Correlation between copy number variation genes (focal) and selected clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C18913VG
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Thyroid Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C18913VG
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 26 arm-level results and 15 clinical features across 421 patients, 13 significant findings detected with Q value < 0.25.

  • Amp Peak 1(Xq22.3) cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • Del Peak 2(2p23.1) cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • Del Peak 3(2q35) cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.

  • Del Peak 6(6q22.31) cnv correlated to 'Time to Death'.

  • Del Peak 12(8q24.22) cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • Del Peak 13(9q21.13) cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • Del Peak 16(11p15.1) cnv correlated to 'AGE' and 'NEOPLASM.DISEASESTAGE'.

  • Del Peak 17(13q12.3) cnv correlated to 'RADIATIONEXPOSURE'.

  • Del Peak 25(19p13.2) cnv correlated to 'Time to Death'.

  • Del Peak 34(Xq22.3) cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 26 arm-level results and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 13 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		RADIATIONEXPOSURE DISTANT
METASTASIS 		EXTRATHYROIDAL
EXTENSION 		LYMPH
NODE
METASTASIS 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE 		MULTIFOCALITY TUMOR
SIZE
nCNV (%) nWild-Type logrank test t-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 Chi-square test Fisher's exact test t-test t-test Chi-square test Fisher's exact test t-test
Del Peak 3(2q35) 0 (0%) 412 0.00119
(0.413) 		0.00609
(1.00) 		1
(1.00) 		0.0899
(1.00) 		1
(1.00) 		0.294
(1.00) 		0.0909
(1.00) 		0.607
(1.00) 		0.0951
(1.00) 		0.192
(1.00) 		1.08e-21
(3.91e-19) 		6.34e-06
(0.00224) 		1
(1.00) 		0.154
(1.00)
Del Peak 16(11p15 1) 0 (0%) 414 0.00162
(0.557) 		0.000427
(0.15) 		0.0132
(1.00) 		0.831
(1.00) 		0.212
(1.00) 		1
(1.00) 		0.0955
(1.00) 		0.548
(1.00) 		0.584
(1.00) 		0.493
(1.00) 		0.0855
(1.00) 		1.36e-06
(0.000484) 		0.704
(1.00) 		0.0337
(1.00)
Del Peak 34(Xq22 3) 0 (0%) 417 0.879
(1.00) 		0.0702
(1.00) 		0.0523
(1.00) 		1
(1.00) 		1
(1.00) 		0.122
(1.00) 		0.105
(1.00) 		0.416
(1.00) 		0.307
(1.00) 		0.294
(1.00) 		1.13e-21
(4.07e-19) 		2.05e-06
(0.000727) 		1
(1.00) 		0.835
(1.00)
Amp Peak 1(Xq22 3) 0 (0%) 408 0.147
(1.00) 		0.162
(1.00) 		0.0453
(1.00) 		0.649
(1.00) 		1
(1.00) 		1
(1.00) 		0.539
(1.00) 		0.0205
(1.00) 		0.35
(1.00) 		0.859
(1.00) 		2.88e-05
(0.0102) 		0.00903
(1.00) 		0.573
(1.00) 		0.996
(1.00)
Del Peak 2(2p23 1) 0 (0%) 412 0.817
(1.00) 		0.169
(1.00) 		0.459
(1.00) 		0.0899
(1.00) 		1
(1.00) 		1
(1.00) 		0.0909
(1.00) 		0.152
(1.00) 		0.093
(1.00) 		0.603
(1.00) 		1.06e-21
(3.84e-19) 		0.00121
(0.418) 		1
(1.00) 		0.419
(1.00)
Del Peak 6(6q22 31) 0 (0%) 416 1.81e-09
(6.46e-07) 		0.112
(1.00) 		0.605
(1.00) 		0.585
(1.00) 		0.156
(1.00) 		0.159
(1.00) 		0.0282
(1.00) 		0.437
(1.00) 		0.542
(1.00) 		1
(1.00) 		0.00185
(0.637) 		0.0569
(1.00) 		0.39
(1.00) 		0.0482
(1.00)
Del Peak 12(8q24 22) 0 (0%) 416 0.882
(1.00) 		0.0612
(1.00) 		0.107
(1.00) 		0.585
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.376
(1.00) 		0.364
(1.00) 		1.16e-21
(4.15e-19) 		0.00729
(1.00) 		1
(1.00) 		0.253
(1.00)
Del Peak 13(9q21 13) 0 (0%) 406 0.0079
(1.00) 		0.0124
(1.00) 		0.546
(1.00) 		0.796
(1.00) 		0.403
(1.00) 		0.459
(1.00) 		0.139
(1.00) 		0.0681
(1.00) 		0.391
(1.00) 		0.758
(1.00) 		0.731
(1.00) 		2.4e-13
(8.58e-11) 		0.798
(1.00) 		0.151
(1.00)
Del Peak 17(13q12 3) 0 (0%) 409 0.316
(1.00) 		0.00765
(1.00) 		0.0839
(1.00) 		0.345
(1.00) 		0.337
(1.00) 		0.000592
(0.207) 		0.285
(1.00) 		1
(1.00) 		0.272
(1.00) 		0.828
(1.00) 		0.0727
(1.00) 		0.0667
(1.00) 		0.381
(1.00) 		0.503
(1.00)
Del Peak 25(19p13 2) 0 (0%) 417 2.95e-05
(0.0104) 		0.0286
(1.00) 		0.268
(1.00) 		1
(1.00) 		1
