Correlation between gene mutation status and selected clinical features
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.

Summary

Testing the association between mutation status of 36 genes and 17 clinical features across 492 patients, 11 significant findings detected with Q value < 0.25.

  • BRAF mutation correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.

  • NRAS mutation correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • HRAS mutation correlated to 'HISTOLOGICAL_TYPE'.

  • RANBP9 mutation correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 36 genes and 17 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 11 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		RADIATION
EXPOSURE 		EXTRATHYROIDAL
EXTENSION 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		MULTIFOCALITY TUMOR
SIZE 		RACE ETHNICITY
nMutated (%) nWild-Type logrank test Wilcoxon-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 Fisher's exact test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
BRAF 290 (59%) 202 0.221
(1.00) 		0.488
(1.00) 		0.00021
(0.0184) 		0.00126
(0.0964) 		1.68e-06
(0.000839) 		0.728
(1.00) 		1
(1.00) 		0.923
(1.00) 		1e-05
(0.00122) 		0.316
(1.00) 		1e-05
(0.00122) 		0.341
(1.00) 		0.00291
(0.171) 		1
(1.00) 		0.407
(1.00) 		0.863
(1.00) 		0.118
(0.977)
NRAS 40 (8%) 452 0.406
(1.00) 		0.279
(1.00) 		0.0507
(0.839) 		0.574
(1.00) 		5.6e-05
(0.00571) 		0.125
(0.977) 		0.853
(1.00) 		0.5
(1.00) 		1e-05
(0.00122) 		1
(1.00) 		0.206
(1.00) 		0.444
(1.00) 		0.00263
(0.171) 		0.509
(1.00) 		0.859
(1.00) 		0.483
(1.00) 		0.0309
(0.655)
HRAS 16 (3%) 476 0.487
(1.00) 		0.413
(1.00) 		0.424
(1.00) 		0.738
(1.00) 		0.172
(1.00) 		0.254
(1.00) 		0.773
(1.00) 		0.0585
(0.867) 		0.00307
(0.171) 		1
(1.00) 		0.496
(1.00) 		0.307
(1.00) 		0.354
(1.00) 		1
(1.00) 		0.434
(1.00) 		0.101
(0.977) 		0.378
(1.00)
RANBP9 3 (1%) 489 2.74e-06
(0.000839) 		0.398
(1.00) 		0.0552
(0.867) 		0.159
(1.00) 		1
(1.00) 		0.0316
(0.655) 		0.172
(1.00) 		0.295
(1.00) 		1
(1.00) 		1
(1.00) 		0.134
(0.977) 		0.235
(1.00) 		0.595
(1.00) 		1
(1.00)
NUDT11 10 (2%) 482 0.642
(1.00) 		0.787
(1.00) 		0.42
(1.00) 		0.418
(1.00) 		0.285
(1.00) 		1
(1.00) 		0.139
(0.977) 		1
(1.00) 		0.0743
(0.912) 		0.0273
(0.655) 		0.824
(1.00) 		0.804
(1.00) 		0.336
(1.00) 		0.524
(1.00) 		0.686
(1.00) 		1
(1.00) 		1
(1.00)
RPTN 10 (2%) 482 0.663
(1.00) 		0.301
(1.00) 		0.802
(1.00) 		0.466
(1.00) 		0.337
(1.00) 		1
(1.00) 		1
(1.00) 		0.00733
(0.345) 		0.878
(1.00) 		0.306
(1.00) 		0.365
(1.00) 		0.803
(1.00) 		0.123
(0.977) 		0.356
(1.00) 		0.485
(1.00) 		0.35
(1.00) 		0.564
(1.00)
EMG1 11 (2%) 481 0.627
(1.00) 		0.475
(1.00) 		1
(1.00) 		0.713
(1.00) 		0.22
(1.00) 		1
(1.00) 		0.303
(1.00) 		0.222
(1.00) 		0.433
(1.00) 		1
(1.00) 		0.189
(1.00) 		0.034
(0.655) 		0.264
(1.00) 		0.56
(1.00) 		0.411
(1.00) 		0.776
(1.00) 		0.608
(1.00)
FAM47C 14 (3%) 478 0.517
(1.00) 		0.294
(1.00) 		0.453
(1.00) 		0.92
(1.00) 		0.259
(1.00) 		1
(1.00) 		0.373
(1.00) 		0.781
(1.00) 		0.654
(1.00) 		1
(1.00) 		1
(1.00) 		0.883
(1.00) 		0.474
(1.00) 		0.425
(1.00) 		0.886
(1.00) 		0.774
(1.00) 		0.143
(0.981)
EIF1AX 7 (1%) 485 0.0327
(0.655) 		0.031
(0.655) 		0.884
(1.00) 		1
(1.00) 		0.215
(1.00) 		1
(1.00) 		0.388
(1.00) 		0.433
(1.00) 		0.0277
(0.655) 		1
(1.00) 		0.757
(1.00) 		0.397
(1.00) 		0.393
(1.00) 		0.419
