Correlation between copy number variations of arm-level result and selected clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C11Z42SP
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 variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C11Z42SP
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 55 arm-level events and 15 clinical features across 475 patients, 57 significant findings detected with Q value < 0.25.

  • 1Q GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.T.STAGE', and 'EXTRATHYROIDAL.EXTENSION'.

  • 4P GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 4Q GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 5P GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 5Q GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

  • 7P GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 7Q GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 8Q GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 9Q GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 11P GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 11Q GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 12P GAIN MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.M.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 12Q GAIN MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.M.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 13Q GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 16P GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 16Q GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 17P GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 17Q GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 18P GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 18Q GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 19P GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 19Q GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 20P GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

  • 20Q GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

  • 21Q GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • XQ GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 2P LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 2Q LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 3Q LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 6Q LOSS MUTATION ANALYSIS cnv correlated to 'Time to Death'.

  • 8P LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 8Q LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 9Q LOSS MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 10P LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 10Q LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 11P LOSS MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 11Q LOSS MUTATION ANALYSIS cnv correlated to 'AGE' and 'NEOPLASM.DISEASESTAGE'.

  • 13Q LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 17Q LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • XQ LOSS MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 55 arm-level events and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 57 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		RADIATIONEXPOSURE EXTRATHYROIDAL
EXTENSION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		MULTIFOCALITY TUMOR
SIZE
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 Fisher's exact test Fisher's exact test t-test Fisher's exact test t-test
1Q GAIN MUTATION ANALYSIS 23 (5%) 452 0.147
(1.00) 		0.000629
(0.473) 		6.31e-06
(0.00491) 		0.000144
(0.11) 		0.00345
(1.00) 		0.68
(1.00) 		0.339
(1.00) 		0.0253
(1.00) 		0.506
(1.00) 		0.591
(1.00) 		0.000255
(0.193) 		0.0178
(1.00) 		0.548
(1.00) 		0.055
(1.00) 		0.0507
(1.00)
5Q GAIN MUTATION ANALYSIS 15 (3%) 460 0.0194
(1.00) 		0.00985
(1.00) 		5.66e-05
(0.0436) 		0.633
(1.00) 		0.0107
(1.00) 		1.37e-05
(0.0106) 		0.555
(1.00) 		0.0309
(1.00) 		0.366
(1.00) 		1
(1.00) 		0.0356
(1.00) 		0.516
(1.00) 		3.57e-25
(2.9e-22) 		0.607
(1.00) 		0.147
(1.00)
20P GAIN MUTATION ANALYSIS 12 (3%) 463 0.33
(1.00) 		0.0901
(1.00) 		5.85e-05
(0.045) 		0.496
(1.00) 		0.0678
(1.00) 		0.000173
(0.132) 		0.524
(1.00) 		0.00495
(1.00) 		1
(1.00) 		1
(1.00) 		0.0231
(1.00) 		0.846
(1.00) 		3.83e-25
(3.09e-22) 		0.779
(1.00) 		0.129
(1.00)
20Q GAIN MUTATION ANALYSIS 12 (3%) 463 0.33
(1.00) 		0.0901
(1.00) 		5.85e-05
(0.045) 		0.496
(1.00) 		0.0678
(1.00) 		0.000173
(0.132) 		0.524
(1.00) 		0.00495
