ALL | 63 | 54 | 89
DEL PEAK 2(1P32.3) MUTATED | 7 | 8 | 59
DEL PEAK 2(1P32.3) WILD-TYPE | 56 | 46 | 30

Figure S8. Get High-res Image Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 2(1p32.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000489 (Fisher's exact test), Q value = 0.14

Table S9. Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 104 | 103
DEL PEAK 2(1P32.3) MUTATED | 25 | 49
DEL PEAK 2(1P32.3) WILD-TYPE | 79 | 54

Figure S9. Get High-res Image Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 13(9p21.3) mutation analysis' versus 'Time to Death'

P value = 3.01e-05 (logrank test), Q value = 0.0089

Table S10. Gene #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 206 | 51 | 0.0 - 211.2 (13.4)
DEL PEAK 13(9P21.3) MUTATED | 73 | 26 | 0.1 - 117.4 (14.7)
DEL PEAK 13(9P21.3) WILD-TYPE | 133 | 25 | 0.0 - 211.2 (13.4)

Figure S10. Get High-res Image Gene #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 13(9p21.3) mutation analysis' versus 'AGE'

P value = 0.000488 (t-test), Q value = 0.14

Table S11. Gene #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 207 | 43.1 (13.4)
DEL PEAK 13(9P21.3) MUTATED | 74 | 47.5 (13.2)
DEL PEAK 13(9P21.3) WILD-TYPE | 133 | 40.7 (13.0)

Figure S11. Get High-res Image Gene #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 13(9p21.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000267 (Fisher's exact test), Q value = 0.077

Table S12. Gene #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 104 | 103
DEL PEAK 13(9P21.3) MUTATED | 50 | 24
DEL PEAK 13(9P21.3) WILD-TYPE | 54 | 79

Figure S12. Get High-res Image Gene #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 14(10q26.2) mutation analysis' versus 'Time to Death'

P value = 0.000151 (logrank test), Q value = 0.044

Table S13. Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 206 | 51 | 0.0 - 211.2 (13.4)
DEL PEAK 14(10Q26.2) MUTATED | 65 | 29 | 0.1 - 156.2 (12.4)
DEL PEAK 14(10Q26.2) WILD-TYPE | 141 | 22 | 0.0 - 211.2 (14.3)

Figure S13. Get High-res Image Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 25(19q13.42) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.51e-08 (Fisher's exact test), Q value = 2.8e-05

Table S14. Gene #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA
--- | --- | --- | ---
ALL | 63 | 54 | 89
DEL PEAK 25(19Q13.42) MUTATED | 20 | 23 | 67
DEL PEAK 25(19Q13.42) WILD-TYPE | 43 | 31 | 22

Figure S14. Get High-res Image Gene #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

- Mutation data file = all_lesions.conf_99.cnv.cluster.txt

- Clinical data file = LGG-TP.clin.merged.picked.txt

- Number of patients = 207

- Number of significantly arm-level cnvs = 43

- Number of selected clinical features = 7

- Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

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

Student's t-test analysis

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

Fisher's exact test

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

Q value calculation

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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[4] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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