(1.00) 		0.251
(1.00) 		1
(1.00)
DLX6 7 (1%) 485 0.729
(1.00) 		0.805
(1.00) 		0.272
(1.00) 		0.615
(1.00) 		0.0672
(0.887) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.816
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.116
(0.977) 		1
(1.00) 		0.524
(1.00) 		1
(1.00) 		1
(1.00)
GPR44 4 (1%) 488 0.657
(1.00) 		0.965
(1.00) 		0.644
(1.00) 		0.0299
(0.655) 		0.371
(1.00) 		1
(1.00) 		0.286
(1.00) 		0.633
(1.00) 		0.705
(1.00) 		1
(1.00) 		0.0972
(0.977) 		0.0682
(0.887) 		0.129
(0.977) 		0.0196
(0.655) 		0.583
(1.00) 		1
(1.00)
TMEM184A 5 (1%) 487 0.824
(1.00) 		0.403
(1.00) 		0.71
(1.00) 		0.128
(0.977) 		1
(1.00) 		1
(1.00) 		0.611
(1.00) 		1
(1.00) 		0.565
(1.00) 		1
(1.00) 		0.138
(0.977) 		0.392
(1.00) 		0.66
(1.00) 		1
(1.00) 		0.582
(1.00) 		1
(1.00)
NUP93 4 (1%) 488 0.851
(1.00) 		0.524
(1.00) 		0.736
(1.00) 		0.742
(1.00) 		0.623
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.013
(0.532) 		1
(1.00) 		1
(1.00) 		0.557
(1.00) 		0.504
(1.00) 		0.336
(1.00) 		0.988
(1.00) 		0.23
(1.00) 		1
(1.00)
GAGE2A 4 (1%) 488 0.871
(1.00) 		0.00664
(0.339) 		0.839
(1.00) 		0.872
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.633
(1.00) 		0.706
(1.00) 		1
(1.00) 		0.612
(1.00) 		0.454
(1.00) 		0.965
(1.00) 		1
(1.00) 		0.349
(1.00) 		0.479
(1.00) 		1
(1.00)
ABL1 5 (1%) 487 0.617
(1.00) 		0.0199
(0.655) 		0.58
(1.00) 		0.893
(1.00) 		1
(1.00) 		0.121
(0.977) 		0.332
(1.00) 		0.655
(1.00) 		0.74
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.857
(1.00) 		0.381
(1.00) 		0.559
(1.00) 		0.582
(1.00) 		0.404
(1.00)
LMTK2 4 (1%) 488 0.523
(1.00) 		0.845
(1.00) 		0.141
(0.977) 		0.168
(1.00) 		0.622
(1.00) 		0.0921
(0.977) 		1
(1.00) 		1
(1.00) 		0.455
(1.00) 		1
(1.00) 		0.154
(1.00) 		0.0696
(0.887) 		0.129
(0.977) 		0.0904
(0.977) 		1
(1.00) 		0.338
(1.00)
SRPX 4 (1%) 488 0.829
(1.00) 		0.289
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.248
(1.00) 		1
(1.00) 		0.577
(1.00) 		0.633
(1.00) 		0.225
(1.00) 		1
(1.00) 		0.425
(1.00) 		1
(1.00) 		0.248
(1.00) 		0.336
(1.00) 		0.421
(1.00) 		0.479
(1.00) 		0.266
(1.00)
PPM1D 6 (1%) 486 0.684
(1.00) 		0.231
(1.00) 		0.0954
(0.977) 		0.337
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.633
(1.00) 		0.615
(1.00) 		1
(1.00) 		0.192
(1.00) 		0.391
(1.00) 		0.744
(1.00) 		1
(1.00) 		0.744
(1.00) 		1
(1.00) 		1
(1.00)
TG 20 (4%) 472 0.436
(1.00) 		0.301
(1.00) 		0.266
(1.00) 		0.175
(1.00) 		0.47
(1.00) 		0.325
(1.00) 		1
(1.00) 		0.817
(1.00) 		0.0407
(0.732) 		1
(1.00) 		0.214
(1.00) 		0.906
(1.00) 		0.926
(1.00) 		0.653
(1.00) 		0.789
(1.00) 		0.893
(1.00) 		0.225
(1.00)
PTCD1 3 (1%) 489 0.0316
(0.655) 		0.363
(1.00) 		0.416
(1.00) 		0.16
(1.00) 		0.499
(1.00) 		1
(1.00) 		1
(1.00) 		0.559
(1.00) 		0.649
(1.00) 		1
(1.00) 		0.0806
(0.948) 		0.236
(1.00) 		0.254
(1.00) 		0.123
(0.977) 		0.186
(1.00)
TSC22D1 4 (1%) 488 0.615
(1.00) 		0.547
(1.00) 		0.109
(0.977) 		0.633
(1.00) 		0.371
(1.00) 		0.121
(0.977) 		0.286
(1.00) 		0.302
(1.00) 		0.137
(0.977) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.45
(1.00) 		0.629
(1.00) 		0.578
(1.00) 		1
(1.00) 		1
(1.00)
AKT1 5 (1%) 487 0.837
(1.00) 		0.172
(1.00) 		0.111
(0.977) 		0.401
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.128
(0.977) 		1
(1.00) 		0.096
(0.977) 		0.0256
(0.655) 		0.715
(1.00) 		1
(1.00) 		0.594
(1.00) 		1
(1.00) 		0.404
(1.00)
