Correlation between copy number variation genes (focal events) and selected clinical features
Rectum Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1KH0KPH
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1KH0KPH
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 62 focal events and 11 clinical features across 162 patients, one significant finding detected with Q value < 0.25.

  • DEL PEAK 30(18Q21.2) MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 62 focal events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test t-test
DEL PEAK 30(18Q21 2) MUTATION ANALYSIS 143 (88%) 19 0.549
(1.00) 		0.443
(1.00) 		0.0438
(1.00) 		0.00589
(1.00) 		0.0607
(1.00) 		0.208
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.673
(1.00) 		0.00019
(0.13)
AMP PEAK 1(1Q21 3) MUTATION ANALYSIS 48 (30%) 114 0.806
(1.00) 		0.951
(1.00) 		0.803
(1.00) 		0.117
(1.00) 		0.443
(1.00) 		0.102
(1.00) 		0.863
(1.00) 		1
(1.00) 		0.0639
(1.00) 		0.691
(1.00) 		0.203
(1.00)
AMP PEAK 2(1Q32 2) MUTATION ANALYSIS 48 (30%) 114 0.123
(1.00) 		0.645
(1.00) 		0.715
(1.00) 		0.0291
(1.00) 		0.251
(1.00) 		0.36
(1.00) 		1
(1.00) 		1
(1.00) 		0.362
(1.00) 		0.64
(1.00) 		0.0158
(1.00)
AMP PEAK 3(5Q22 3) MUTATION ANALYSIS 19 (12%) 143 0.42
(1.00) 		0.383
(1.00) 		0.565
(1.00) 		0.881
(1.00) 		0.753
(1.00) 		0.743
(1.00) 		0.81
(1.00) 		0.37
(1.00) 		1
(1.00) 		0.806
(1.00) 		0.412
(1.00)
AMP PEAK 4(6P21 1) MUTATION ANALYSIS 52 (32%) 110 0.484
(1.00) 		0.528
(1.00) 		0.206
(1.00) 		0.441
(1.00) 		0.00799
(1.00) 		0.00684
(1.00) 		0.4
(1.00) 		0.0626
(1.00) 		0.0844
(1.00) 		0.0957
(1.00) 		0.0734
(1.00)
AMP PEAK 5(8P11 23) MUTATION ANALYSIS 52 (32%) 110 0.059
(1.00) 		0.264
(1.00) 		0.144
(1.00) 		0.219
(1.00) 		0.449
(1.00) 		0.299
(1.00) 		0.0635
(1.00) 		0.222
(1.00) 		1
(1.00) 		0.0229
(1.00) 		0.294
(1.00)
AMP PEAK 6(8P11 21) MUTATION ANALYSIS 69 (43%) 93 0.429
(1.00) 		0.541
(1.00) 		0.104
(1.00) 		0.411
(1.00) 		0.828
(1.00) 		0.195
(1.00) 		0.637
(1.00) 		0.154
(1.00) 		0.241
(1.00) 		0.00288
(1.00) 		0.618
(1.00)
AMP PEAK 7(8Q24 21) MUTATION ANALYSIS 107 (66%) 55 0.373
(1.00) 		0.228
(1.00) 		0.215
(1.00) 		0.499
(1.00) 		0.702
(1.00) 		0.538
(1.00) 		0.868
(1.00) 		0.0326
(1.00) 		0.665
(1.00) 		0.372
(1.00) 		0.831
(1.00)
AMP PEAK 8(10Q22 2) MUTATION ANALYSIS 11 (7%) 151 0.299
(1.00) 		0.686
(1.00) 		0.938
(1.00) 		0.935
(1.00) 		0.914
(1.00) 		0.743
(1.00) 		0.551
(1.00) 		0.592
(1.00) 		0.349
(1.00) 		1
(1.00) 		0.918
(1.00)