(1.00) 		1
(1.00) 		1
(1.00) 		0.0231
(1.00) 		0.846
(1.00) 		3.83e-25
(3.09e-22) 		0.779
(1.00) 		0.129
(1.00)
7P GAIN MUTATION ANALYSIS 16 (3%) 459 0.353
(1.00) 		0.0414
(1.00) 		3.81e-05
(0.0295) 		0.844
(1.00) 		0.00569
(1.00) 		0.00183
(1.00) 		1
(1.00) 		0.0126
(1.00) 		1
(1.00) 		1
(1.00) 		0.0123
(1.00) 		0.516
(1.00) 		3.49e-25
(2.84e-22) 		0.802
(1.00) 		0.633
(1.00)
7Q GAIN MUTATION ANALYSIS 18 (4%) 457 0.368
(1.00) 		0.0284
(1.00) 		0.000208
(0.158) 		0.938
(1.00) 		0.00569
(1.00) 		0.0041
(1.00) 		0.792
(1.00) 		0.00881
(1.00) 		1
(1.00) 		1
(1.00) 		0.0278
(1.00) 		0.215
(1.00) 		3.49e-25
(2.84e-22) 		0.811
(1.00) 		0.583
(1.00)
12P GAIN MUTATION ANALYSIS 13 (3%) 462 0.521
(1.00) 		0.154
(1.00) 		0.0302
(1.00) 		1
(1.00) 		0.00358
(1.00) 		9.15e-05
(0.0701) 		1
(1.00) 		0.011
(1.00) 		1
(1.00) 		1
(1.00) 		0.26
(1.00) 		0.276
(1.00) 		3.66e-25
(2.96e-22) 		0.586
(1.00) 		0.903
(1.00)
12Q GAIN MUTATION ANALYSIS 14 (3%) 461 0.521
(1.00) 		0.129
(1.00) 		0.0527
(1.00) 		0.968
(1.00) 		0.00358
(1.00) 		4.78e-05
(0.0369) 		1
(1.00) 		0.00429
(1.00) 		1
(1.00) 		1
(1.00) 		0.237
(1.00) 		0.232
(1.00) 		3.66e-25
(2.96e-22) 		0.791
(1.00) 		0.903
(1.00)
16Q GAIN MUTATION ANALYSIS 12 (3%) 463 0.202
(1.00) 		0.102
(1.00) 		7.51e-05
(0.0577) 		0.697
(1.00) 		0.0678
(1.00) 		0.00321
(1.00) 		1
(1.00) 		0.0266
(1.00) 		1
(1.00) 		1
(1.00) 		0.0231
(1.00) 		0.333
(1.00) 		3.83e-25
(3.09e-22) 		0.779
(1.00) 		0.663
(1.00)
17P GAIN MUTATION ANALYSIS 16 (3%) 459 0.424
(1.00) 		0.0976
(1.00) 		3.81e-05
(0.0295) 		0.844
(1.00) 		0.036
(1.00) 		0.00838
(1.00) 		1
(1.00) 		0.0472
(1.00) 		1
(1.00) 		1
(1.00) 		0.76
(1.00) 		0.289
(1.00) 		1.44e-06
(0.00112) 		1
(1.00) 		0.399
(1.00)
17Q GAIN MUTATION ANALYSIS 17 (4%) 458 0.424
(1.00) 		0.16
(1.00) 		0.000103
(0.0783) 		0.855
(1.00) 		0.0205
(1.00) 		0.00601
(1.00) 		1
(1.00) 		0.0765
(1.00) 		1
(1.00) 		1
(1.00) 		0.685
(1.00) 		0.319
(1.00) 		2.02e-07
(0.000158) 		0.806
(1.00) 		0.574
(1.00)
11Q LOSS MUTATION ANALYSIS 9 (2%) 466 0.00379
(1.00) 		8.99e-05
(0.069) 		7.2e-06
(0.00559) 		0.188
(1.00) 		0.503
(1.00) 		0.145
(1.00) 		0.00169
(1.00) 		1
(1.00) 		0.238
(1.00) 		1
(1.00) 		0.793
(1.00) 		0.49
(1.00) 		0.252
(1.00) 		1
(1.00) 		0.0132
(1.00)
XQ LOSS MUTATION ANALYSIS 4 (1%) 471 0.748
(1.00) 		0.0809
(1.00) 		1.57e-06
(0.00122) 		0.056
(1.00) 		0.123
(1.00) 		0.103
(1.00) 		0.0577
(1.00) 		1
(1.00) 		1
(1.00) 		0.117
(1.00) 		0.636
(1.00) 		0.298
(1.00) 		4.19e-25
(3.34e-22) 		1
(1.00) 		0.863
(1.00)
4P GAIN MUTATION ANALYSIS 5 (1%) 470 0.0297
(1.00) 		0.0531
(1.00) 		0.372
(1.00) 		0.625
(1.00) 		0.061
(1.00) 		0.0444
(1.00) 		1
(1.00) 		0.192
(1.00) 		0.139
(1.00) 		1
(1.00) 		1
(1.00) 		0.371
(1.00) 		4.1e-25
(3.28e-22) 		0.185
(1.00) 		0.299
(1.00)
4Q GAIN MUTATION ANALYSIS 5 (1%) 470 0.0297
(1.00) 		0.0531
(1.00) 		0.372
(1.00) 		0.625
(1.00) 		0.061
(1.00) 		0.0444
(1.00) 		1
(1.00) 		0.192
(1.00) 		0.139
(1.00) 		1
(1.00) 		1
(1.00) 		0.371
(1.00) 		4.1e-25
(3.28e-22) 		0.185
(1.00) 		0.299
(1.00)
5P GAIN MUTATION ANALYSIS 18 (4%) 457 0.0737
(1.00) 		0.000897
(0.673) 		0.000238
(0.18) 		0.476
(1.00) 		0.172
(1.00) 		0.000347
(0.262) 		0.585
(1.00) 		0.0999
(1.00) 		0.422
(1.00) 		1
(1.00) 		0.0324
(1.00) 		0.533
(1.00) 		0.0121
(1.00) 		1
(1.00) 		0.102
(1.00)
8Q GAIN MUTATION ANALYSIS 7 (1%) 468 0.0949
(1.00) 		0.362
(1.00) 		3.05e-06
(0.00237) 		0.397
(1.00) 		1
(1.00) 		0.0928
(1.00) 		0.682
(1.00) 		0.827
(1.00) 		1
(1.00) 		1
(1.00) 		0.00795
(1.00) 		0.362
(1.00) 		0.002
(1.00) 		0.13
(1.00) 		0.274
(1.00)
9Q GAIN MUTATION ANALYSIS 4 (1%) 471 0.693
(1.00) 		0.0152
(1.00) 		0.0697
(1.00) 		0.623
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.284
(1.00) 		0.472
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.000155
(0.118) 		0.338
(1.00) 		0.00973
(1.00)
11P GAIN MUTATION ANALYSIS 6 (1%) 469 0.563
(1.00) 		0.791
(1.00) 		0.942
(1.00) 		0.692
(1.00) 		0.123
(1.00) 		0.182
(1.00) 		0.19
(1.00) 		0.263
(1.00) 		1
(1.00) 		1
(1.00) 		0.348
(1.00) 		0.44
(1.00) 		4.19e-25
(3.34e-22) 		0.225
(1.00) 		0.556
(1.00)
11Q GAIN MUTATION ANALYSIS 5 (1%) 470 0.567
(1.00) 		0.82
(1.00) 		0.964
(1.00) 		0.794
(1.00) 		0.248
(1.00) 		0.245
(1.00) 		0.611
(1.00) 		0.579
(1.00) 		1
(1.00) 		1
(1.00) 		0.438
(1.00) 		0.371
(1.00) 		4.28e-25
(3.38e-22) 		0.0651
(1.00) 		0.822
(1.00)
13Q GAIN MUTATION ANALYSIS 5 (1%) 470 0.726
(1.00) 		0.162
(1.00) 		0.0172
(1.00) 		0.699