ZNF878 3 (1%) 489 0.714
(1.00) 		0.808
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.295
(1.00) 		0.646
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.254
(1.00) 		1
(1.00) 		1
(1.00)
RBM10 4 (1%) 488 0.836
(1.00) 		0.792
(1.00) 		0.735
(1.00) 		1
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.577
(1.00) 		1
(1.00) 		0.0343
(0.655) 		1
(1.00) 		0.42
(1.00) 		0.313
(1.00) 		0.87
(1.00) 		0.0432
(0.755) 		0.139
(0.977) 		1
(1.00) 		0.266
(1.00)
EP400 3 (1%) 489 0.768
(1.00) 		0.647
(1.00) 		1
(1.00) 		0.159
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0821
(0.948) 		1
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.631
(1.00) 		1
(1.00)
ABCD1 4 (1%) 488 0.842
(1.00) 		0.154
(1.00) 		0.476
(1.00) 		0.199
(1.00) 		0.0605
(0.867) 		1
(1.00) 		1
(1.00) 		0.633
(1.00) 		0.14
(0.977) 		1
(1.00) 		0.644
(1.00) 		0.0494
(0.839) 		0.0745
(0.912) 		0.595
(1.00) 		0.588
(1.00) 		1
(1.00) 		0.266
(1.00)
MYH10 4 (1%) 488 0.768
(1.00) 		0.551
(1.00) 		0.201
(1.00) 		0.453
(1.00) 		0.123
(0.977) 		1
(1.00) 		0.577
(1.00) 		1
(1.00) 		0.703
(1.00) 		1
(1.00) 		0.153
(1.00) 		1
(1.00) 		0.662
(1.00) 		1
(1.00) 		0.479
(1.00) 		1
(1.00)
NLRP6 4 (1%) 488 0.683
(1.00) 		0.565
(1.00) 		0.4
(1.00) 		0.0613
(0.867) 		0.623
(1.00) 		1
(1.00) 		0.302
(1.00) 		1
(1.00) 		1
(1.00) 		0.423
(1.00) 		0.314
(1.00) 		0.13
(0.977) 		0.336
(1.00) 		0.0228
(0.655) 		0.0238
(0.655) 		1
(1.00)
IGSF3 4 (1%) 488 0.714
(1.00) 		0.129
(0.977) 		0.175
(1.00) 		0.0286
(0.655) 		1
(1.00) 		0.0623
(0.867) 		0.286
(1.00) 		1
(1.00) 		0.111
(0.977) 		1
(1.00) 		1
(1.00) 		0.0682
(0.887) 		0.857
(1.00) 		0.629
(1.00) 		0.982
(1.00) 		1
(1.00)
PRMT8 3 (1%) 489 0.856
(1.00) 		0.302
(1.00) 		0.508
(1.00) 		0.312
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.649
(1.00) 		1
(1.00) 		0.612
(1.00) 		1
(1.00) 		0.252
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ARMCX3 3 (1%) 489 0.824
(1.00) 		0.528
(1.00) 		0.788
(1.00) 		0.313
(1.00) 		0.122
(0.977) 		1
(1.00) 		0.569
(1.00) 		0.0523
(0.842) 		0.647
(1.00) 		1
(1.00) 		0.611
(1.00) 		1
(1.00) 		1
(1.00) 		0.107
(0.977) 		1
(1.00)
RYR1 7 (1%) 485 0.647
(1.00) 		0.0389
(0.722) 		0.592
(1.00) 		0.506
(1.00) 		0.121
(0.977) 		1
(1.00) 		0.388
(1.00) 		0.204
(1.00) 		0.656
(1.00) 		1
(1.00) 		0.258
(1.00) 		0.462
(1.00) 		0.117
(0.977) 		1
(1.00) 		0.735
(1.00) 		0.539
(1.00) 		1
(1.00)
TNRC18 4 (1%) 488 0.786
(1.00) 		0.417
(1.00) 		0.0284
(0.655) 		0.636
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.302
(1.00) 		0.013
(0.532) 		1
(1.00) 		0.424
(1.00) 		1
(1.00) 		0.76
(1.00) 		0.336
(1.00) 		0.478
(1.00) 		0.478
(1.00) 		1
(1.00)
TMEM90B 3 (1%) 489 0.839
(1.00) 		0.622
(1.00) 		0.416
(1.00) 		0.587
(1.00) 		0.622
(1.00) 		1
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.336
(1.00) 		1
(1.00) 		0.287
(1.00) 		1
(1.00) 		0.504
(1.00) 		0.0951
(0.977) 		0.478
(1.00) 		1
(1.00)
ZC3H11A 3 (1%) 489 0.885
(1.00) 		0.0791
(0.948) 		0.788
(1.00) 		0.696
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.0623
(0.867) 		1
(1.00)
DGCR8 3 (1%) 489 0.857
(1.00) 		0.287
(1.00) 		0.607
(1.00) 		0.492
(1.00) 		1
(1.00) 		1
(1.00) 		0.569
(1.00) 		0.559
(1.00) 		0.227
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.664
(1.00) 		1
(1.00)
'BRAF MUTATION STATUS' versus 'PATHOLOGIC_STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.018

