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 55 focal events and 12 clinical features across 242 patients, one significant finding detected with Q value < 0.25.

  • AMP PEAK 19(15Q26.2) MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 55 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.

Clinical
Features 		Time
from
Specimen
Diagnosis
to
Death 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		MELANOMA
ULCERATION 		MELANOMA
PRIMARY
KNOWN 		BRESLOW
THICKNESS 		GENDER
nCNV (%) nWild-Type logrank test logrank test t-test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test t-test Fisher's exact test
AMP PEAK 19(15Q26 2) MUTATION ANALYSIS 78 (32%) 164 0.89
(1.00) 		0.202
(1.00) 		0.346
(1.00) 		0.223
(1.00) 		0.000183
(0.121) 		0.123
(1.00) 		0.444
(1.00) 		0.286
(1.00) 		0.264
(1.00) 		0.21
(1.00) 		0.587
(1.00) 		1
(1.00)
AMP PEAK 1(1P12) MUTATION ANALYSIS 75 (31%) 167 0.365
(1.00) 		0.1
(1.00) 		0.708
(1.00) 		0.284
(1.00) 		0.279
(1.00) 		0.256
(1.00) 		0.73
(1.00) 		0.494
(1.00) 		0.594
(1.00) 		1
(1.00) 		0.421
(1.00) 		0.776
(1.00)
AMP PEAK 2(1Q21 3) MUTATION ANALYSIS 123 (51%) 119 0.848
(1.00) 		0.7
(1.00) 		0.817
(1.00) 		0.503
(1.00) 		0.746
(1.00) 		0.878
(1.00) 		0.493
(1.00) 		0.411
(1.00) 		0.322
(1.00) 		0.846
(1.00) 		0.859
(1.00) 		0.896
(1.00)
AMP PEAK 3(1Q44) MUTATION ANALYSIS 130 (54%) 112 0.65
(1.00) 		0.0733
(1.00) 		0.871
(1.00) 		0.348
(1.00) 		0.748
(1.00) 		0.982
(1.00) 		0.982
(1.00) 		0.461
(1.00) 		0.32
(1.00) 		0.845
(1.00) 		0.866
(1.00) 		0.692
(1.00)
AMP PEAK 4(3P13) MUTATION ANALYSIS 60 (25%) 182 0.0544
(1.00) 		0.0057
(1.00) 		0.0501
(1.00) 		0.842
(1.00) 		0.099
(1.00) 		0.15
(1.00) 		0.815
(1.00) 		0.659
(1.00) 		1
(1.00) 		0.653
(1.00) 		0.108
(1.00) 		0.127
(1.00)
AMP PEAK 5(4Q12) MUTATION ANALYSIS 41 (17%) 201 0.61
(1.00) 		0.903
(1.00) 		0.0885
(1.00) 		0.596
(1.00) 		0.183
(1.00) 		0.919
(1.00) 		0.646
(1.00) 		0.291
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.869
(1.00) 		0.599
(1.00)
AMP PEAK 6(5P15 33) MUTATION ANALYSIS 77 (32%) 165 0.541
(1.00) 		0.108
(1.00) 		0.308
(1.00) 		0.288
(1.00) 		0.384
(1.00) 		0.359
(1.00) 		0.166
(1.00) 		0.369
(1.00) 		0.716
(1.00) 		0.208
(1.00) 		0.196
(1.00) 		0.888
(1.00)
AMP PEAK 7(5Q35 3) MUTATION ANALYSIS 36 (15%) 206 0.0881
(1.00) 		0.655
(1.00) 		0.382
(1.00) 		0.195
(1.00) 		0.662
(1.00) 		0.596
(1.00) 		0.979
(1.00) 		0.274
