Correlation between copy number variation genes (focal events) and selected clinical features
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 30 focal events and 11 clinical features across 516 patients, 21 significant findings detected with Q value < 0.25.

  • amp_3q26.32 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • del_3p26.3 cnv correlated to 'RACE'.

  • del_3p22.2 cnv correlated to 'PATHOLOGY.T.STAGE' and 'RACE'.

  • del_3p12.2 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_13q14.2 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 30 focal events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 21 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 3 157 (30%) 359 0.241
(1.00) 		0.0442
(1.00) 		1e-05
(0.00311) 		1e-05
(0.00311) 		0.03
(1.00) 		0.00014
(0.0419) 		0.00047
(0.138) 		0.546
(1.00) 		0.797
(1.00) 		0.109
(1.00) 		0.826
(1.00)
del 14q31 1 223 (43%) 293 0.131
(1.00) 		0.112
(1.00) 		2e-05
(0.00608) 		0.00014
(0.0419) 		0.000109
(0.0328) 		0.00109
(0.316) 		0.139
(1.00) 		0.184
(1.00) 		0.251
(1.00) 		0.0173
(1.00) 		1
(1.00)
amp 3q26 32 86 (17%) 430 0.222
(1.00) 		0.983
(1.00) 		0.00011
(0.033) 		0.0002
(0.0594) 		0.0577
(1.00) 		0.00087
(0.253) 		0.807
(1.00) 		0.395
(1.00) 		0.605
(1.00) 		1
(1.00)
del 3p22 2 456 (88%) 60 0.8
(1.00) 		0.37
(1.00) 		0.0257
(1.00) 		0.00032
(0.0944) 		1
(1.00) 		0.582
(1.00) 		1
(1.00) 		0.322
(1.00) 		0.4
(1.00) 		2e-05
(0.00608) 		1
(1.00)
del 4q34 3 78 (15%) 438 0.857
(1.00) 		0.566
(1.00) 		2e-05
(0.00608) 		1e-05
(0.00311) 		0.725
(1.00) 		0.0111
(1.00) 		0.309
(1.00) 		0.477
(1.00) 		0.0892
(1.00) 		0.59
(1.00)
del 9p23 149 (29%) 367 0.465
(1.00) 		0.0246
(1.00) 		1e-05
(0.00311) 		1e-05
(0.00311) 		0.103
(1.00) 		0.00315
(0.898) 		0.00166
(0.477) 		0.546
(1.00) 		0.797
(1.00) 		0.293
(1.00) 		0.654
(1.00)
del 13q14 2 81 (16%) 435 0.0145
(1.00) 		0.757
(1.00) 		1e-05
(0.00311) 		1e-05
(0.00311) 		0.33
(1.00) 		0.0553
(1.00) 		0.802
(1.00) 		0.949
(1.00) 		0.12
(1.00) 		0.399
(1.00)
del 3p26 3 446 (86%) 70 0.205
(1.00) 		0.326
(1.00) 		0.148
(1.00) 		0.0116
(1.00) 		0.731
(1.00) 		0.856
(1.00) 		0.79
(1.00) 		0.169
(1.00) 		0.4
(1.00) 		0.00033
(0.097) 		0.397
(1.00)
del 3p12 2 298 (58%) 218 0.19
(1.00) 		0.741
(1.00) 		0.668
(1.00) 		0.224
(1.00) 		0.623
(1.00) 		0.501
(1.00) 		0.000814
(0.238) 		0.394
(1.00) 		0.517
(1.00) 		0.22
(1.00) 		0.538
(1.00)
del 3q11 2 158 (31%) 358 0.444
(1.00) 		0.0244
(1.00) 		0.356
(1.00) 		0.0863
(1.00) 		0.599
(1.00) 		0.742
(1.00) 		1.8e-07
(5.62e-05) 		0.485
(1.00) 		0.779
(1.00) 		0.186
(1.00) 		0.371
(1.00)
del 10q23 31 94 (18%) 422 0.228
(1.00) 		0.587
(1.00) 		0.00875
(1.00) 		0.00021
(0.0622) 		1
(1.00) 		0.0577
(1.00) 		0.043
(1.00) 		0.589
(1.00) 		0.133
(1.00) 		0.427
(1.00)
amp 1q24 1 62 (12%) 454 0.14
(1.00) 		0.0811
(1.00) 		0.173
(1.00) 		0.121
(1.00) 		0.0803
(1.00) 		0.337
(1.00) 		0.574
(1.00) 		0.763
(1.00) 		0.857
(1.00) 		0.529
(1.00)
amp 1q32 1 62 (12%) 454 0.155
(1.00) 		0.0215
(1.00) 		0.108
(1.00) 		0.106
(1.00) 		0.711
(1.00) 		0.494
(1.00) 		0.574