AMP PEAK 9(11P15 5) MUTATION ANALYSIS 43 (27%) 119 0.423
(1.00) 		0.969
(1.00) 		0.677
(1.00) 		0.916
(1.00) 		0.191
(1.00) 		0.852
(1.00) 		1
(1.00) 		0.188
(1.00) 		0.656
(1.00) 		0.938
(1.00) 		0.671
(1.00)
AMP PEAK 10(11Q13 3) MUTATION ANALYSIS 26 (16%) 136 0.565
(1.00) 		0.0577
(1.00) 		0.576
(1.00) 		0.499
(1.00) 		0.377
(1.00) 		0.288
(1.00) 		1
(1.00) 		0.697
(1.00) 		0.591
(1.00) 		0.66
(1.00) 		0.0323
(1.00)
AMP PEAK 11(12P13 33) MUTATION ANALYSIS 41 (25%) 121 0.694
(1.00) 		0.246
(1.00) 		0.739
(1.00) 		0.425
(1.00) 		0.548
(1.00) 		0.102
(1.00) 		0.589
(1.00) 		0.308
(1.00) 		0.171
(1.00) 		0.274
(1.00) 		0.349
(1.00)
AMP PEAK 12(12P12 1) MUTATION ANALYSIS 40 (25%) 122 0.931
(1.00) 		0.334
(1.00) 		0.609
(1.00) 		0.376
(1.00) 		0.542
(1.00) 		0.0879
(1.00) 		0.716
(1.00) 		0.191
(1.00) 		0.161
(1.00) 		0.219
(1.00) 		0.106
(1.00)
AMP PEAK 13(13Q12 13) MUTATION ANALYSIS 121 (75%) 41 0.0316
(1.00) 		0.113
(1.00) 		0.0876
(1.00) 		0.0666
(1.00) 		0.0178
(1.00) 		0.239
(1.00) 		0.718
(1.00) 		0.00387
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.459
(1.00)
AMP PEAK 14(13Q12 2) MUTATION ANALYSIS 120 (74%) 42 0.0393
(1.00) 		0.0514
(1.00) 		0.124
(1.00) 		0.0629
(1.00) 		0.0276
(1.00) 		0.303
(1.00) 		0.369
(1.00) 		0.00467
(1.00) 		0.181
(1.00) 		1
(1.00) 		0.459
(1.00)
AMP PEAK 15(13Q22 1) MUTATION ANALYSIS 117 (72%) 45 0.135
(1.00) 		0.337
(1.00) 		0.808
(1.00) 		0.201
(1.00) 		0.134
(1.00) 		0.279
(1.00) 		0.482
(1.00) 		0.00132
(0.896) 		0.67
(1.00) 		0.801
(1.00) 		0.928
(1.00)
AMP PEAK 16(15Q26 1) MUTATION ANALYSIS 15 (9%) 147 0.818
(1.00) 		0.944
(1.00) 		0.413
(1.00) 		0.221
(1.00) 		0.423
(1.00) 		0.446
(1.00) 		0.106
(1.00) 		0.362
(1.00) 		0.0967
(1.00) 		0.375
(1.00) 		0.473
(1.00)
AMP PEAK 17(16P11 2) MUTATION ANALYSIS 45 (28%) 117 0.358
(1.00) 		0.323
(1.00) 		0.137
(1.00) 		0.624
(1.00) 		0.146
(1.00) 		0.0796
(1.00) 		0.862
(1.00) 		0.0205
(1.00) 		0.67
(1.00) 		0.0597
(1.00) 		0.968
(1.00)
AMP PEAK 18(17Q12) MUTATION ANALYSIS 43 (27%) 119 0.877
(1.00) 		0.676
(1.00) 		0.637
(1.00) 		0.745
(1.00) 		0.357
(1.00) 		0.348
(1.00) 		0.215
(1.00) 		0.517
(1.00) 		0.343
(1.00) 		0.173
(1.00) 		0.3
(1.00)
AMP PEAK 19(17Q24 1) MUTATION ANALYSIS 37 (23%) 125 0.926
(1.00) 		0.423
(1.00) 		0.42
(1.00) 		0.255
(1.00) 		0.265
(1.00) 		0.185
(1.00) 		1
(1.00) 		0.0401
(1.00) 		0.338
(1.00) 		0.221
(1.00) 		0.238
(1.00)
AMP PEAK 20(19P13 2) MUTATION ANALYSIS 32 (20%) 130 0.0127
(1.00) 		0.451
(1.00) 		0.36