(1.00) 		0.464
(1.00) 		0.785
(1.00) 		0.222
(1.00) 		0.579
(1.00)
AMP PEAK 8(6P25 1) MUTATION ANALYSIS 134 (55%) 108 0.000965
(0.635) 		0.0277
(1.00) 		0.0183
(1.00) 		0.0854
(1.00) 		0.131
(1.00) 		0.281
(1.00) 		0.593
(1.00) 		0.373
(1.00) 		0.617
(1.00) 		0.846
(1.00) 		0.695
(1.00) 		0.597
(1.00)
AMP PEAK 9(6Q12) MUTATION ANALYSIS 52 (21%) 190 0.77
(1.00) 		0.733
(1.00) 		0.369
(1.00) 		0.19
(1.00) 		0.178
(1.00) 		0.275
(1.00) 		0.303
(1.00) 		0.53
(1.00) 		0.157
(1.00) 		0.813
(1.00) 		0.241
(1.00) 		0.749
(1.00)
AMP PEAK 10(7P22 3) MUTATION ANALYSIS 130 (54%) 112 0.984
(1.00) 		0.842
(1.00) 		0.417
(1.00) 		0.649
(1.00) 		0.198
(1.00) 		0.513
(1.00) 		0.634
(1.00) 		0.473
(1.00) 		0.511
(1.00) 		0.329
(1.00) 		0.189
(1.00) 		0.895
(1.00)
AMP PEAK 11(7Q34) MUTATION ANALYSIS 141 (58%) 101 0.891
(1.00) 		0.998
(1.00) 		0.142
(1.00) 		0.36
(1.00) 		0.0176
(1.00) 		0.405
(1.00) 		0.432
(1.00) 		0.633
(1.00) 		0.402
(1.00) 		0.693
(1.00) 		0.389
(1.00) 		0.144
(1.00)
AMP PEAK 12(8Q11 21) MUTATION ANALYSIS 104 (43%) 138 0.279
(1.00) 		0.124
(1.00) 		0.0166
(1.00) 		0.137
(1.00) 		0.43
(1.00) 		0.395
(1.00) 		0.313
(1.00) 		0.306
(1.00) 		0.865
(1.00) 		0.435
(1.00) 		0.949
(1.00) 		0.69
(1.00)
AMP PEAK 13(8Q24 21) MUTATION ANALYSIS 122 (50%) 120 0.959
(1.00) 		0.193
(1.00) 		0.0146
(1.00) 		0.272
(1.00) 		0.402
(1.00) 		0.269
(1.00) 		0.363
(1.00) 		0.617
(1.00) 		0.869
(1.00) 		0.846
(1.00) 		0.941
(1.00) 		0.693
(1.00)
AMP PEAK 14(9P24 1) MUTATION ANALYSIS 23 (10%) 219 0.965
(1.00) 		0.771
(1.00) 		0.685
(1.00) 		0.0014
(0.921) 		0.173
(1.00) 		0.41
(1.00) 		0.654
(1.00) 		0.566
(1.00) 		0.0286
(1.00) 		1
(1.00) 		0.00346
(1.00) 		1
(1.00)
AMP PEAK 15(11Q13 3) MUTATION ANALYSIS 43 (18%) 199 0.965
(1.00) 		0.923
(1.00) 		0.98
(1.00) 		0.0984
(1.00) 		0.118
(1.00) 		0.361
(1.00) 		0.751
(1.00) 		0.631
(1.00) 		0.317
(1.00) 		0.443
(1.00) 		0.452
(1.00) 		0.864
(1.00)
AMP PEAK 16(11Q13 4) MUTATION ANALYSIS 40 (17%) 202 0.983
(1.00) 		0.847
(1.00) 		0.554
(1.00) 		0.0492
(1.00) 		0.762
(1.00) 		0.512
(1.00) 		0.261
(1.00) 		0.448
(1.00) 		0.15
(1.00) 		0.601
(1.00) 		0.332
(1.00) 		0.598
(1.00)
AMP PEAK 17(12Q14 1) MUTATION ANALYSIS 41 (17%) 201 0.725
(1.00) 		0.491
(1.00) 		0.62
(1.00) 		0.54
(1.00) 		0.459
(1.00) 		0.281
(1.00) 		0.341
(1.00) 		0.633
(1.00) 		0.413
(1.00) 		0.434
(1.00) 		0.144
(1.00) 		0.599
(1.00)