(1.00) 		0.763
(1.00) 		0.857
(1.00) 		0.213
(1.00)
amp 4q32 1 16 (3%) 500 0.375
(1.00) 		0.295
(1.00) 		0.654
(1.00) 		0.4
(1.00) 		0.57
(1.00) 		0.852
(1.00) 		0.599
(1.00) 		0.104
(1.00) 		1
(1.00) 		1
(1.00)
amp 5q35 1 326 (63%) 190 0.0703
(1.00) 		0.152
(1.00) 		0.509
(1.00) 		0.312
(1.00) 		0.31
(1.00) 		0.336
(1.00) 		0.072
(1.00) 		0.819
(1.00) 		0.135
(1.00) 		0.00329
(0.934) 		1
(1.00)
amp 7q36 3 173 (34%) 343 0.475
(1.00) 		0.562
(1.00) 		0.0208
(1.00) 		0.0611
(1.00) 		0.447
(1.00) 		0.0103
(1.00) 		0.0196
(1.00) 		0.108
(1.00) 		0.345
(1.00) 		0.084
(1.00) 		0.27
(1.00)
amp 8q24 22 78 (15%) 438 0.322
(1.00) 		0.00626
(1.00) 		0.00171
(0.489) 		0.0014
(0.403) 		0.737
(1.00) 		0.107
(1.00) 		0.0739
(1.00) 		0.765
(1.00) 		0.331
(1.00) 		0.231
(1.00)
amp 10p14 20 (4%) 496 0.926
(1.00) 		0.0427
(1.00) 		0.4
(1.00) 		0.0319
(1.00) 		0.212
(1.00) 		0.69
(1.00) 		0.642
(1.00) 		0.244
(1.00) 		0.45
(1.00) 		1
(1.00)
amp xp22 2 30 (6%) 486 0.229
(1.00) 		0.796
(1.00) 		0.05
(1.00) 		0.0953
(1.00) 		1
(1.00) 		0.16
(1.00) 		1
(1.00) 		1
(1.00) 		0.0232
(1.00) 		0.613
(1.00)
amp xp11 4 32 (6%) 484 0.284
(1.00) 		0.953
(1.00) 		0.0414
(1.00) 		0.114
(1.00) 		1
(1.00) 		0.099
(1.00) 		1
(1.00) 		1
(1.00) 		0.0717
(1.00) 		0.381
(1.00)
amp xq11 2 28 (5%) 488 0.626
(1.00) 		0.301
(1.00) 		0.394
(1.00) 		0.431
(1.00) 		1
(1.00) 		0.577
(1.00) 		1
(1.00) 		1
(1.00) 		0.0737
(1.00) 		0.611
(1.00)
amp xq28 36 (7%) 480 0.936
(1.00) 		0.482
(1.00) 		0.616
(1.00) 		0.762
(1.00) 		1
(1.00) 		0.0949
(1.00) 		0.721
(1.00) 		1
(1.00) 		1
(1.00) 		0.392
(1.00)
del 1p36 23 101 (20%) 415 0.0309
(1.00) 		0.113
(1.00) 		0.321
(1.00) 		0.1
(1.00) 		1
(1.00) 		0.117
(1.00) 		0.105
(1.00) 		0.793
(1.00) 		1
(1.00) 		0.217
(1.00)
del 1p31 1 75 (15%) 441 0.264
(1.00) 		0.138
(1.00) 		0.651
(1.00) 		0.0392
(1.00) 		0.492
(1.00) 		0.158
(1.00) 		0.0193
(1.00) 		0.793
(1.00) 		0.575
(1.00) 		0.0902
(1.00)
del 1q43 40 (8%) 476 0.387
(1.00) 		0.71
(1.00) 		1
(1.00) 		0.15
(1.00) 		1
(1.00) 		0.496
(1.00) 		1
(1.00) 		0.943
(1.00) 		0.441
(1.00) 		0.719
(1.00)
del 2q37 3 50 (10%) 466 0.0717
(1.00) 		0.712
(1.00) 		0.491
(1.00) 		0.74
(1.00) 		1
(1.00) 		0.653
(1.00) 		0.162
(1.00) 		0.589
(1.00) 		0.492
(1.00)
del 3p14 1 365 (71%) 151 0.971
(1.00) 		0.964
(1.00) 		0.261
(1.00) 		0.0531
(1.00) 		0.428
(1.00) 		0.548
(1.00) 		0.00122
(0.351) 		0.899
(1.00) 		0.517
(1.00) 		0.0796
(1.00) 		0.827
(1.00)
del 6q26 150 (29%) 366 0.773
(1.00) 		0.248
(1.00) 		0.454
(1.00) 		0.642
(1.00) 		0.00907
(1.00) 		0.838
(1.00) 		0.0155
(1.00) 		0.36
(1.00) 		0.0591
(1.00) 		0.258
(1.00) 		0.178
(1.00)
del 6q26 150 (29%) 366 0.468
(1.00) 		0.204
(1.00) 		0.453
(1.00) 		0.639
(1.00) 		0.00907
(1.00) 		0.84
(1.00) 		0.00869
(1.00) 		0.36
(1.00) 		0.0591
(1.00) 		0.259
(1.00) 		0.178
(1.00)
del 8p23 2 152 (29%) 364 0.237
(1.00) 		0.177
(1.00) 		0.1
(1.00) 		0.0736
(1.00) 		1
(1.00) 		0.137
(1.00) 		0.191
(1.00) 		0.694
(1.00) 		0.731
(1.00) 		0.0906
(1.00) 		0.0371
(1.00)
'amp_3q26.32' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.033