(1.00) 		0.242
(1.00) 		0.543
(1.00) 		0.578
(1.00) 		0.693
(1.00) 		0.0717
(1.00) 		0.599
(1.00) 		0.511
(1.00) 		0.522
(1.00)
AMP PEAK 21(20Q11 21) MUTATION ANALYSIS 143 (88%) 19 0.171
(1.00) 		0.099
(1.00) 		0.25
(1.00) 		0.55
(1.00) 		0.0991
(1.00) 		0.547
(1.00) 		1
(1.00) 		0.000738
(0.5) 		0.533
(1.00) 		0.581
(1.00) 		0.514
(1.00)
AMP PEAK 22(20Q11 23) MUTATION ANALYSIS 144 (89%) 18 0.172
(1.00) 		0.179
(1.00) 		0.273
(1.00) 		0.603
(1.00) 		0.0305
(1.00) 		0.433
(1.00) 		1
(1.00) 		0.000498
(0.339) 		0.513
(1.00) 		0.581
(1.00) 		0.514
(1.00)
AMP PEAK 23(20Q13 31) MUTATION ANALYSIS 145 (90%) 17 0.178
(1.00) 		0.239
(1.00) 		0.315
(1.00) 		0.614
(1.00) 		0.0498
(1.00) 		0.493
(1.00) 		0.8
(1.00) 		0.000498
(0.339) 		0.492
(1.00) 		0.55
(1.00) 		0.474
(1.00)
AMP PEAK 24(XP22 2) MUTATION ANALYSIS 33 (20%) 129 0.777
(1.00) 		0.427
(1.00) 		0.0552
(1.00) 		0.722
(1.00) 		0.677
(1.00) 		0.465
(1.00) 		0.0771
(1.00) 		0.303
(1.00) 		0.348
(1.00) 		0.273
(1.00) 		0.407
(1.00)
AMP PEAK 25(XQ27 3) MUTATION ANALYSIS 38 (23%) 124 0.404
(1.00) 		0.225
(1.00) 		0.556
(1.00) 		0.343
(1.00) 		0.749
(1.00) 		0.688
(1.00) 		0.356
(1.00) 		0.3
(1.00) 		0.337
(1.00) 		0.685
(1.00) 		0.862
(1.00)
DEL PEAK 1(1P36 11) MUTATION ANALYSIS 71 (44%) 91 0.822
(1.00) 		0.617
(1.00) 		0.559
(1.00) 		0.0983
(1.00) 		0.223
(1.00) 		0.412
(1.00) 		0.751
(1.00) 		0.56
(1.00) 		1
(1.00) 		0.333
(1.00) 		0.0385
(1.00)
DEL PEAK 2(1P33) MUTATION ANALYSIS 49 (30%) 113 0.73
(1.00) 		0.652
(1.00) 		0.877
(1.00) 		0.537
(1.00) 		0.253
(1.00) 		0.778
(1.00) 		1
(1.00) 		0.11
(1.00) 		0.368
(1.00) 		0.547
(1.00) 		0.594
(1.00)
DEL PEAK 3(1P13 2) MUTATION ANALYSIS 51 (31%) 111 0.888
(1.00) 		0.646
(1.00) 		0.131
(1.00) 		0.144
(1.00) 		0.807
(1.00) 		0.518
(1.00) 		0.735
(1.00) 		0.347
(1.00) 		0.38
(1.00) 		0.688
(1.00) 		0.217
(1.00)
DEL PEAK 4(2P12) MUTATION ANALYSIS 17 (10%) 145 0.413
(1.00) 		0.175
(1.00) 		0.193
(1.00) 		0.364
(1.00) 		0.66
(1.00) 		0.285
(1.00) 		0.8
(1.00) 		1
(1.00) 		0.492
(1.00) 		1
(1.00) 		0.457
(1.00)
DEL PEAK 5(3P14 2) MUTATION ANALYSIS 29 (18%) 133 0.0127
(1.00) 		0.811
(1.00) 		0.131
(1.00) 		0.186
(1.00) 		0.962
(1.00) 		0.285
(1.00) 		0.013
(1.00) 		0.456
(1.00) 		0.292
(1.00) 		0.0853
(1.00) 		0.389
(1.00)
DEL PEAK 6(3Q26 31) MUTATION ANALYSIS 17 (10%) 145 0.00281
(1.00) 		0.705
(1.00) 		0.0368
(1.00) 		0.216
(1.00) 		0.554
(1.00) 		0.2
(1.00) 		0.0036
(1.00) 		0.0303
(1.00) 		0.121
(1.00) 		0.0387
(1.00) 		0.242