AMP PEAK 18(12Q15) MUTATION ANALYSIS 38 (16%) 204 0.177
(1.00) 		0.51
(1.00) 		0.594
(1.00) 		0.351
(1.00) 		0.86
(1.00) 		0.153
(1.00) 		0.239
(1.00) 		0.834
(1.00) 		1
(1.00) 		0.435
(1.00) 		0.478
(1.00) 		0.473
(1.00)
AMP PEAK 20(17Q25 3) MUTATION ANALYSIS 83 (34%) 159 0.613
(1.00) 		0.818
(1.00) 		0.0074
(1.00) 		0.472
(1.00) 		0.364
(1.00) 		0.389
(1.00) 		0.972
(1.00) 		0.977
(1.00) 		0.117
(1.00) 		1
(1.00) 		0.609
(1.00) 		0.335
(1.00)
AMP PEAK 21(19P13 2) MUTATION ANALYSIS 47 (19%) 195 0.571
(1.00) 		0.163
(1.00) 		0.976
(1.00) 		0.752
(1.00) 		0.773
(1.00) 		0.795
(1.00) 		0.893
(1.00) 		0.00759
(1.00) 		1
(1.00) 		0.323
(1.00) 		0.801
(1.00) 		1
(1.00)
AMP PEAK 22(20Q13 33) MUTATION ANALYSIS 121 (50%) 121 0.767
(1.00) 		0.259
(1.00) 		0.0873
(1.00) 		0.204
(1.00) 		0.0828
(1.00) 		0.302
(1.00) 		0.191
(1.00) 		0.119
(1.00) 		0.621
(1.00) 		0.846
(1.00) 		0.2
(1.00) 		0.599
(1.00)
AMP PEAK 23(22Q13 2) MUTATION ANALYSIS 101 (42%) 141 0.234
(1.00) 		0.313
(1.00) 		0.786
(1.00) 		0.492
(1.00) 		0.619
(1.00) 		0.078
(1.00) 		0.61
(1.00) 		0.995
(1.00) 		0.319
(1.00) 		1
(1.00) 		0.725
(1.00) 		1
(1.00)
DEL PEAK 1(1P36 31) MUTATION ANALYSIS 55 (23%) 187 0.317
(1.00) 		0.739
(1.00) 		0.381
(1.00) 		0.606
(1.00) 		0.382
(1.00) 		0.862
(1.00) 		0.942
(1.00) 		0.0973
(1.00) 		1
(1.00) 		0.819
(1.00) 		0.439
(1.00) 		0.209
(1.00)
DEL PEAK 2(1P22 1) MUTATION ANALYSIS 61 (25%) 181 0.695
(1.00) 		0.252
(1.00) 		0.0217
(1.00) 		0.578
(1.00) 		0.0342
(1.00) 		0.93
(1.00) 		0.0649
(1.00) 		0.0994
(1.00) 		0.0851
(1.00) 		1
(1.00) 		0.83
(1.00) 		0.367
(1.00)
DEL PEAK 3(2Q37 3) MUTATION ANALYSIS 58 (24%) 184 0.416
(1.00) 		0.897
(1.00) 		0.858
(1.00) 		0.471
(1.00) 		0.891
(1.00) 		0.0454
(1.00) 		0.147
(1.00) 		0.0905
(1.00) 		0.706
(1.00) 		0.37
(1.00) 		0.771
(1.00) 		0.758
(1.00)
DEL PEAK 4(3P21 2) MUTATION ANALYSIS 41 (17%) 201 0.235
(1.00) 		0.405
(1.00) 		0.0537
(1.00) 		0.894
(1.00) 		0.601
(1.00) 		0.194
(1.00) 		0.042
(1.00) 		0.834
(1.00) 		0.634
(1.00) 		0.608
(1.00) 		0.00307
(1.00) 		0.38
(1.00)
DEL PEAK 5(3Q23) MUTATION ANALYSIS 36 (15%) 206 0.281
(1.00) 		0.944
(1.00) 		0.301
(1.00) 		0.683
(1.00) 		0.356
(1.00) 		0.19
(1.00) 		0.243
(1.00) 		0.0418
(1.00) 		0.363
(1.00) 		0.586
(1.00) 		0.196
(1.00) 		0.854
(1.00)
DEL PEAK 6(4Q34 3) MUTATION ANALYSIS 59 (24%) 183 0.762
(1.00) 		0.518
(1.00) 		0.197
(1.00) 		0.634
(1.00) 		0.312
(1.00) 		0.209
(1.00) 		0.638