Table S1.  Gene #3: 'amp_3q26.32' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 253 57 126 80
AMP PEAK 3(3Q26.32) MUTATED 28 6 27 25
AMP PEAK 3(3Q26.32) WILD-TYPE 225 51 99 55

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 = 2e-04 (Fisher's exact test), Q value = 0.059

Table S2.  Gene #3: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
AMP PEAK 3(3Q26.32) MUTATED 29 8 45 4
AMP PEAK 3(3Q26.32) WILD-TYPE 229 61 133 7

Figure S2.  Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_3p26.3' versus 'RACE'

P value = 0.00033 (Fisher's exact test), Q value = 0.097

Table S3.  Gene #17: 'del_3p26.3' versus Clinical Feature #10: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 44 457
DEL PEAK 5(3P26.3) MUTATED 6 29 404
DEL PEAK 5(3P26.3) WILD-TYPE 2 15 53

Figure S3.  Get High-res Image Gene #17: 'del_3p26.3' versus Clinical Feature #10: 'RACE'

'del_3p22.2' versus 'PATHOLOGY.T.STAGE'

P value = 0.00032 (Fisher's exact test), Q value = 0.094

Table S4.  Gene #18: 'del_3p22.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
DEL PEAK 6(3P22.2) MUTATED 221 61 168 6
DEL PEAK 6(3P22.2) WILD-TYPE 37 8 10 5

Figure S4.  Get High-res Image Gene #18: 'del_3p22.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_3p22.2' versus 'RACE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0061

Table S5.  Gene #18: 'del_3p22.2' versus Clinical Feature #10: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 44 457
DEL PEAK 6(3P22.2) MUTATED 6 29 414
DEL PEAK 6(3P22.2) WILD-TYPE 2 15 43

Figure S5.  Get High-res Image Gene #18: 'del_3p22.2' versus Clinical Feature #10: 'RACE'

'del_3p12.2' versus 'GENDER'

P value = 0.000814 (Fisher's exact test), Q value = 0.24

Table S6.  Gene #20: 'del_3p12.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 186 330
DEL PEAK 8(3P12.2) MUTATED 89 209
DEL PEAK 8(3P12.2) WILD-TYPE 97 121

Figure S6.  Get High-res Image Gene #20: 'del_3p12.2' versus Clinical Feature #7: 'GENDER'

'del_3q11.2' versus 'GENDER'

P value = 1.8e-07 (Fisher's exact test), Q value = 5.6e-05

Table S7.  Gene #21: 'del_3q11.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 186 330
DEL PEAK 9(3Q11.2) MUTATED 31 127
DEL PEAK 9(3Q11.2) WILD-TYPE 155 203

