Correlation between gene mutation status and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1HM56JG
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 gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1HM56JG
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 32 genes and 10 molecular subtypes across 323 patients, 26 significant findings detected with P value < 0.05 and Q value < 0.25.

  • NRAS mutation correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • BRAF mutation correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • HRAS mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 32 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 26 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type 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 Fisher's exact test
BRAF 183 (57%) 140 0.0194
(1.00) 		9.33e-39
(2.63e-36) 		9.4e-07
(0.000256) 		2.51e-11
(6.89e-09) 		7.79e-49
(2.24e-46) 		1.22e-48
(3.5e-46) 		2.35e-40
(6.66e-38) 		3.32e-43
(9.42e-41) 		5.44e-44
(1.55e-41) 		1.44e-45
(4.12e-43)
HRAS 12 (4%) 311 0.000222
(0.0586) 		2.28e-06
(0.000613) 		9.23e-05
(0.0245) 		0.00529
(1.00) 		1.46e-05
(0.00389) 		3.74e-06
(0.001) 		1.69e-06
(0.000455) 		9.25e-06
(0.00247) 		1.22e-06
(0.000331) 		3.38e-07
(9.23e-05)
NRAS 26 (8%) 297 0.00692
(1.00) 		7.17e-14
(2.01e-11) 		1
(1.00) 		0.000583
(0.153) 		8.63e-13
(2.39e-10) 		7.02e-14
(1.97e-11) 		1.87e-12
(5.16e-10) 		3.3e-12
(9.09e-10) 		8.08e-13
(2.25e-10) 		2.01e-13
(5.62e-11)
EMG1 6 (2%) 317 0.548
(1.00) 		1
(1.00) 		0.327
(1.00) 		0.0846
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
PTTG1IP 4 (1%) 319 1
(1.00) 		1
(1.00) 		0.199
(1.00) 		0.418
(1.00) 		0.471
(1.00) 		0.396
(1.00) 		0.467
(1.00) 		0.556
(1.00)
RPTN 8 (2%) 315 0.805
(1.00) 		0.436
(1.00) 		0.265
(1.00) 		0.801
(1.00) 		0.0385
(1.00) 		0.22
(1.00) 		0.74
(1.00) 		0.672
(1.00) 		0.821
(1.00) 		1
(1.00)
TG 16 (5%) 307 1
(1.00) 		0.0226
(1.00) 		0.34
(1.00) 		0.492
(1.00) 		0.129
(1.00) 		0.0519
(1.00) 		0.0453
(1.00) 		0.021
(1.00) 		0.0428
(1.00) 		0.0235
(1.00)
TMCO2 3 (1%) 320 1
(1.00) 		0.41
(1.00) 		0.778
(1.00) 		0.2
(1.00) 		0.508
(1.00) 		0.325
(1.00) 		0.418
(1.00) 		0.778
(1.00) 		0.394
(1.00) 		0.778
(1.00)
R3HDM2 4 (1%) 319 0.0124
(1.00) 		0.0607
(1.00) 		0.136
(1.00) 		0.0869
(1.00) 		0.021
(1.00) 		0.00694
(1.00) 		0.0184
(1.00) 		0.00788
(1.00)
PRB2 6 (2%) 317 1
(1.00) 		0.633
(1.00) 		0.0801
(1.00) 		0.851
(1.00) 		0.374
(1.00) 		0.572
(1.00) 		0.529
(1.00) 		0.518
(1.00) 		0.52
(1.00) 		0.523
(1.00)
LYPD3 3 (1%) 320 0.547
(1.00) 		0.41
(1.00) 		0.508
(1.00) 		0.439
(1.00) 		0.653
(1.00) 		0.778
(1.00) 		0.64
(1.00) 		0.778
(1.00)
IL32 3 (1%) 320 1
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.858
(1.00) 		0.209
(1.00) 		1
(1.00) 		1
(1.00) 		0.644
(1.00)
PPM1D 5 (2%) 318 1
(1.00) 		1
(1.00) 		0.778
(1.00) 		0.125