(1.00) 		0.141
(1.00) 		0.574
(1.00) 		0.821
(1.00) 		0.136
(1.00) 		0.00896
(1.00)
DEL PEAK 7(5P15 31) MUTATION ANALYSIS 47 (19%) 195 0.95
(1.00) 		0.909
(1.00) 		0.119
(1.00) 		0.735
(1.00) 		0.421
(1.00) 		0.0346
(1.00) 		0.993
(1.00) 		0.854
(1.00) 		0.00215
(1.00) 		0.219
(1.00) 		0.625
(1.00) 		0.138
(1.00)
DEL PEAK 8(5Q11 2) MUTATION ANALYSIS 66 (27%) 176 0.536
(1.00) 		0.487
(1.00) 		0.29
(1.00) 		0.721
(1.00) 		0.381
(1.00) 		0.16
(1.00) 		0.657
(1.00) 		0.133
(1.00) 		0.0953
(1.00) 		0.389
(1.00) 		0.562
(1.00) 		0.769
(1.00)
DEL PEAK 9(5Q31 3) MUTATION ANALYSIS 89 (37%) 153 0.985
(1.00) 		0.845
(1.00) 		0.984
(1.00) 		0.822
(1.00) 		0.781
(1.00) 		0.0973
(1.00) 		0.278
(1.00) 		0.175
(1.00) 		1
(1.00) 		0.312
(1.00) 		0.804
(1.00) 		0.786
(1.00)
DEL PEAK 10(6Q22 31) MUTATION ANALYSIS 143 (59%) 99 0.0682
(1.00) 		0.623
(1.00) 		0.393
(1.00) 		0.727
(1.00) 		0.884
(1.00) 		0.641
(1.00) 		0.61
(1.00) 		0.995
(1.00) 		0.403
(1.00) 		0.694
(1.00) 		0.118
(1.00) 		0.0445
(1.00)
DEL PEAK 11(6Q25 3) MUTATION ANALYSIS 150 (62%) 92 0.0897
(1.00) 		0.712
(1.00) 		0.717
(1.00) 		0.835
(1.00) 		0.711
(1.00) 		0.658
(1.00) 		0.587
(1.00) 		0.989
(1.00) 		0.396
(1.00) 		0.689
(1.00) 		0.641
(1.00) 		0.177
(1.00)
DEL PEAK 12(6Q26) MUTATION ANALYSIS 146 (60%) 96 0.0946
(1.00) 		0.564
(1.00) 		0.532
(1.00) 		0.881
(1.00) 		0.685
(1.00) 		0.668
(1.00) 		0.483
(1.00) 		0.993
(1.00) 		0.398
(1.00) 		0.551
(1.00) 		0.112
(1.00) 		0.044
(1.00)
DEL PEAK 13(8P23 3) MUTATION ANALYSIS 57 (24%) 185 0.0976
(1.00) 		0.596
(1.00) 		0.2
(1.00) 		0.201
(1.00) 		0.34
(1.00) 		0.116
(1.00) 		0.604
(1.00) 		0.603
(1.00) 		0.698
(1.00) 		0.365
(1.00) 		0.228
(1.00) 		0.536
(1.00)
DEL PEAK 14(9P23) MUTATION ANALYSIS 165 (68%) 77 0.0177
(1.00) 		0.403
(1.00) 		0.745
(1.00) 		0.528
(1.00) 		0.5
(1.00) 		0.38
(1.00) 		0.414
(1.00) 		0.058
(1.00) 		0.601
(1.00) 		0.536
(1.00) 		0.791
(1.00) 		0.0905
(1.00)
DEL PEAK 15(9P21 3) MUTATION ANALYSIS 186 (77%) 56 0.0335
(1.00) 		0.89
(1.00) 		0.367
(1.00) 		0.143
(1.00) 		0.635
(1.00) 		0.549
(1.00) 		0.537
(1.00) 		0.538
(1.00) 		1
(1.00) 		0.247
(1.00) 		0.409
(1.00) 		0.0301
(1.00)
DEL PEAK 16(10P15 3) MUTATION ANALYSIS 129 (53%) 113 0.148
(1.00) 		0.557
(1.00) 		0.0334
(1.00) 		0.127
(1.00) 		0.973
(1.00) 		0.22
(1.00) 		0.743
(1.00) 		0.467
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.532
(1.00) 		0.187
(1.00)