Figure S7.  Get High-res Image Gene #21: 'del_3q11.2' versus Clinical Feature #7: 'GENDER'

'del_4q34.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0061

Table S8.  Gene #22: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 253 57 126 80
DEL PEAK 10(4Q34.3) MUTATED 19 7 31 21
DEL PEAK 10(4Q34.3) WILD-TYPE 234 50 95 59

Figure S8.  Get High-res Image Gene #22: '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 = 0.0031

Table S9.  Gene #22: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
DEL PEAK 10(4Q34.3) MUTATED 20 9 43 6
DEL PEAK 10(4Q34.3) WILD-TYPE 238 60 135 5

Figure S9.  Get High-res Image Gene #22: '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 = 0.0031

Table S10.  Gene #26: 'del_9p23' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 253 57 126 80
DEL PEAK 14(9P23) MUTATED 50 12 51 36
DEL PEAK 14(9P23) WILD-TYPE 203 45 75 44

Figure S10.  Get High-res Image Gene #26: 'del_9p23' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_9p23' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S11.  Gene #26: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
DEL PEAK 14(9P23) MUTATED 53 16 75 5
DEL PEAK 14(9P23) WILD-TYPE 205 53 103 6

Figure S11.  Get High-res Image Gene #26: '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 = 0.0031

Table S12.  Gene #27: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 253 57 126 80
DEL PEAK 15(9P21.3) MUTATED 51 11 55 40
DEL PEAK 15(9P21.3) WILD-TYPE 202 46 71 40

Figure S12.  Get High-res Image Gene #27: '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 = 0.0031

Table S13.  Gene #27: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
DEL PEAK 15(9P21.3) MUTATED 54 15 82 6
DEL PEAK 15(9P21.3) WILD-TYPE 204 54 96 5

Figure S13.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

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

P value = 0.00014 (Fisher's exact test), Q value = 0.042

Table S14.  Gene #27: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 417 78 19
DEL PEAK 15(9P21.3) MUTATED 115 39 3
DEL PEAK 15(9P21.3) WILD-TYPE 302 39 16

Figure S14.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'del_9p21.3' versus 'GENDER'

P value = 0.00047 (Fisher's exact test), Q value = 0.14

Table S15.  Gene #27: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 186 330
DEL PEAK 15(9P21.3) MUTATED 39 118
DEL PEAK 15(9P21.3) WILD-TYPE 147 212

Figure S15.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

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

P value = 0.00021 (Fisher's exact test), Q value = 0.062

Table S16.  Gene #28: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
DEL PEAK 16(10Q23.31) MUTATED 32 12 44 6
DEL PEAK 16(10Q23.31) WILD-TYPE 226 57 134 5

Figure S16.  Get High-res Image Gene #28: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_13q14.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S17.  Gene #29: 'del_13q14.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 253 57 126 80
DEL PEAK 17(13Q14.2) MUTATED 26 3 31 21
DEL PEAK 17(13Q14.2) WILD-TYPE 227 54 95 59

Figure S17.  Get High-res Image Gene #29: 'del_13q14.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_13q14.2' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S18.  Gene #29: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
DEL PEAK 17(13Q14.2) MUTATED 28 4 42 7
DEL PEAK 17(13Q14.2) WILD-TYPE 230 65 136 4

Figure S18.  Get High-res Image Gene #29: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_14q31.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0061

Table S19.  Gene #30: 'del_14q31.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 253 57 126 80
DEL PEAK 18(14Q31.1) MUTATED 82 27 67 47
DEL PEAK 18(14Q31.1) WILD-TYPE 171 30 59 33

Figure S19.  Get High-res Image Gene #30: 'del_14q31.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 0.00014 (Fisher's exact test), Q value = 0.042

Table S20.  Gene #30: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
DEL PEAK 18(14Q31.1) MUTATED 87 35 97 4
DEL PEAK 18(14Q31.1) WILD-TYPE 171 34 81 7

Figure S20.  Get High-res Image Gene #30: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

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

P value = 0.000109 (Fisher's exact test), Q value = 0.033

Table S21.  Gene #30: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients 0 1
ALL 231 18
DEL PEAK 18(14Q31.1) MUTATED 97 16
DEL PEAK 18(14Q31.1) WILD-TYPE 134 2

Figure S21.  Get High-res Image Gene #30: '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 = 516

  • Number of significantly focal cnvs = 30

  • 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.

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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