(1.00) 		0.455
(1.00) 		0.249
(1.00) 		0.869
(1.00) 		0.328
(1.00) 		0.864
(1.00) 		0.329
(1.00)
EIF1AX 5 (2%) 318 0.731
(1.00) 		0.0268
(1.00) 		0.444
(1.00) 		0.132
(1.00) 		0.0584
(1.00) 		0.0304
(1.00) 		0.0634
(1.00) 		0.199
(1.00) 		0.056
(1.00) 		0.235
(1.00)
PPTC7 3 (1%) 320 0.0791
(1.00) 		0.0615
(1.00) 		0.173
(1.00) 		0.108
(1.00) 		0.312
(1.00) 		0.292
(1.00) 		0.294
(1.00) 		0.301
(1.00)
SCUBE2 3 (1%) 320 1
(1.00) 		0.273
(1.00) 		0.322
(1.00) 		0.608
(1.00) 		0.653
(1.00) 		0.643
(1.00) 		0.64
(1.00) 		0.522
(1.00)
MUC7 5 (2%) 318 0.731
(1.00) 		0.362
(1.00) 		0.683
(1.00) 		0.26
(1.00) 		0.805
(1.00) 		0.915
(1.00) 		0.869
(1.00) 		0.631
(1.00) 		0.864
(1.00) 		0.63
(1.00)
TMEM90B 3 (1%) 320 0.135
(1.00) 		1
(1.00) 		1
(1.00) 		0.858
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
CCDC15 5 (2%) 318 0.731
(1.00) 		0.147
(1.00) 		1
(1.00) 		0.381
(1.00) 		0.143
(1.00) 		0.271
(1.00) 		0.627
(1.00) 		0.108
(1.00) 		0.632
(1.00) 		0.531
(1.00)
ATAD2 4 (1%) 319 1
(1.00) 		0.645
(1.00) 		0.814
(1.00) 		1
(1.00) 		0.694
(1.00) 		1
(1.00) 		0.689
(1.00) 		1
(1.00)
ZNF878 4 (1%) 319 1
(1.00) 		0.48
(1.00) 		0.048
(1.00) 		0.643
(1.00) 		0.694
(1.00) 		1
(1.00) 		0.689
(1.00) 		1
(1.00)
ARMCX3 3 (1%) 320 0.547
(1.00) 		0.569
(1.00) 		0.443
(1.00) 		0.181
(1.00) 		0.533
(1.00) 		0.2
(1.00) 		0.514
(1.00) 		0.202
(1.00)
TSC22D1 3 (1%) 320 1
(1.00) 		1
(1.00) 		0.753
(1.00) 		1
(1.00) 		1
(1.00) 		0.512
(1.00) 		0.779
(1.00) 		0.644
(1.00)
TROAP 3 (1%) 320 1
(1.00) 		0.569
(1.00) 		0.778
(1.00) 		0.535
(1.00) 		0.753
(1.00) 		1
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.294
(1.00) 		0.301
(1.00)
SYNPO2L 3 (1%) 320 0.547
(1.00) 		1
(1.00) 		1
(1.00) 		0.858
(1.00) 		1
(1.00) 		1
(1.00) 		0.779
(1.00) 		1
(1.00)
ZNF443 4 (1%) 319 0.144
(1.00) 		0.29
(1.00) 		1
(1.00) 		1
(1.00) 		0.515
(1.00) 		0.371
(1.00) 		0.167
(1.00) 		0.107
(1.00) 		0.152
(1.00) 		0.113
(1.00)
SLC26A11 3 (1%) 320 0.0791
(1.00) 		1
(1.00) 		0.382
(1.00) 		0.858
(1.00) 		0.776
(1.00) 		0.398
(1.00) 		0.779
(1.00) 		0.401
(1.00)
CDC27 3 (1%) 320 1
(1.00) 		1
(1.00) 		0.382
(1.00) 		0.143
(1.00) 		0.776
(1.00) 		0.398
(1.00) 		0.779
(1.00) 		0.401
(1.00)
CHD2 4 (1%) 319 1
(1.00) 		0.376
(1.00) 		0.639
(1.00) 		0.535
(1.00) 		0.74
(1.00) 		0.0637
(1.00) 		1
(1.00) 		0.84
(1.00) 		1
(1.00) 		0.837
(1.00)
SREBF2 3 (1%) 320 1
(1.00) 		0.569
(1.00) 		0.583
(1.00) 		0.325
(1.00) 		0.418
(1.00) 		0.778
(1.00) 		0.394
(1.00) 		0.778
(1.00)
ACD 3 (1%) 320 0.547
(1.00) 		1
(1.00) 		0.382
(1.00) 		0.143
(1.00) 		0.209
(1.00) 		1
(1.00) 		0.199
(1.00) 		0.644
(1.00)
DNMT3A 5 (2%) 318 0.465
(1.00) 		1
(1.00) 		0.505
(1.00) 		1
(1.00) 		0.484
(1.00) 		0.782
(1.00) 		0.743
(1.00) 		0.861
(1.00) 		0.74
(1.00) 		0.864
(1.00)
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 7.17e-14 (Fisher's exact test), Q value = 2e-11