(1.00) 		0.123
(1.00) 		0.245
(1.00) 		1
(1.00) 		0.192
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		4.19e-25
(3.34e-22) 		0.665
(1.00) 		0.65
(1.00)
16P GAIN MUTATION ANALYSIS 14 (3%) 461 0.21
(1.00) 		0.151
(1.00) 		0.000536
(0.403) 		0.789
(1.00) 		0.0371
(1.00) 		0.00562
(1.00) 		1
(1.00) 		0.0899
(1.00) 		1
(1.00) 		1
(1.00) 		0.0376
(1.00) 		0.164
(1.00) 		3.74e-25
(3.02e-22) 		1
(1.00) 		0.674
(1.00)
18P GAIN MUTATION ANALYSIS 6 (1%) 469 0.625
(1.00) 		0.727
(1.00) 		0.942
(1.00) 		0.692
(1.00) 		0.061
(1.00) 		0.471
(1.00) 		0.656
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.371
(1.00) 		4.19e-25
(3.34e-22) 		0.691
(1.00) 		0.605
(1.00)
18Q GAIN MUTATION ANALYSIS 6 (1%) 469 0.625
(1.00) 		0.727
(1.00) 		0.942
(1.00) 		0.692
(1.00) 		0.061
(1.00) 		0.471
(1.00) 		0.656
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.371
(1.00) 		4.19e-25
(3.34e-22) 		0.691
(1.00) 		0.605
(1.00)
19P GAIN MUTATION ANALYSIS 8 (2%) 467 0.728
(1.00) 		0.076
(1.00) 		0.881
(1.00) 		0.572
(1.00) 		0.0302
(1.00) 		0.00453
(1.00) 		0.216
(1.00) 		0.0097
(1.00) 		1
(1.00) 		1
(1.00) 		0.588
(1.00) 		0.429
(1.00) 		3.92e-25
(3.14e-22) 		0.151
(1.00) 		0.216
(1.00)
19Q GAIN MUTATION ANALYSIS 10 (2%) 465 0.0385
(1.00) 		0.0268
(1.00) 		0.771
(1.00) 		0.33
(1.00) 		0.0149
(1.00) 		0.00094
(0.704) 		0.138
(1.00) 		0.00621
(1.00) 		0.261
(1.00) 		1
(1.00) 		0.507
(1.00) 		0.665
(1.00) 		3.83e-25
(3.09e-22) 		0.524
(1.00) 		0.142
(1.00)
21Q GAIN MUTATION ANALYSIS 5 (1%) 470 0.625
(1.00) 		0.0455
(1.00) 		0.767
(1.00) 		0.552
(1.00) 		0.248
(1.00) 		0.688
(1.00) 		0.611
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.636
(1.00) 		0.298
(1.00) 		4.28e-25
(3.38e-22) 		0.0651
(1.00) 		0.318
(1.00)
XQ GAIN MUTATION ANALYSIS 8 (2%) 467 0.302
(1.00) 		0.192
(1.00) 		8.88e-06
(0.00689) 		0.469
(1.00) 		0.685
(1.00) 		0.00453
(1.00) 		0.118
(1.00) 		0.261
(1.00) 		1
(1.00) 		1
(1.00) 		0.0273
(1.00) 		0.429
(1.00) 		0.964
(1.00) 		0.479
(1.00) 		0.21
(1.00)
2P LOSS MUTATION ANALYSIS 10 (2%) 465 0.714
(1.00) 		0.272
(1.00) 		0.00327
(1.00) 		0.686
(1.00) 		0.00731
(1.00) 		0.0177
(1.00) 		0.727
(1.00) 		0.00621
(1.00) 		1
(1.00) 		1
(1.00) 		0.137
(1.00) 		0.534
(1.00) 		3.74e-25
(3.02e-22) 		1
(1.00) 		0.713
(1.00)
2Q LOSS MUTATION ANALYSIS 9 (2%) 466 0.714
(1.00) 		0.134
(1.00) 		0.00103
(0.769) 		0.677
(1.00) 		0.0149
(1.00) 		0.0226
(1.00) 		0.704
(1.00) 		0.00224
(1.00) 		1
(1.00) 		1
(1.00) 		0.15
(1.00) 		0.49
(1.00) 		3.83e-25
(3.09e-22) 		0.738
(1.00) 		0.823
(1.00)
3Q LOSS MUTATION ANALYSIS 3 (1%) 472 0.755
(1.00) 		0.229
(1.00) 		0.0435
(1.00) 		0.804
(1.00) 		0.248
(1.00) 		0.134
(1.00) 		1
(1.00) 		0.24
(1.00) 		1
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00) 		4.28e-25
(3.38e-22) 		0.597
(1.00) 		0.237
(1.00)
6Q LOSS MUTATION ANALYSIS 6 (1%) 469 9.71e-05
(0.0743) 		0.0478
(1.00) 		0.185
(1.00) 		0.904
(1.00) 		0.372
(1.00) 		0.0169
(1.00) 		0.19
(1.00) 		0.789
(1.00) 		0.165
(1.00) 		0.188
(1.00) 		0.348
(1.00) 		0.682
(1.00) 		0.002
(1.00) 		0.691
(1.00) 		0.0497
(1.00)
8P LOSS MUTATION ANALYSIS 4 (1%) 471 0.867
(1.00) 		0.998
(1.00) 		0.188
(1.00) 		1
(1.00) 		0.248
(1.00) 		0.373
(1.00) 		0.0577
(1.00) 		0.472
(1.00) 		1
(1.00) 		1
(1.00) 		0.636
(1.00) 		1
(1.00) 		4.19e-25
(3.34e-22) 		1
(1.00) 		0.879
(1.00)
8Q LOSS MUTATION ANALYSIS 4 (1%) 471 0.867
(1.00) 		0.998
(1.00) 		0.188
(1.00) 		1
(1.00) 		0.248
(1.00) 		0.373
(1.00) 		0.0577
(1.00) 		0.472
(1.00) 		1
(1.00) 		1
(1.00) 		0.636
(1.00) 		1
(1.00) 		4.19e-25
(3.34e-22) 		1
(1.00) 		0.879
(1.00)
9Q LOSS MUTATION ANALYSIS 19 (4%) 456 0.0702
(1.00) 		0.0091
(1.00) 		5.93e-11
(4.65e-08) 		0.314
(1.00) 		0.8
(1.00) 		0.0319
(1.00) 		0.117
(1.00) 		0.673
(1.00) 		0.44
(1.00) 		0.534
(1.00) 		0.0686
(1.00) 		0.741
(1.00) 		0.418
(1.00) 		0.817
(1.00) 		0.168
(1.00)
10P LOSS MUTATION ANALYSIS 6 (1%) 469 0.741
(1.00) 		0.11
(1.00) 		0.0362
(1.00) 		0.445
(1.00) 		0.0302
(1.00) 		0.182
(1.00) 		0.19
(1.00) 		0.263
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		4.1e-25
(3.28e-22) 		0.421
(1.00) 		0.111
(1.00)
10Q LOSS MUTATION ANALYSIS 5 (1%) 470 0.881
(1.00) 		0.108
(1.00) 		0.243
(1.00) 		0.456
(1.00) 		0.061
(1.00) 		0.245
(1.00) 		0.117
(1.00) 		0.579
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		4.19e-25
(3.34e-22) 		0.185
(1.00) 		0.111
(1.00)
11P LOSS MUTATION ANALYSIS 7 (1%) 468 0.00188
(1.00) 		0.000502
(0.379) 		2.17e-07