(1.00)
DEL PEAK 7(4P13) MUTATION ANALYSIS 58 (36%) 104 0.699
(1.00) 		0.877
(1.00) 		0.644
(1.00) 		0.769
(1.00) 		0.326
(1.00) 		0.98
(1.00) 		0.0996
(1.00) 		0.38
(1.00) 		0.00177
(1.00) 		0.399
(1.00) 		0.671
(1.00)
DEL PEAK 8(4Q22 1) MUTATION ANALYSIS 72 (44%) 90 0.413
(1.00) 		0.378
(1.00) 		0.409
(1.00) 		0.288
(1.00) 		0.722
(1.00) 		0.858
(1.00) 		0.153
(1.00) 		0.393
(1.00) 		0.0892
(1.00) 		0.223
(1.00) 		0.0753
(1.00)
DEL PEAK 9(4Q35 1) MUTATION ANALYSIS 72 (44%) 90 0.804
(1.00) 		0.645
(1.00) 		0.319
(1.00) 		0.455
(1.00) 		0.573
(1.00) 		0.98
(1.00) 		0.428
(1.00) 		0.15
(1.00) 		0.0892
(1.00) 		0.121
(1.00) 		0.332
(1.00)
DEL PEAK 10(5Q11 2) MUTATION ANALYSIS 49 (30%) 113 0.688
(1.00) 		0.836
(1.00) 		0.689
(1.00) 		0.966
(1.00) 		0.874
(1.00) 		0.339
(1.00) 		0.233
(1.00) 		0.347
(1.00) 		0.01
(1.00) 		0.888
(1.00) 		0.713
(1.00)
DEL PEAK 11(5Q22 2) MUTATION ANALYSIS 55 (34%) 107 0.244
(1.00) 		0.56
(1.00) 		0.423
(1.00) 		0.51
(1.00) 		0.432
(1.00) 		0.922
(1.00) 		0.405
(1.00) 		0.222
(1.00) 		0.0176
(1.00) 		1
(1.00) 		0.377
(1.00)
DEL PEAK 12(6P25 3) MUTATION ANALYSIS 24 (15%) 138 0.0811
(1.00) 		0.391
(1.00) 		0.315
(1.00) 		0.216
(1.00) 		0.388
(1.00) 		0.67
(1.00) 		0.825
(1.00) 		0.386
(1.00) 		0.217
(1.00) 		0.66
(1.00) 		0.944
(1.00)
DEL PEAK 13(6Q26) MUTATION ANALYSIS 30 (19%) 132 0.166
(1.00) 		0.852
(1.00) 		0.379
(1.00) 		0.395
(1.00) 		0.077
(1.00) 		0.677
(1.00) 		0.158
(1.00) 		0.0138
(1.00) 		0.308
(1.00) 		0.588
(1.00) 		0.205
(1.00)
DEL PEAK 14(7Q31 1) MUTATION ANALYSIS 4 (2%) 158 0.174
(1.00) 		0.93
(1.00) 		1
(1.00) 		0.528
(1.00) 		1
(1.00) 		1
(1.00) 		0.296
(1.00) 		1
(1.00) 		1
(1.00) 		0.544
(1.00)
DEL PEAK 15(8P23 2) MUTATION ANALYSIS 100 (62%) 62 0.754
(1.00) 		0.494
(1.00) 		0.45
(1.00) 		0.205
(1.00) 		0.557
(1.00) 		0.827
(1.00) 		0.872
(1.00) 		0.564
(1.00) 		0.0831
(1.00) 		0.386
(1.00) 		0.116
(1.00)
DEL PEAK 16(8P11 21) MUTATION ANALYSIS 24 (15%) 138 0.956
(1.00) 		0.184
(1.00) 		0.471
(1.00) 		0.755
(1.00) 		0.837
(1.00) 		0.0829
(1.00) 		0.506
(1.00) 		1
(1.00) 		0.217
(1.00) 		0.742
(1.00) 		0.105
(1.00)
DEL PEAK 17(10Q21 1) MUTATION ANALYSIS 37 (23%) 125 0.83
(1.00) 		0.261
(1.00) 		0.356
(1.00) 		0.858
(1.00) 		0.579
(1.00) 		0.102
(1.00) 		0.574
(1.00) 		0.179
(1.00) 		0.0249
(1.00) 		0.109
(1.00) 		0.854
(1.00)
DEL PEAK 18(10Q25 2) MUTATION ANALYSIS 47 (29%) 115 0.27
(1.00) 		0.369
(1.00) 		0.484
(1.00) 		0.14
(1.00) 		0.895
(1.00) 		0.599
(1.00) 		0.864
(1.00) 		0.0535