Table S1.  Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 50 167
NRAS MUTATED 26 0 0
NRAS WILD-TYPE 80 50 167

Figure S1.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.000583 (Fisher's exact test), Q value = 0.15

Table S2.  Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 32 89
NRAS MUTATED 9 5 0
NRAS WILD-TYPE 87 27 89

Figure S2.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 8.63e-13 (Fisher's exact test), Q value = 2.4e-10

Table S3.  Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 39 77 94
NRAS MUTATED 26 0 0 0
NRAS WILD-TYPE 79 39 77 94

Figure S3.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.02e-14 (Fisher's exact test), Q value = 2e-11

Table S4.  Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 124 96 34
NRAS MUTATED 0 0 26 0
NRAS WILD-TYPE 61 124 70 34

Figure S4.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.87e-12 (Fisher's exact test), Q value = 5.2e-10

Table S5.  Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 114 102
NRAS MUTATED 25 0 1
NRAS WILD-TYPE 81 114 101

Figure S5.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.3e-12 (Fisher's exact test), Q value = 9.1e-10

Table S6.  Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 116 112
NRAS MUTATED 24 1 1
NRAS WILD-TYPE 70 115 111

Figure S6.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.08e-13 (Fisher's exact test), Q value = 2.2e-10

Table S7.  Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 121 96
NRAS MUTATED 25 0 1
NRAS WILD-TYPE 80 121 95

Figure S7.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.01e-13 (Fisher's exact test), Q value = 5.6e-11

Table S8.  Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 97 107
NRAS MUTATED 1 25 0
NRAS WILD-TYPE 117 72 107

Figure S8.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 9.33e-39 (Fisher's exact test), Q value = 2.6e-36

Table S9.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 50 167
BRAF MUTATED 10 29 144
BRAF WILD-TYPE 96 21 23

Figure S9.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 9.4e-07 (Fisher's exact test), Q value = 0.00026

Table S10.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 76 79
BRAF MUTATED 19 57 42
BRAF WILD-TYPE 43 19 37

Figure S10.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 2.51e-11 (Fisher's exact test), Q value = 6.9e-09

Table S11.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 32 89
BRAF MUTATED 30 16 72
BRAF WILD-TYPE 66 16 17

Figure S11.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 7.79e-49 (Fisher's exact test), Q value = 2.2e-46

Table S12.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 39 77 94
BRAF MUTATED 5 21 63 89
BRAF WILD-TYPE 100 18 14 5

Figure S12.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.22e-48 (Fisher's exact test), Q value = 3.5e-46

Table S13.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 124 96 34
BRAF MUTATED 47 111 1 19
BRAF WILD-TYPE 14 13 95 15

Figure S13.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2.35e-40 (Fisher's exact test), Q value = 6.7e-38

Table S14.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 114 102
BRAF MUTATED 7 98 77
BRAF WILD-TYPE 99 16 25

Figure S14.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.32e-43 (Fisher's exact test), Q value = 9.4e-41

Table S15.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 116 112
BRAF MUTATED 1 92 89
BRAF WILD-TYPE 93 24 23

Figure S15.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.44e-44 (Fisher's exact test), Q value = 1.5e-41

Table S16.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 121 96
BRAF MUTATED 5 106 71
BRAF WILD-TYPE 100 15 25

Figure S16.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.44e-45 (Fisher's exact test), Q value = 4.1e-43

Table S17.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 97 107
BRAF MUTATED 92 1 89
BRAF WILD-TYPE 26 96 18

Figure S17.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000222 (Fisher's exact test), Q value = 0.059

Table S18.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 246 49
HRAS MUTATED 0 4 8
HRAS WILD-TYPE 25 242 41

Figure S18.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.28e-06 (Fisher's exact test), Q value = 0.00061

Table S19.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 50 167
HRAS MUTATED 12 0 0
HRAS WILD-TYPE 94 50 167

Figure S19.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.024

Table S20.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 76 79
HRAS MUTATED 9 2 0
HRAS WILD-TYPE 53 74 79

Figure S20.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.0039

Table S21.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 39 77 94
HRAS MUTATED 12 0 0 0
HRAS WILD-TYPE 93 39 77 94

Figure S21.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.74e-06 (Fisher's exact test), Q value = 0.001

Table S22.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 124 96 34
HRAS MUTATED 0 0 12 0
HRAS WILD-TYPE 61 124 84 34

Figure S22.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.69e-06 (Fisher's exact test), Q value = 0.00045

Table S23.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 114 102
HRAS MUTATED 12 0 0
HRAS WILD-TYPE 94 114 102

Figure S23.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.25e-06 (Fisher's exact test), Q value = 0.0025

Table S24.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 116 112
HRAS MUTATED 11 0 1
HRAS WILD-TYPE 83 116 111

Figure S24.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.22e-06 (Fisher's exact test), Q value = 0.00033

Table S25.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 121 96
HRAS MUTATED 12 0 0
HRAS WILD-TYPE 93 121 96

Figure S25.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.38e-07 (Fisher's exact test), Q value = 9.2e-05

Table S26.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 97 107
HRAS MUTATED 0 12 0
HRAS WILD-TYPE 118 85 107

Figure S26.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Mutation data file = THCA-TP.mutsig.cluster.txt

  • Molecular subtypes file = THCA-TP.transferedmergedcluster.txt

  • Number of patients = 323

  • Number of significantly mutated genes = 32

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

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

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] 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)
[2] 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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