(0.00017) 		0.189
(1.00) 		0.449
(1.00) 		0.0928
(1.00) 		0.0155
(1.00) 		0.827
(1.00) 		0.19
(1.00) 		1
(1.00) 		0.536
(1.00) 		0.504
(1.00) 		0.0804
(1.00) 		0.708
(1.00) 		0.0349
(1.00)
13Q LOSS MUTATION ANALYSIS 12 (3%) 463 0.118
(1.00) 		0.0411
(1.00) 		0.42
(1.00) 		0.721
(1.00) 		0.0201
(1.00) 		0.306
(1.00) 		0.315
(1.00) 		0.371
(1.00) 		0.305
(1.00) 		0.000342
(0.259) 		0.69
(1.00) 		0.415
(1.00) 		1.18e-14
(9.23e-12) 		0.399
(1.00) 		0.266
(1.00)
17Q LOSS MUTATION ANALYSIS 4 (1%) 471 0.81
(1.00) 		0.377
(1.00) 		0.795
(1.00) 		0.623
(1.00) 		0.123
(1.00) 		0.373
(1.00) 		1
(1.00) 		0.472
(1.00) 		0.113
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		4.28e-25
(3.38e-22) 		1
(1.00) 		0.479
(1.00)
1P GAIN MUTATION ANALYSIS 3 (1%) 472 0.916
(1.00) 		0.297
(1.00) 		0.0159
(1.00) 		1
(1.00) 		1
(1.00) 		0.134
(1.00) 		1
(1.00) 		0.349
(1.00) 		1
(1.00) 		0.0798
(1.00) 		1
(1.00) 		0.222
(1.00) 		0.15
(1.00) 		1
(1.00)
8P GAIN MUTATION ANALYSIS 6 (1%) 469 0.636
(1.00) 		0.624
(1.00) 		0.942
(1.00) 		0.904
(1.00) 		0.623
(1.00) 		0.182
(1.00) 		1
(1.00) 		0.789
(1.00) 		1
(1.00) 		1
(1.00) 		0.348
(1.00) 		0.44
(1.00) 		0.002
(1.00) 		0.225
(1.00) 		0.416
(1.00)
9P GAIN MUTATION ANALYSIS 3 (1%) 472 0.698
(1.00) 		0.0778
(1.00) 		0.0435
(1.00) 		0.804
(1.00) 		0.248
(1.00) 		0.609
(1.00) 		1
(1.00) 		0.24
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.597
(1.00) 		0.0605
(1.00)
14Q GAIN MUTATION ANALYSIS 11 (2%) 464 0.539
(1.00) 		0.0276
(1.00) 		0.00238
(1.00) 		0.369
(1.00) 		0.0678
(1.00) 		0.0323
(1.00) 		0.302
(1.00) 		0.067
(1.00) 		1
(1.00) 		1
(1.00) 		0.821
(1.00) 		0.469
(1.00) 		0.0173
(1.00) 		0.122
(1.00) 		0.305
(1.00)
22Q GAIN MUTATION ANALYSIS 3 (1%) 472 0.677
(1.00) 		0.809
(1.00) 		0.811
(1.00) 		0.298
(1.00) 		0.499
(1.00) 		0.609
(1.00) 		0.57
(1.00) 		0.653
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.768
(1.00)
1P LOSS MUTATION ANALYSIS 3 (1%) 472 0.769
(1.00) 		0.206
(1.00) 		0.0435
(1.00) 		0.804
(1.00) 		0.248
(1.00) 		0.609
(1.00) 		0.57
(1.00) 		0.24
(1.00) 		1
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00) 		1
(1.00)
6P LOSS MUTATION ANALYSIS 3 (1%) 472 0.208
(1.00) 		0.615
(1.00) 		1
(1.00) 		1
(1.00) 		0.134
(1.00) 		1
(1.00) 		0.653
(1.00) 		1
(1.00) 		1
(1.00) 		0.607
(1.00) 		0.434
(1.00) 		0.597
(1.00)
9P LOSS MUTATION ANALYSIS 15 (3%) 460 0.684
(1.00) 		0.12
(1.00) 		0.00167
(1.00) 		0.416
(1.00) 		1
(1.00) 		0.0694
(1.00) 		0.0787
(1.00) 		0.75
(1.00) 		1
(1.00) 		1
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.0298
(1.00) 		0.794
(1.00) 		0.282
(1.00)
15Q LOSS MUTATION ANALYSIS 6 (1%) 469 0.692
(1.00) 		0.548
(1.00) 		0.0617
(1.00) 		0.445
(1.00) 		0.215
(1.00) 		0.0271
(1.00) 		1
(1.00) 		0.0101
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.386
(1.00) 		1
(1.00) 		0.191
(1.00)
17P LOSS MUTATION ANALYSIS 7 (1%) 468 0.597
(1.00) 		0.701
(1.00) 		0.517
(1.00) 		0.132
(1.00) 		0.449
(1.00) 		0.335
(1.00) 		0.682
(1.00) 		0.16
(1.00) 		0.0156
(1.00) 		0.254
(1.00) 		0.176
(1.00) 		0.737
(1.00) 		0.929
(1.00) 		1
(1.00) 		0.0909
(1.00)
18P LOSS MUTATION ANALYSIS 4 (1%) 471 0.754
(1.00) 		0.555
(1.00) 		0.188
(1.00) 		0.334
(1.00) 		1
(1.00) 		0.373
(1.00) 		1
(1.00) 		0.472
(1.00) 		1
(1.00) 		1
(1.00) 		0.636
(1.00) 		1
(1.00) 		0.002
(1.00) 		0.628
(1.00) 		0.24
(1.00)
18Q LOSS MUTATION ANALYSIS 4 (1%) 471 0.754
(1.00) 		0.555
(1.00) 		0.188
(1.00) 		0.334
(1.00) 		1
(1.00) 		0.373
(1.00) 		1
(1.00) 		0.472
(1.00) 		1
(1.00) 		1
(1.00) 		0.636
(1.00) 		1
(1.00) 		0.002
(1.00) 		0.628
(1.00) 		0.24
(1.00)
19P LOSS MUTATION ANALYSIS 4 (1%) 471 0.00071
(0.533) 		0.178
(1.00) 		0.188
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.284
(1.00) 		1
(1.00) 		1
(1.00) 		0.00892
(1.00) 		1
(1.00) 		0.533
(1.00) 		0.628
(1.00)
21Q LOSS MUTATION ANALYSIS 8 (2%) 467 0.855
(1.00) 		0.0931
(1.00) 		0.00857
(1.00) 		0.168
(1.00) 		0.724
(1.00) 		1
(1.00) 		0.439
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.21
(1.00) 		1
(1.00) 		0.98
(1.00) 		0.151
(1.00) 		0.659
(1.00)
22Q LOSS MUTATION ANALYSIS 82 (17%) 393 0.607
(1.00) 		0.847
(1.00) 		0.675
(1.00) 		0.378
(1.00) 		0.255
(1.00) 		0.503
(1.00) 		0.494
(1.00) 		0.262
(1.00) 		0.481
(1.00) 		0.331
(1.00) 		0.113
(1.00) 		0.536
(1.00) 		0.244
(1.00) 		0.14
(1.00) 		0.899
(1.00)
'1Q GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.31e-06 (Chi-square test), Q value = 0.0049