(1.00) 		0.159
(1.00) 		1
(1.00) 		1
(1.00) 		0.0593
(1.00) 		0.294
(1.00) 		0.212
(1.00) 		0.134
(1.00)
Del Peak 4(5p15 2) 0 (0%) 418 0.917
(1.00) 		0.306
(1.00) 		0.574
(1.00) 		0.356
(1.00) 		1
(1.00) 		1
(1.00) 		0.304
(1.00) 		0.285
(1.00) 		0.177
(1.00) 		0.0509
(1.00) 		0.439
(1.00) 		0.706
(1.00) 		0.084
(1.00) 		0.411
(1.00)
Del Peak 8(7q34) 0 (0%) 417 0.73
(1.00) 		0.774
(1.00) 		1
(1.00) 		0.145
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.416
(1.00) 		0.689
(1.00) 		1
(1.00) 		0.235
(1.00) 		0.797
(1.00) 		0.634
(1.00) 		0.193
(1.00)
Del Peak 14(10q21 2) 0 (0%) 411 0.727
(1.00) 		0.814
(1.00) 		0.719
(1.00) 		0.617
(1.00) 		0.29
(1.00) 		1
(1.00) 		0.795
(1.00) 		1
(1.00) 		0.898
(1.00) 		1
(1.00) 		0.676
(1.00) 		0.872
(1.00) 		0.514
(1.00) 		0.211
(1.00)
Del Peak 15(10q23 31) 0 (0%) 412 0.762
(1.00) 		0.0097
(1.00) 		0.241
(1.00) 		0.566
(1.00) 		1
(1.00) 		1
(1.00) 		0.313
(1.00) 		1
(1.00) 		0.11
(1.00) 		0.798
(1.00) 		0.00551
(1.00) 		0.0321
(1.00) 		0.735
(1.00) 		0.0709
(1.00)
Del Peak 18(13q21 31) 0 (0%) 407 0.327
(1.00) 		0.0995
(1.00) 		0.207
(1.00) 		0.199
(1.00) 		0.0744
(1.00) 		0.000865
(0.302) 		0.251
(1.00) 		0.6
(1.00) 		0.233
(1.00) 		0.844
(1.00) 		0.00276
(0.944) 		0.526
(1.00) 		0.0869
(1.00) 		0.842
(1.00)
Del Peak 19(15q25 3) 0 (0%) 415 0.777
(1.00) 		0.909
(1.00) 		0.345
(1.00) 		0.0614
(1.00) 		1
(1.00) 		1
(1.00) 		0.0277
(1.00) 		1
(1.00) 		0.358
(1.00) 		0.662
(1.00) 		0.397
(1.00) 		0.0395
(1.00) 		1
(1.00) 		0.73
(1.00)
Del Peak 21(16q23 3) 0 (0%) 416 0.717
(1.00) 		0.0711
(1.00) 		1
(1.00) 		0.116
(1.00) 		1
(1.00) 		0.195
(1.00) 		1
(1.00) 		0.034
(1.00) 		0.921
(1.00) 		0.203
(1.00) 		0.745
(1.00) 		0.0292
(1.00) 		0.658
(1.00) 		0.893
(1.00)
Del Peak 22(17p13 1) 0 (0%) 416 0.696
(1.00) 		0.969
(1.00) 		0.336
(1.00) 		0.178
(1.00) 		0.00971
(1.00) 		1
(1.00) 		0.246
(1.00) 		0.186
(1.00) 		0.437
(1.00) 		1
(1.00) 		0.162
(1.00) 		0.268
(1.00) 		0.39
(1.00) 		0.371
(1.00)
Del Peak 23(18p11 21) 0 (0%) 418 0.879
(1.00) 		0.939
(1.00) 		0.574
(1.00) 		0.653
(1.00) 		1
(1.00) 		1
(1.00) 		0.603
(1.00) 		0.604
(1.00) 		0.797
(1.00) 		1
(1.00) 		0.0277
(1.00) 		0.0664
(1.00) 		1
(1.00) 		0.389
(1.00)
Del Peak 24(18q22 2) 0 (0%) 417 0.787
(1.00) 		0.522
(1.00) 		0.576
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.416
(1.00) 		0.689
(1.00) 		1
(1.00) 		0.00185
(0.637) 		0.197
(1.00) 		0.634
(1.00) 		0.757
(1.00)
Del Peak 28(21q21 1) 0 (0%) 412 0.872
(1.00) 		0.0536
(1.00) 		0.699
(1.00) 		0.772
(1.00) 		1
(1.00) 		1
(1.00) 		0.586
(1.00) 		0.607
(1.00) 		0.391
(1.00) 		0.332
(1.00) 		0.912
(1.00) 		0.00823
(1.00) 		0.19
(1.00) 		0.621
(1.00)
Del Peak 29(22q13 1) 0 (0%) 351 0.248
(1.00) 		0.628
(1.00) 		0.881
(1.00) 		0.228
(1.00) 		0.482
(1.00) 		0.325
(1.00) 		0.485
(1.00) 		0.204
(1.00) 		0.514
(1.00) 		0.371
(1.00) 		0.0841
(1.00) 		0.689
(1.00) 		0.183
(1.00) 		1
(1.00)
Del Peak 30(22q13 2) 0 (0%) 351 0.248
(1.00) 		0.628
(1.00) 		0.881
(1.00) 		0.228
(1.00) 		0.482
(1.00) 		0.325
(1.00) 		0.485
(1.00) 		0.204
(1.00) 		0.514
(1.00) 		0.371
(1.00) 		0.0841
(1.00) 		0.689
(1.00) 		0.183
(1.00) 		1
(1.00)
Del Peak 31(22q13 31) 0 (0%) 351 0.248
(1.00) 		0.628
(1.00) 		0.881
(1.00) 		0.228
(1.00) 		0.482
(1.00) 		0.325
(1.00) 		0.485
(1.00) 		0.204
(1.00) 		0.514
(1.00) 		0.371
(1.00) 		0.0841
(1.00) 		0.689
(1.00) 		0.183
(1.00) 		1
(1.00)
Del Peak 32(22q13 32) 0 (0%) 350 0.248
(1.00) 		0.668
(1.00) 		0.881
(1.00) 		0.147
(1.00) 		0.481
(1.00) 		0.324
(1.00) 		0.574
(1.00) 		0.204
(1.00) 		0.448
(1.00) 		0.371
(1.00) 		0.0674
(1.00) 		0.708
(1.00) 		0.145
(1.00) 		1
(1.00)
Del Peak 33(Xq22 1) 0 (0%) 415 0.829
(1.00) 		0.186
(1.00) 		0.0387
(1.00) 		1
(1.00) 		1
(1.00) 		0.195
(1.00) 		0.188
(1.00) 		0.344
(1.00) 		0.647
(1.00) 		0.269
(1.00) 		0.804
(1.00) 		0.000937
(0.326) 		0.412
(1.00) 		0.495
(1.00)
'Amp Peak 1(Xq22.3)' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.88e-05 (t-test), Q value = 0.01