(1.00) 		0.00819
(1.00) 		0.204
(1.00) 		0.975
(1.00)
DEL PEAK 19(11Q22 3) MUTATION ANALYSIS 37 (23%) 125 0.584
(1.00) 		0.453
(1.00) 		0.563
(1.00) 		0.647
(1.00) 		0.967
(1.00) 		0.0597
(1.00) 		0.71
(1.00) 		0.0322
(1.00) 		0.133
(1.00) 		0.164
(1.00) 		0.233
(1.00)
DEL PEAK 20(12P13 1) MUTATION ANALYSIS 33 (20%) 129 0.0417
(1.00) 		0.894
(1.00) 		0.263
(1.00) 		0.936
(1.00) 		0.142
(1.00) 		0.28
(1.00) 		0.845
(1.00) 		0.465
(1.00) 		1
(1.00) 		0.568
(1.00) 		0.463
(1.00)
DEL PEAK 21(12Q21 33) MUTATION ANALYSIS 28 (17%) 134 0.285
(1.00) 		0.292
(1.00) 		0.0542
(1.00) 		0.735
(1.00) 		0.888
(1.00) 		0.677
(1.00) 		1
(1.00) 		0.469
(1.00) 		0.277
(1.00) 		0.314
(1.00) 		0.806
(1.00)
DEL PEAK 22(14Q11 2) MUTATION ANALYSIS 67 (41%) 95 0.327
(1.00) 		0.427
(1.00) 		0.535
(1.00) 		0.615
(1.00) 		0.278
(1.00) 		0.714
(1.00) 		0.427
(1.00) 		0.0746
(1.00) 		0.232
(1.00) 		0.101
(1.00) 		0.54
(1.00)
DEL PEAK 23(14Q31 1) MUTATION ANALYSIS 69 (43%) 93 0.31
(1.00) 		0.84
(1.00) 		0.167
(1.00) 		0.166
(1.00) 		0.0557
(1.00) 		0.622
(1.00) 		0.27
(1.00) 		0.00787
(1.00) 		1
(1.00) 		0.424
(1.00) 		0.533
(1.00)
DEL PEAK 24(15Q22 33) MUTATION ANALYSIS 75 (46%) 87 0.92
(1.00) 		0.86
(1.00) 		0.0913
(1.00) 		0.0108
(1.00) 		0.268
(1.00) 		0.767
(1.00) 		0.344
(1.00) 		1
(1.00) 		0.0966
(1.00) 		0.608
(1.00) 		0.0324
(1.00)
DEL PEAK 25(16P13 3) MUTATION ANALYSIS 13 (8%) 149 0.0157
(1.00) 		0.433
(1.00) 		0.0816
(1.00) 		0.788
(1.00) 		0.181
(1.00) 		0.797
(1.00) 		1
(1.00) 		0.263
(1.00) 		1
(1.00) 		1
(1.00) 		0.302
(1.00)
DEL PEAK 26(16Q23 1) MUTATION ANALYSIS 23 (14%) 139 0.945
(1.00) 		0.585
(1.00) 		0.0104
(1.00) 		0.606
(1.00) 		0.0146
(1.00) 		0.841
(1.00) 		0.826
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0773
(1.00)
DEL PEAK 27(17P12) MUTATION ANALYSIS 110 (68%) 52 0.751
(1.00) 		0.0943
(1.00) 		0.561
(1.00) 		0.0145
(1.00) 		0.924
(1.00) 		0.918
(1.00) 		0.866
(1.00) 		0.122
(1.00) 		1
(1.00) 		0.854
(1.00) 		0.733
(1.00)
DEL PEAK 28(17P11 2) MUTATION ANALYSIS 102 (63%) 60 0.843
(1.00) 		0.201
(1.00) 		0.87
(1.00) 		0.0845
(1.00) 		0.705
(1.00) 		0.372
(1.00) 		0.514
(1.00) 		0.0783
(1.00) 		0.671
(1.00) 		0.862
(1.00) 		0.683
(1.00)
DEL PEAK 29(17Q25 3) MUTATION ANALYSIS 24 (15%) 138 0.0274
(1.00) 		0.696
(1.00) 		0.868
(1.00) 		0.366
(1.00) 		0.874
(1.00) 		0.13
(1.00) 		0.119
(1.00) 		1
(1.00) 		0.217
(1.00) 		0.102
(1.00) 		0.665
(1.00)
DEL PEAK 31(18Q22 1) MUTATION ANALYSIS 138 (85%) 24 0.545
(1.00) 		0.227