Table S1.  Gene #2: '1Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
1Q GAIN MUTATED 6 0 9 1 7 0
1Q GAIN WILD-TYPE 264 49 97 1 34 5

Figure S1.  Get High-res Image Gene #2: '1Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'1Q GAIN MUTATION STATUS' versus 'PATHOLOGY.T.STAGE'

P value = 0.000144 (Fisher's exact test), Q value = 0.11

Table S2.  Gene #2: '1Q GAIN MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 137 159 158 19
1Q GAIN MUTATED 2 3 14 4
1Q GAIN WILD-TYPE 135 156 144 15

Figure S2.  Get High-res Image Gene #2: '1Q GAIN MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'1Q GAIN MUTATION STATUS' versus 'EXTRATHYROIDAL.EXTENSION'

P value = 0.000255 (Fisher's exact test), Q value = 0.19

Table S3.  Gene #2: '1Q GAIN MUTATION STATUS' versus Clinical Feature #11: 'EXTRATHYROIDAL.EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 124 15 320 1
1Q GAIN MUTATED 10 3 9 1
1Q GAIN WILD-TYPE 114 12 311 0

Figure S3.  Get High-res Image Gene #2: '1Q GAIN MUTATION STATUS' versus Clinical Feature #11: 'EXTRATHYROIDAL.EXTENSION'

'4P GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.1e-25 (t-test), Q value = 3.3e-22

Table S4.  Gene #3: '4P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
4P GAIN MUTATED 5 0.0 (0.0)
4P GAIN WILD-TYPE 374 3.6 (6.3)

Figure S4.  Get High-res Image Gene #3: '4P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'4Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.1e-25 (t-test), Q value = 3.3e-22

Table S5.  Gene #4: '4Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
4Q GAIN MUTATED 5 0.0 (0.0)
4Q GAIN WILD-TYPE 374 3.6 (6.3)