Table S1.  Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 278 50 108 2 46 6
BRAF MUTATED 157 19 74 0 35 4
BRAF WILD-TYPE 121 31 34 2 11 2

Figure S1.  Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'BRAF MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 0.00126 (Fisher's exact test), Q value = 0.096

Table S2.  Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 141 162 164 23
BRAF MUTATED 78 81 112 18
BRAF WILD-TYPE 63 81 52 5

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

'BRAF MUTATION STATUS' versus 'PATHOLOGY_N_STAGE'

P value = 1.68e-06 (Fisher's exact test), Q value = 0.00084

Table S3.  Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 220 222
BRAF MUTATED 108 159
BRAF WILD-TYPE 112 63

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

'BRAF MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S4.  Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL 7 348 102 35
BRAF MUTATED 4 238 16 32
BRAF WILD-TYPE 3 110 86 3

Figure S4.  Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'BRAF MUTATION STATUS' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S5.  Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 130 18 328 1
BRAF MUTATED 99 16 170 0
BRAF WILD-TYPE 31 2 158 1

Figure S5.  Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'BRAF MUTATION STATUS' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00291 (Wilcoxon-test), Q value = 0.17

Table S6.  Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 378 3.7 (6.2)
BRAF MUTATED 236 3.9 (5.9)
BRAF WILD-TYPE 142 3.5 (6.8)

Figure S6.  Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'NRAS MUTATION STATUS' versus 'PATHOLOGY_N_STAGE'

P value = 5.6e-05 (Fisher's exact test), Q value = 0.0057

Table S7.  Gene #2: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 220 222
NRAS MUTATED 30 7
NRAS WILD-TYPE 190 215

Figure S7.  Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'NRAS MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S8.  Gene #2: 'NRAS MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL 7 348 102 35
NRAS MUTATED 0 14 26 0
NRAS WILD-TYPE 7 334 76 35

Figure S8.  Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'NRAS MUTATION STATUS' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00263 (Wilcoxon-test), Q value = 0.17

Table S9.  Gene #2: 'NRAS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 378 3.7 (6.2)
NRAS MUTATED 30 1.7 (3.8)
NRAS WILD-TYPE 348 3.9 (6.4)

Figure S9.  Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'HRAS MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00307 (Fisher's exact test), Q value = 0.17

Table S10.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL 7 348 102 35
HRAS MUTATED 0 6 10 0
HRAS WILD-TYPE 7 342 92 35

Figure S10.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'RANBP9 MUTATION STATUS' versus 'Time to Death'

P value = 2.74e-06 (logrank test), Q value = 0.00084

Table S11.  Gene #35: 'RANBP9 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 491 14 0.2 - 178.3 (31.1)
RANBP9 MUTATED 3 1 17.5 - 48.1 (17.5)
RANBP9 WILD-TYPE 488 13 0.2 - 178.3 (31.2)

Figure S11.  Get High-res Image Gene #35: 'RANBP9 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/22815544/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THCA-TP/22507188/THCA-TP.merged_data.txt

  • Number of patients = 492

  • Number of significantly mutated genes = 36

  • Number of selected clinical features = 17

  • 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

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.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] 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)
[3] 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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