Table S1.  Gene #1: 'Amp Peak 1(Xq22.3)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 328 3.5 (6.2)
AMP PEAK 1(XQ22.3) CNV 7 0.4 (1.1)
AMP PEAK 1(XQ22.3) WILD-TYPE 321 3.6 (6.3)

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(Xq22.3)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 2(2p23.1)' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.06e-21 (t-test), Q value = 3.8e-19

Table S2.  Gene #2: 'Del Peak 2(2p23.1)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 328 3.5 (6.2)
DEL PEAK 2(2P23.1) CNV 7 0.0 (0.0)
DEL PEAK 2(2P23.1) WILD-TYPE 321 3.6 (6.2)

Figure S2.  Get High-res Image Gene #2: 'Del Peak 2(2p23.1)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 3(2q35)' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.08e-21 (t-test), Q value = 3.9e-19

Table S3.  Gene #3: 'Del Peak 3(2q35)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 328 3.5 (6.2)
DEL PEAK 3(2Q35) CNV 6 0.0 (0.0)
DEL PEAK 3(2Q35) WILD-TYPE 322 3.6 (6.2)

Figure S3.  Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 3(2q35)' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.34e-06 (Chi-square test), Q value = 0.0022

Table S4.  Gene #3: 'Del Peak 3(2q35)' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 237 44 94 2 36 5
DEL PEAK 3(2Q35) CNV 1 6 2 0 0 0
DEL PEAK 3(2Q35) WILD-TYPE 236 38 92 2 36 5

Figure S4.  Get High-res Image Gene #3: 'Del Peak 3(2q35)' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'Del Peak 6(6q22.31)' versus 'Time to Death'