Figure S5.  Get High-res Image Gene #4: '4Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'5P GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000238 (Chi-square test), Q value = 0.18

Table S6.  Gene #5: '5P GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
5P GAIN MUTATED 4 5 7 1 1 0
5P GAIN WILD-TYPE 266 44 99 1 40 5

Figure S6.  Get High-res Image Gene #5: '5P GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'5Q GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.66e-05 (Chi-square test), Q value = 0.044

Table S7.  Gene #6: '5Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
5Q GAIN MUTATED 4 5 5 1 0 0
5Q GAIN WILD-TYPE 266 44 101 1 41 5

Figure S7.  Get High-res Image Gene #6: '5Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'5Q GAIN MUTATION STATUS' versus 'PATHOLOGY.M.STAGE'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.011

Table S8.  Gene #6: '5Q GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 258 8 208
5Q GAIN MUTATED 0 0 15
5Q GAIN WILD-TYPE 258 8 193

Figure S8.  Get High-res Image Gene #6: '5Q GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'5Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.57e-25 (t-test), Q value = 2.9e-22

Table S9.  Gene #6: '5Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
5Q GAIN MUTATED 11 0.0 (0.0)
5Q GAIN WILD-TYPE 368 3.7 (6.3)

Figure S9.  Get High-res Image Gene #6: '5Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'7P GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.81e-05 (Chi-square test), Q value = 0.03

Table S10.  Gene #7: '7P GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
7P GAIN MUTATED 6 6 3 1 0 0
7P GAIN WILD-TYPE 264 43 103 1 41 5

Figure S10.  Get High-res Image Gene #7: '7P GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'7P GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.49e-25 (t-test), Q value = 2.8e-22

Table S11.  Gene #7: '7P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
7P GAIN MUTATED 12 0.0 (0.0)
7P GAIN WILD-TYPE 367 3.7 (6.3)

Figure S11.  Get High-res Image Gene #7: '7P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'7Q GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000208 (Chi-square test), Q value = 0.16

Table S12.  Gene #8: '7Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
7Q GAIN MUTATED 7 6 4 1 0 0
7Q GAIN WILD-TYPE 263 43 102 1 41 5

Figure S12.  Get High-res Image Gene #8: '7Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'7Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.49e-25 (t-test), Q value = 2.8e-22

Table S13.  Gene #8: '7Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
7Q GAIN MUTATED 12 0.0 (0.0)
7Q GAIN WILD-TYPE 367 3.7 (6.3)

Figure S13.  Get High-res Image Gene #8: '7Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'8Q GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.05e-06 (Chi-square test), Q value = 0.0024

Table S14.  Gene #10: '8Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
8Q GAIN MUTATED 3 1 2 1 0 0
8Q GAIN WILD-TYPE 267 48 104 1 41 5

Figure S14.  Get High-res Image Gene #10: '8Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000155 (t-test), Q value = 0.12

Table S15.  Gene #12: '9Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
9Q GAIN MUTATED 3 0.3 (0.6)
9Q GAIN WILD-TYPE 376 3.6 (6.3)

Figure S15.  Get High-res Image Gene #12: '9Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'11P GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.19e-25 (t-test), Q value = 3.3e-22

Table S16.  Gene #13: '11P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
11P GAIN MUTATED 4 0.0 (0.0)
11P GAIN WILD-TYPE 375 3.6 (6.3)

Figure S16.  Get High-res Image Gene #13: '11P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'11Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.28e-25 (t-test), Q value = 3.4e-22

Table S17.  Gene #14: '11Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
11Q GAIN MUTATED 3 0.0 (0.0)
11Q GAIN WILD-TYPE 376 3.6 (6.2)

Figure S17.  Get High-res Image Gene #14: '11Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'12P GAIN MUTATION STATUS' versus 'PATHOLOGY.M.STAGE'

P value = 9.15e-05 (Fisher's exact test), Q value = 0.07

Table S18.  Gene #15: '12P GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 258 8 208
12P GAIN MUTATED 0 0 13
12P GAIN WILD-TYPE 258 8 195

Figure S18.  Get High-res Image Gene #15: '12P GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'12P GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.66e-25 (t-test), Q value = 3e-22

Table S19.  Gene #15: '12P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
12P GAIN MUTATED 10 0.0 (0.0)
12P GAIN WILD-TYPE 369 3.7 (6.3)

Figure S19.  Get High-res Image Gene #15: '12P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'12Q GAIN MUTATION STATUS' versus 'PATHOLOGY.M.STAGE'

P value = 4.78e-05 (Fisher's exact test), Q value = 0.037

Table S20.  Gene #16: '12Q GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 258 8 208
12Q GAIN MUTATED 0 0 14
12Q GAIN WILD-TYPE 258 8 194

Figure S20.  Get High-res Image Gene #16: '12Q GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'12Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.66e-25 (t-test), Q value = 3e-22

Table S21.  Gene #16: '12Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
12Q GAIN MUTATED 10 0.0 (0.0)
12Q GAIN WILD-TYPE 369 3.7 (6.3)

Figure S21.  Get High-res Image Gene #16: '12Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'13Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.19e-25 (t-test), Q value = 3.3e-22

Table S22.  Gene #17: '13Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
13Q GAIN MUTATED 4 0.0 (0.0)
13Q GAIN WILD-TYPE 375 3.6 (6.3)

Figure S22.  Get High-res Image Gene #17: '13Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'16P GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.74e-25 (t-test), Q value = 3e-22

Table S23.  Gene #19: '16P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
16P GAIN MUTATED 9 0.0 (0.0)
16P GAIN WILD-TYPE 370 3.6 (6.3)

Figure S23.  Get High-res Image Gene #19: '16P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'16Q GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 7.51e-05 (Chi-square test), Q value = 0.058

