Correlation between copy number variation genes (focal events) and selected clinical features
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C12R3QDG
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C12R3QDG
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 29 focal events and 11 clinical features across 505 patients, 20 significant findings detected with Q value < 0.25.

  • 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'.

  • del_13q13.3 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • del_14q31.1 cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.T.STAGE', and 'PATHOLOGY.N.STAGE'.

Results
Overview of the results

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)
'amp_3q26.32' versus 'NEOPLASM.DISEASESTAGE'

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'

'amp_3q26.32' versus 'PATHOLOGY.T.STAGE'

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'

'amp_3q26.32' versus 'PATHOLOGY.M.STAGE'

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'

'del_3p25.3' versus 'RACE'

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'

'del_3p11.2' versus 'GENDER'

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'

'del_3q11.2' versus 'GENDER'

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'

'del_4q34.3' versus 'NEOPLASM.DISEASESTAGE'

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'

'del_4q34.3' versus 'PATHOLOGY.T.STAGE'

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'

'del_9p23' versus 'NEOPLASM.DISEASESTAGE'

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'

'del_9p23' versus 'PATHOLOGY.T.STAGE'

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'

'del_9p21.3' versus 'NEOPLASM.DISEASESTAGE'

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'

'del_9p21.3' versus 'PATHOLOGY.T.STAGE'

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'

'del_9p21.3' versus 'PATHOLOGY.M.STAGE'

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'

'del_9p21.3' versus 'GENDER'

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'

'del_10q23.31' versus 'PATHOLOGY.T.STAGE'

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'

'del_13q13.3' versus 'NEOPLASM.DISEASESTAGE'

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'

'del_13q13.3' versus 'PATHOLOGY.T.STAGE'

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'

'del_14q31.1' versus 'NEOPLASM.DISEASESTAGE'

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'

'del_14q31.1' versus 'PATHOLOGY.T.STAGE'

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'

'del_14q31.1' versus 'PATHOLOGY.N.STAGE'

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'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = KIRC-TP.merged_data.txt

  • Number of patients = 505

  • Number of significantly focal cnvs = 29

  • Number of selected clinical features = 11

  • 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

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

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.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] 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)
[3] 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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