Stomach Adenocarcinoma: Correlation between gene mutation status and selected clinical features
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

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

Summary

Testing the association between mutation status of 87 genes and 9 clinical features across 132 patients, one significant finding detected with Q value < 0.25.

  • ANAPC1 mutation correlated to 'AGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 87 genes and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.

Clinical
Features 		Time
to
Death 		AGE GENDER HISTOLOGICAL
TYPE 		PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) TUMOR
STAGE 		NEOADJUVANT
THERAPY
nMutated (%) nWild-Type logrank test t-test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
ANAPC1 12 (9%) 120 0.711
(1.00) 		0.000135
(0.102) 		0.762
(1.00) 		0.767
(1.00) 		0.144
(1.00) 		0.718
(1.00) 		0.392
(1.00) 		0.909
(1.00) 		1
(1.00)
ACVR2A 17 (13%) 115 0.00155
(1.00) 		0.0992
(1.00) 		0.114
(1.00) 		0.18
(1.00) 		0.15
(1.00) 		1
(1.00) 		0.529
(1.00) 		0.787
(1.00) 		0.596
(1.00)
CBWD1 17 (13%) 115 0.303
(1.00) 		0.0208
(1.00) 		0.294
(1.00) 		0.298
(1.00) 		0.0009
(0.677) 		0.54
(1.00) 		0.529
(1.00) 		0.408
(1.00) 		0.596
(1.00)
DNAJC15 3 (2%) 129 0.0291
(1.00) 		0.564
(1.00) 		0.81
(1.00) 		1
(1.00) 		0.114
(1.00) 		1
(1.00)
KRAS 17 (13%) 115 0.353
(1.00) 		0.241
(1.00) 		0.114
(1.00) 		0.668
(1.00) 		0.811
(1.00) 		0.502
(1.00) 		0.645
(1.00) 		0.339
(1.00) 		0.596
(1.00)
RPL22 10 (8%) 122 0.478
(1.00) 		0.0186
(1.00) 		0.522
(1.00) 		0.613
(1.00) 		0.0588
(1.00) 		0.235
(1.00) 		0.000928
(0.697) 		0.0811
(1.00) 		1
(1.00)
SFRS12IP1 5 (4%) 127 0.00167
(1.00) 		0.648
(1.00) 		0.782
(1.00) 		0.236
(1.00) 		0.606
(1.00) 		1
(1.00) 		0.368
(1.00) 		1
(1.00)
SMAP1 5 (4%) 127 0.0768
(1.00) 		0.39
(1.00) 		0.782
(1.00) 		0.0317
(1.00) 		0.606
(1.00) 		1
(1.00) 		0.132
(1.00) 		1
(1.00)
TP53 61 (46%) 71 0.0826
(1.00) 		0.714
(1.00) 		0.285
(1.00) 		0.0533
(1.00) 		0.759
(1.00) 		0.908
(1.00) 		0.128
(1.00) 		0.751
(1.00) 		0.47
(1.00)
TRIM48 14 (11%) 118 0.322
(1.00) 		0.12
(1.00) 		0.566
(1.00) 		0.299
(1.00) 		0.0982
(1.00) 		0.304
(1.00) 		0.0874
(1.00) 		0.166
(1.00) 		0.599
(1.00)
ZNF48 3 (2%) 129 0.0763
(1.00) 		0.564
(1.00) 		0.953
(1.00) 		0.151
(1.00) 		1
(1.00) 		1
(1.00)
PGM5 18 (14%) 114 0.962
(1.00) 		0.000669
(0.504) 		0.0192
(1.00) 		0.505
(1.00) 		0.00714
(1.00) 		0.584
(1.00) 		0.551
(1.00) 		0.413
(1.00) 		1
(1.00)
ARID1A 26 (20%) 106 0.225
(1.00) 		0.89
(1.00) 		0.272
(1.00) 		0.268
(1.00) 		0.162
(1.00) 		0.303
(1.00) 		0.0177
(1.00) 		0.118
(1.00) 		0.656
(1.00)
RHOA 7 (5%) 125 0.0968
(1.00) 		0.0721
(1.00) 		0.701
(1.00) 		0.358
(1.00) 		0.541
(1.00) 		0.718
(1.00) 		0.628
(1.00) 		0.203
(1.00) 		0.361
(1.00)
PIK3CA 25 (19%) 107 0.407
(1.00) 		0.591
(1.00) 		0.377
(1.00) 		0.774
(1.00) 		0.722