P value = 1.81e-09 (logrank test), Q value = 6.5e-07

Table S5.  Gene #5: 'Del Peak 6(6q22.31)' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 416 10 0.0 - 147.4 (9.3)
DEL PEAK 6(6Q22.31) CNV 5 2 1.6 - 33.6 (21.4)
DEL PEAK 6(6Q22.31) WILD-TYPE 411 8 0.0 - 147.4 (9.3)

Figure S5.  Get High-res Image Gene #5: 'Del Peak 6(6q22.31)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 12(8q24.22)' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.16e-21 (t-test), Q value = 4.2e-19

Table S6.  Gene #7: 'Del Peak 12(8q24.22)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 328 3.5 (6.2)
DEL PEAK 12(8Q24.22) CNV 3 0.0 (0.0)
DEL PEAK 12(8Q24.22) WILD-TYPE 325 3.6 (6.2)

Figure S6.  Get High-res Image Gene #7: 'Del Peak 12(8q24.22)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 13(9q21.13)' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.4e-13 (Chi-square test), Q value = 8.6e-11

Table S7.  Gene #8: 'Del Peak 13(9q21.13)' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 237 44 94 2 36 5
DEL PEAK 13(9Q21.13) CNV 3 5 2 2 3 0
DEL PEAK 13(9Q21.13) WILD-TYPE 234 39 92 0 33 5

Figure S7.  Get High-res Image Gene #8: 'Del Peak 13(9q21.13)' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'Del Peak 16(11p15.1)' versus 'AGE'

P value = 0.000427 (t-test), Q value = 0.15

Table S8.  Gene #11: 'Del Peak 16(11p15.1)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 421 46.6 (15.6)
DEL PEAK 16(11P15.1) CNV 7 68.1 (8.7)
DEL PEAK 16(11P15.1) WILD-TYPE 414 46.2 (15.4)

Figure S8.  Get High-res Image Gene #11: 'Del Peak 16(11p15.1)' versus Clinical Feature #2: 'AGE'

'Del Peak 16(11p15.1)' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.36e-06 (Chi-square test), Q value = 0.00048

Table S9.  Gene #11: 'Del Peak 16(11p15.1)' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 237 44 94 2 36 5
DEL PEAK 16(11P15.1) CNV 1 1 4 1 0 0
DEL PEAK 16(11P15.1) WILD-TYPE 236 43 90 1 36 5

Figure S9.  Get High-res Image Gene #11: 'Del Peak 16(11p15.1)' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'Del Peak 17(13q12.3)' versus 'RADIATIONEXPOSURE'

P value = 0.000592 (Fisher's exact test), Q value = 0.21

Table S10.  Gene #12: 'Del Peak 17(13q12.3)' versus Clinical Feature #6: 'RADIATIONEXPOSURE'

nPatients NO YES
ALL 363 16
DEL PEAK 17(13Q12.3) CNV 7 4
DEL PEAK 17(13Q12.3) WILD-TYPE 356 12

Figure S10.  Get High-res Image Gene #12: 'Del Peak 17(13q12.3)' versus Clinical Feature #6: 'RADIATIONEXPOSURE'

'Del Peak 25(19p13.2)' versus 'Time to Death'

P value = 2.95e-05 (logrank test), Q value = 0.01

Table S11.  Gene #19: 'Del Peak 25(19p13.2)' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 416 10 0.0 - 147.4 (9.3)
DEL PEAK 25(19P13.2) CNV 4 1 0.9 - 33.5 (11.9)
DEL PEAK 25(19P13.2) WILD-TYPE 412 9 0.0 - 147.4 (9.3)

Figure S11.  Get High-res Image Gene #19: 'Del Peak 25(19p13.2)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 34(Xq22.3)' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.13e-21 (t-test), Q value = 4.1e-19

Table S12.  Gene #26: 'Del Peak 34(Xq22.3)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 328 3.5 (6.2)
DEL PEAK 34(XQ22.3) CNV 4 0.0 (0.0)
DEL PEAK 34(XQ22.3) WILD-TYPE 324 3.6 (6.2)

Figure S12.  Get High-res Image Gene #26: 'Del Peak 34(Xq22.3)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 34(Xq22.3)' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.05e-06 (Chi-square test), Q value = 0.00073

Table S13.  Gene #26: 'Del Peak 34(Xq22.3)' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 237 44 94 2 36 5
DEL PEAK 34(XQ22.3) CNV 0 4 0 0 0 0
DEL PEAK 34(XQ22.3) WILD-TYPE 237 40 94 2 36 5

Figure S13.  Get High-res Image Gene #26: 'Del Peak 34(Xq22.3)' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

Methods & Data
Input

  • Mutation data file = all_lesions.conf_99.cnv.cluster.txt

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

  • Number of patients = 421

  • Number of significantly arm-level cnvs = 26

  • Number of selected clinical features = 15

  • 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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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