Table S24.  Gene #20: '16Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
16Q GAIN MUTATED 5 4 2 1 0 0
16Q GAIN WILD-TYPE 265 45 104 1 41 5

Figure S24.  Get High-res Image Gene #20: '16Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'16Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.83e-25 (t-test), Q value = 3.1e-22

Table S25.  Gene #20: '16Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
16Q GAIN MUTATED 8 0.0 (0.0)
16Q GAIN WILD-TYPE 371 3.6 (6.3)

Figure S25.  Get High-res Image Gene #20: '16Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'17P GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.81e-05 (Chi-square test), Q value = 0.03

Table S26.  Gene #21: '17P GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
17P GAIN MUTATED 6 6 3 1 0 0
17P GAIN WILD-TYPE 264 43 103 1 41 5

Figure S26.  Get High-res Image Gene #21: '17P GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'17P GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.44e-06 (t-test), Q value = 0.0011

Table S27.  Gene #21: '17P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
17P GAIN MUTATED 12 0.6 (1.4)
17P GAIN WILD-TYPE 367 3.7 (6.3)

Figure S27.  Get High-res Image Gene #21: '17P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'17Q GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000103 (Chi-square test), Q value = 0.078

Table S28.  Gene #22: '17Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
17Q GAIN MUTATED 7 6 3 1 0 0
17Q GAIN WILD-TYPE 263 43 103 1 41 5

Figure S28.  Get High-res Image Gene #22: '17Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'17Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.02e-07 (t-test), Q value = 0.00016

Table S29.  Gene #22: '17Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
17Q GAIN MUTATED 13 0.5 (1.3)
17Q GAIN WILD-TYPE 366 3.7 (6.3)

Figure S29.  Get High-res Image Gene #22: '17Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'18P GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.19e-25 (t-test), Q value = 3.3e-22

Table S30.  Gene #23: '18P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
18P GAIN MUTATED 4 0.0 (0.0)
18P GAIN WILD-TYPE 375 3.6 (6.3)

Figure S30.  Get High-res Image Gene #23: '18P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'18Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.19e-25 (t-test), Q value = 3.3e-22

Table S31.  Gene #24: '18Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
18Q GAIN MUTATED 4 0.0 (0.0)
18Q GAIN WILD-TYPE 375 3.6 (6.3)

Figure S31.  Get High-res Image Gene #24: '18Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'19P GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.92e-25 (t-test), Q value = 3.1e-22

Table S32.  Gene #25: '19P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
19P GAIN MUTATED 7 0.0 (0.0)
19P GAIN WILD-TYPE 372 3.6 (6.3)

Figure S32.  Get High-res Image Gene #25: '19P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'19Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.83e-25 (t-test), Q value = 3.1e-22

Table S33.  Gene #26: '19Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
19Q GAIN MUTATED 8 0.0 (0.0)
19Q GAIN WILD-TYPE 371 3.6 (6.3)

Figure S33.  Get High-res Image Gene #26: '19Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'20P GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.85e-05 (Chi-square test), Q value = 0.045

Table S34.  Gene #27: '20P GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
20P GAIN MUTATED 4 4 3 1 0 0
20P GAIN WILD-TYPE 266 45 103 1 41 5

Figure S34.  Get High-res Image Gene #27: '20P GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20P GAIN MUTATION STATUS' versus 'PATHOLOGY.M.STAGE'

P value = 0.000173 (Fisher's exact test), Q value = 0.13

Table S35.  Gene #27: '20P GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 258 8 208
20P GAIN MUTATED 0 0 12
20P GAIN WILD-TYPE 258 8 196

Figure S35.  Get High-res Image Gene #27: '20P GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'20P GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.83e-25 (t-test), Q value = 3.1e-22

Table S36.  Gene #27: '20P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
20P GAIN MUTATED 8 0.0 (0.0)
20P GAIN WILD-TYPE 371 3.6 (6.3)

Figure S36.  Get High-res Image Gene #27: '20P GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'20Q GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.85e-05 (Chi-square test), Q value = 0.045

Table S37.  Gene #28: '20Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
20Q GAIN MUTATED 4 4 3 1 0 0
20Q GAIN WILD-TYPE 266 45 103 1 41 5

Figure S37.  Get High-res Image Gene #28: '20Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20Q GAIN MUTATION STATUS' versus 'PATHOLOGY.M.STAGE'

P value = 0.000173 (Fisher's exact test), Q value = 0.13

Table S38.  Gene #28: '20Q GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 258 8 208
20Q GAIN MUTATED 0 0 12
20Q GAIN WILD-TYPE 258 8 196

Figure S38.  Get High-res Image Gene #28: '20Q GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'20Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.83e-25 (t-test), Q value = 3.1e-22

Table S39.  Gene #28: '20Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
20Q GAIN MUTATED 8 0.0 (0.0)
20Q GAIN WILD-TYPE 371 3.6 (6.3)

Figure S39.  Get High-res Image Gene #28: '20Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'21Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.28e-25 (t-test), Q value = 3.4e-22

Table S40.  Gene #29: '21Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
21Q GAIN MUTATED 3 0.0 (0.0)
21Q GAIN WILD-TYPE 376 3.6 (6.2)

Figure S40.  Get High-res Image Gene #29: '21Q GAIN MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'XQ GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 8.88e-06 (Chi-square test), Q value = 0.0069

Table S41.  Gene #31: 'XQ GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
XQ GAIN MUTATED 3 2 2 1 0 0
XQ GAIN WILD-TYPE 267 47 104 1 41 5

Figure S41.  Get High-res Image Gene #31: 'XQ GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'2P LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.74e-25 (t-test), Q value = 3e-22