(1.00) 		0.133
(1.00) 		0.0487
(1.00) 		0.353
(1.00) 		0.567
(1.00) 		0.825
(1.00) 		0.397
(1.00) 		0.593
(1.00) 		0.585
(1.00) 		0.00254
(1.00)
DEL PEAK 32(19P13 3) MUTATION ANALYSIS 38 (23%) 124 0.507
(1.00) 		0.795
(1.00) 		0.796
(1.00) 		0.295
(1.00) 		0.567
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.734
(1.00) 		1
(1.00) 		0.778
(1.00) 		0.716
(1.00)
DEL PEAK 33(20P12 1) MUTATION ANALYSIS 60 (37%) 102 0.0882
(1.00) 		0.23
(1.00) 		0.782
(1.00) 		0.84
(1.00) 		0.885
(1.00) 		0.468
(1.00) 		0.257
(1.00) 		1
(1.00) 		0.0855
(1.00) 		0.466
(1.00) 		0.603
(1.00)
DEL PEAK 34(20P12 1) MUTATION ANALYSIS 60 (37%) 102 0.0882
(1.00) 		0.23
(1.00) 		0.782
(1.00) 		0.84
(1.00) 		0.885
(1.00) 		0.468
(1.00) 		0.257
(1.00) 		1
(1.00) 		0.0855
(1.00) 		0.466
(1.00) 		0.603
(1.00)
DEL PEAK 35(21Q11 2) MUTATION ANALYSIS 70 (43%) 92 0.523
(1.00) 		0.454
(1.00) 		0.464
(1.00) 		0.139
(1.00) 		0.332
(1.00) 		0.778
(1.00) 		0.633
(1.00) 		0.24
(1.00) 		1
(1.00) 		0.535
(1.00) 		0.286
(1.00)
DEL PEAK 36(22Q13 31) MUTATION ANALYSIS 66 (41%) 96 0.0632
(1.00) 		0.255
(1.00) 		0.162
(1.00) 		0.278
(1.00) 		0.00849
(1.00) 		0.209
(1.00) 		0.339
(1.00) 		0.563
(1.00) 		0.688
(1.00) 		0.246
(1.00) 		0.372
(1.00)
DEL PEAK 37(XP22 33) MUTATION ANALYSIS 33 (20%) 129 0.521
(1.00) 		0.681
(1.00) 		0.887
(1.00) 		0.722
(1.00) 		0.869
(1.00) 		0.596
(1.00) 		0.845
(1.00) 		0.716
(1.00) 		1
(1.00) 		0.682
(1.00) 		0.813
(1.00)
'DEL PEAK 30(18Q21.2) MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.00019 (t-test), Q value = 0.13

Table S1.  Gene #55: 'DEL PEAK 30(18Q21.2) MUTATION STATUS' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 152 2.6 (5.4)
DEL PEAK 30(18Q21.2) MUTATED 133 2.9 (5.6)
DEL PEAK 30(18Q21.2) WILD-TYPE 19 0.6 (1.4)

Figure S1.  Get High-res Image Gene #55: 'DEL PEAK 30(18Q21.2) MUTATION STATUS' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

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

  • Clinical data file = READ-TP.clin.merged.picked.txt

  • Number of patients = 162

  • Number of significantly focal cnvs = 62

  • 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

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

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

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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[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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