DEL PEAK 17(10Q23 31) MUTATION ANALYSIS 147 (61%) 95 0.657
(1.00) 		0.935
(1.00) 		0.0112
(1.00) 		0.0833
(1.00) 		0.744
(1.00) 		0.17
(1.00) 		0.354
(1.00) 		0.223
(1.00) 		0.403
(1.00) 		0.321
(1.00) 		0.964
(1.00) 		0.00691
(1.00)
DEL PEAK 18(10Q26 3) MUTATION ANALYSIS 149 (62%) 93 0.644
(1.00) 		0.637
(1.00) 		0.00071
(0.468) 		0.0642
(1.00) 		0.905
(1.00) 		0.409
(1.00) 		0.694
(1.00) 		0.0546
(1.00) 		0.616
(1.00) 		1
(1.00) 		0.605
(1.00) 		0.0222
(1.00)
DEL PEAK 19(11Q23 3) MUTATION ANALYSIS 133 (55%) 109 0.307
(1.00) 		0.936
(1.00) 		0.516
(1.00) 		0.114
(1.00) 		0.485
(1.00) 		0.405
(1.00) 		0.294
(1.00) 		0.748
(1.00) 		0.409
(1.00) 		0.564
(1.00) 		0.478
(1.00) 		0.0857
(1.00)
DEL PEAK 20(12P13 31) MUTATION ANALYSIS 37 (15%) 205 0.484
(1.00) 		0.631
(1.00) 		0.497
(1.00) 		0.833
(1.00) 		0.891
(1.00) 		0.715
(1.00) 		0.624
(1.00) 		0.0648
(1.00) 		0.235
(1.00) 		0.789
(1.00) 		0.308
(1.00) 		0.368
(1.00)
DEL PEAK 21(12Q23 3) MUTATION ANALYSIS 54 (22%) 188 0.556
(1.00) 		0.835
(1.00) 		0.557
(1.00) 		0.458
(1.00) 		0.924
(1.00) 		0.754
(1.00) 		0.831
(1.00) 		0.462
(1.00) 		0.686
(1.00) 		0.639
(1.00) 		0.537
(1.00) 		0.155
(1.00)
DEL PEAK 22(13Q12 11) MUTATION ANALYSIS 55 (23%) 187 0.807
(1.00) 		0.75
(1.00) 		0.801
(1.00) 		0.377
(1.00) 		0.403
(1.00) 		0.0158
(1.00) 		0.613
(1.00) 		0.0128
(1.00) 		1
(1.00) 		1
(1.00) 		0.0158
(1.00) 		0.276
(1.00)
DEL PEAK 23(13Q34) MUTATION ANALYSIS 57 (24%) 185 0.996
(1.00) 		0.403
(1.00) 		0.822
(1.00) 		0.344
(1.00) 		0.436
(1.00) 		0.192
(1.00) 		0.521
(1.00) 		0.0208
(1.00) 		0.581
(1.00) 		1
(1.00) 		0.0473
(1.00) 		1
(1.00)
DEL PEAK 24(14Q32 2) MUTATION ANALYSIS 78 (32%) 164 0.353
(1.00) 		0.736
(1.00) 		0.357
(1.00) 		0.61
(1.00) 		0.194
(1.00) 		0.293
(1.00) 		0.572
(1.00) 		0.357
(1.00) 		0.728
(1.00) 		1
(1.00) 		0.234
(1.00) 		0.398
(1.00)
DEL PEAK 25(15Q13 3) MUTATION ANALYSIS 55 (23%) 187 0.201
(1.00) 		0.0805
(1.00) 		0.22
(1.00) 		0.979
(1.00) 		0.66
(1.00) 		0.0609
(1.00) 		0.599
(1.00) 		0.791
(1.00) 		0.847
(1.00) 		0.819
(1.00) 		0.887
(1.00) 		0.754
(1.00)
DEL PEAK 26(15Q15 1) MUTATION ANALYSIS 58 (24%) 184 0.118
(1.00) 		0.233
(1.00) 		0.647
(1.00) 		0.98
(1.00) 		0.139
(1.00) 		0.466
(1.00) 		0.508
(1.00) 		0.539
(1.00) 		0.33
(1.00) 		0.656
(1.00) 		0.781
(1.00) 		0.356
(1.00)
DEL PEAK 27(16P13 3) MUTATION ANALYSIS 45 (19%) 197 0.772
(1.00) 		0.871
(1.00) 		0.0946
(1.00) 		0.481