Table S42.  Gene #33: '2P LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
2P LOSS MUTATED 9 0.0 (0.0)
2P LOSS WILD-TYPE 370 3.6 (6.3)

Figure S42.  Get High-res Image Gene #33: '2P LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'2Q LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.83e-25 (t-test), Q value = 3.1e-22

Table S43.  Gene #34: '2Q LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
2Q LOSS MUTATED 8 0.0 (0.0)
2Q LOSS WILD-TYPE 371 3.6 (6.3)

Figure S43.  Get High-res Image Gene #34: '2Q LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'3Q LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.28e-25 (t-test), Q value = 3.4e-22

Table S44.  Gene #35: '3Q LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
3Q LOSS MUTATED 3 0.0 (0.0)
3Q LOSS WILD-TYPE 376 3.6 (6.2)

Figure S44.  Get High-res Image Gene #35: '3Q LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'6Q LOSS MUTATION STATUS' versus 'Time to Death'

P value = 9.71e-05 (logrank test), Q value = 0.074

Table S45.  Gene #37: '6Q LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 13 0.0 - 158.8 (14.2)
6Q LOSS MUTATED 5 2 1.6 - 54.1 (33.6)
6Q LOSS WILD-TYPE 465 11 0.0 - 158.8 (14.0)

Figure S45.  Get High-res Image Gene #37: '6Q LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'8P LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.19e-25 (t-test), Q value = 3.3e-22

Table S46.  Gene #38: '8P LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
8P LOSS MUTATED 4 0.0 (0.0)
8P LOSS WILD-TYPE 375 3.6 (6.3)

Figure S46.  Get High-res Image Gene #38: '8P LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'8Q LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.19e-25 (t-test), Q value = 3.3e-22

Table S47.  Gene #39: '8Q LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
8Q LOSS MUTATED 4 0.0 (0.0)
8Q LOSS WILD-TYPE 375 3.6 (6.3)

Figure S47.  Get High-res Image Gene #39: '8Q LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'9Q LOSS MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.93e-11 (Chi-square test), Q value = 4.6e-08

Table S48.  Gene #41: '9Q LOSS MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
9Q LOSS MUTATED 6 5 3 2 3 0
9Q LOSS WILD-TYPE 264 44 103 0 38 5

Figure S48.  Get High-res Image Gene #41: '9Q LOSS MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'10P LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.1e-25 (t-test), Q value = 3.3e-22

Table S49.  Gene #42: '10P LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
10P LOSS MUTATED 5 0.0 (0.0)
10P LOSS WILD-TYPE 374 3.6 (6.3)

Figure S49.  Get High-res Image Gene #42: '10P LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'10Q LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.19e-25 (t-test), Q value = 3.3e-22

Table S50.  Gene #43: '10Q LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
10Q LOSS MUTATED 4 0.0 (0.0)
10Q LOSS WILD-TYPE 375 3.6 (6.3)

Figure S50.  Get High-res Image Gene #43: '10Q LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'11P LOSS MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.17e-07 (Chi-square test), Q value = 0.00017

Table S51.  Gene #44: '11P LOSS MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
11P LOSS MUTATED 1 1 4 1 0 0
11P LOSS WILD-TYPE 269 48 102 1 41 5

Figure S51.  Get High-res Image Gene #44: '11P LOSS MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'11Q LOSS MUTATION STATUS' versus 'AGE'

P value = 8.99e-05 (t-test), Q value = 0.069

Table S52.  Gene #45: '11Q LOSS MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 475 47.0 (15.5)
11Q LOSS MUTATED 9 67.0 (8.9)
11Q LOSS WILD-TYPE 466 46.6 (15.4)

Figure S52.  Get High-res Image Gene #45: '11Q LOSS MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'11Q LOSS MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 7.2e-06 (Chi-square test), Q value = 0.0056

Table S53.  Gene #45: '11Q LOSS MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
11Q LOSS MUTATED 1 2 4 1 1 0
11Q LOSS WILD-TYPE 269 47 102 1 40 5

Figure S53.  Get High-res Image Gene #45: '11Q LOSS MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'13Q LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.18e-14 (t-test), Q value = 9.2e-12

Table S54.  Gene #46: '13Q LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
13Q LOSS MUTATED 10 0.2 (0.6)
13Q LOSS WILD-TYPE 369 3.7 (6.3)

Figure S54.  Get High-res Image Gene #46: '13Q LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'17Q LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.28e-25 (t-test), Q value = 3.4e-22

Table S55.  Gene #49: '17Q LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
17Q LOSS MUTATED 3 0.0 (0.0)
17Q LOSS WILD-TYPE 376 3.6 (6.2)

Figure S55.  Get High-res Image Gene #49: '17Q LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'XQ LOSS MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.57e-06 (Chi-square test), Q value = 0.0012

Table S56.  Gene #55: 'XQ LOSS MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 270 49 106 2 41 5
XQ LOSS MUTATED 0 4 0 0 0 0
XQ LOSS WILD-TYPE 270 45 106 2 41 5

Figure S56.  Get High-res Image Gene #55: 'XQ LOSS MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'XQ LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.19e-25 (t-test), Q value = 3.3e-22

Table S57.  Gene #55: 'XQ LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 379 3.6 (6.2)
XQ LOSS MUTATED 4 0.0 (0.0)
XQ LOSS WILD-TYPE 375 3.6 (6.3)

Figure S57.  Get High-res Image Gene #55: 'XQ LOSS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

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

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

  • Number of patients = 475

  • Number of significantly arm-level cnvs = 55

  • Number of selected clinical features = 15

  • Exclude regions 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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