(1.00) 		0.924
(1.00) 		0.829
(1.00) 		0.692
(1.00) 		0.533
(1.00) 		0.541
(1.00) 		0.082
(1.00) 		0.381
(1.00) 		0.0419
(1.00)
DEL PEAK 28(16Q12 1) MUTATION ANALYSIS 76 (31%) 166 0.504
(1.00) 		0.227
(1.00) 		0.352
(1.00) 		0.139
(1.00) 		0.143
(1.00) 		0.748
(1.00) 		0.602
(1.00) 		0.508
(1.00) 		0.862
(1.00) 		0.402
(1.00) 		0.889
(1.00) 		0.0898
(1.00)
DEL PEAK 29(16Q24 3) MUTATION ANALYSIS 82 (34%) 160 0.448
(1.00) 		0.158
(1.00) 		0.122
(1.00) 		0.284
(1.00) 		0.0132
(1.00) 		0.591
(1.00) 		0.095
(1.00) 		0.72
(1.00) 		0.733
(1.00) 		0.417
(1.00) 		0.861
(1.00) 		0.126
(1.00)
DEL PEAK 30(17Q21 31) MUTATION ANALYSIS 51 (21%) 191 0.181
(1.00) 		0.0286
(1.00) 		0.838
(1.00) 		0.209
(1.00) 		0.518
(1.00) 		0.953
(1.00) 		0.987
(1.00) 		0.21
(1.00) 		0.845
(1.00) 		1
(1.00) 		0.556
(1.00) 		1
(1.00)
DEL PEAK 31(19P13 3) MUTATION ANALYSIS 69 (29%) 173 0.334
(1.00) 		0.594
(1.00) 		0.816
(1.00) 		0.216
(1.00) 		0.646
(1.00) 		0.494
(1.00) 		0.631
(1.00) 		0.33
(1.00) 		0.72
(1.00) 		0.666
(1.00) 		0.0909
(1.00) 		0.189
(1.00)
DEL PEAK 32(22Q13 1) MUTATION ANALYSIS 24 (10%) 218 0.235
(1.00) 		0.38
(1.00) 		0.252
(1.00) 		0.441
(1.00) 		0.389
(1.00) 		0.771
(1.00) 		0.578
(1.00) 		0.332
(1.00) 		0.282
(1.00) 		1
(1.00) 		0.255
(1.00) 		0.828
(1.00)
'AMP PEAK 19(15Q26.2) MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000183 (Chi-square test), Q value = 0.12

Table S1.  Gene #19: 'AMP PEAK 19(15Q26.2) MUTATION STATUS' versus Clinical Feature #5: 'NEOPLASM.DISEASESTAGE'

nPatients I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
ALL 9 4 20 10 22 17 10 12 9 20 10 21 39 10
AMP PEAK 19(15Q26.2) MUTATED 9 1 9 4 4 7 2 2 2 5 6 8 7 0
AMP PEAK 19(15Q26.2) WILD-TYPE 0 3 11 6 18 10 8 10 7 15 4 13 32 10

Figure S1.  Get High-res Image Gene #19: 'AMP PEAK 19(15Q26.2) MUTATION STATUS' versus Clinical Feature #5: 'NEOPLASM.DISEASESTAGE'

Methods & Data
Input

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

  • Clinical data file = SKCM-TM.clin.merged.picked.txt

  • Number of patients = 242

  • Number of significantly focal cnvs = 55

  • Number of selected clinical features = 12

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] 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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] 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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