(1.00) 		0.63
(1.00) 		0.879
(1.00) 		0.405
(1.00) 		1
(1.00)
INO80E 9 (7%) 123 0.677
(1.00) 		0.338
(1.00) 		0.156
(1.00) 		0.694
(1.00) 		0.000819
(0.617) 		0.199
(1.00) 		0.192
(1.00) 		0.122
(1.00) 		1
(1.00)
FGF22 4 (3%) 128 0.0132
(1.00) 		1
(1.00) 		0.691
(1.00) 		0.288
(1.00) 		0.843
(1.00) 		0.428
(1.00) 		1
(1.00) 		1
(1.00)
OR8H3 10 (8%) 122 0.626
(1.00) 		0.386
(1.00) 		0.739
(1.00) 		0.0282
(1.00) 		0.731
(1.00) 		0.0678
(1.00) 		0.707
(1.00) 		0.705
(1.00) 		0.477
(1.00)
ZNF804B 21 (16%) 111 0.909
(1.00) 		0.238
(1.00) 		0.629
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.0734
(1.00) 		0.395
(1.00) 		0.0128
(1.00) 		1
(1.00)
CDH1 13 (10%) 119 0.516
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.142
(1.00) 		0.681
(1.00) 		0.819
(1.00) 		1
(1.00) 		0.378
(1.00) 		1
(1.00)
TUSC3 11 (8%) 121 0.76
(1.00) 		0.575
(1.00) 		1
(1.00) 		0.786
(1.00) 		0.606
(1.00) 		0.457
(1.00) 		0.356
(1.00) 		0.552
(1.00) 		0.511
(1.00)
PRRT2 5 (4%) 127 0.277
(1.00) 		1
(1.00) 		0.571
(1.00) 		0.00291
(1.00) 		0.418
(1.00) 		0.213
(1.00) 		1
(1.00)
PTH2 3 (2%) 129 0.833
(1.00) 		0.564
(1.00) 		0.756
(1.00) 		1
(1.00) 		0.418
(1.00) 		1
(1.00) 		0.774
(1.00) 		0.172
(1.00)
C17ORF63 4 (3%) 128 0.806
(1.00) 		1
(1.00) 		0.907
(1.00) 		0.273
(1.00) 		0.705
(1.00) 		1
(1.00) 		0.526
(1.00) 		1
(1.00)
IAPP 4 (3%) 128 0.461
(1.00) 		0.649
(1.00) 		0.907
(1.00) 		1
(1.00) 		0.887
(1.00) 		0.162
(1.00) 		0.132
(1.00) 		1
(1.00)
IRF2 8 (6%) 124 0.74
(1.00) 		0.209
(1.00) 		0.0597
(1.00) 		0.873
(1.00) 		0.0186
(1.00) 		0.87
(1.00) 		0.25
(1.00) 		1
(1.00) 		1
(1.00)
RNF43 15 (11%) 117 0.0257
(1.00) 		0.0137
(1.00) 		0.279
(1.00) 		0.154
(1.00) 		0.0955
(1.00) 		0.97
(1.00) 		0.49
(1.00) 		0.199
(1.00) 		0.596
(1.00)
HLA-B 10 (8%) 122 0.963
(1.00) 		0.473
(1.00) 		0.0886
(1.00) 		0.533
(1.00) 		0.158
(1.00) 		0.114
(1.00) 		0.32
(1.00) 		0.3
(1.00) 		1
(1.00)
HLA-A 9 (7%) 123 0.354
(1.00) 		0.985
(1.00) 		0.483
(1.00) 		0.117
(1.00) 		0.603
(1.00) 		0.783
(1.00) 		0.697
(1.00) 		0.952
(1.00) 		0.441
(1.00)
SMAD4 8 (6%) 124 0.103
(1.00) 		0.043
(1.00) 		1
(1.00) 		0.666
(1.00) 		0.898
(1.00) 		1
(1.00) 		0.155
(1.00) 		0.952
(1.00) 		1
(1.00)
UPF3A 7 (5%) 125 0.647
(1.00) 		0.13
(1.00) 		0.438
(1.00) 		0.864
(1.00) 		0.0014
(1.00) 		0.589
(1.00) 		0.216
(1.00) 		0.254
(1.00) 		1
(1.00)
CCDC43 4 (3%) 128 0.252
(1.00) 		1
(1.00) 		0.691
(1.00) 		0.428
(1.00) 		0.79
(1.00) 		1
(1.00) 		0.162
(1.00) 		1
(1.00)
PHF2 13 (10%) 119 0.905
(1.00) 		0.00617
(1.00) 		0.374
(1.00) 		0.435
(1.00) 		0.012
(1.00) 		0.59
(1.00) 		0.00341
(1.00) 		0.101
(1.00) 		1
(1.00)
PCDH15 23 (17%) 109 0.855
(1.00) 		0.802
(1.00) 		0.485
(1.00) 		0.797
(1.00) 		0.285
(1.00) 		0.714
(1.00) 		0.533
(1.00) 		0.204
(1.00) 		0.628
(1.00)
SPRYD5 8 (6%) 124 0.143
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.925
(1.00) 		0.0509
(1.00) 		0.718
(1.00) 		0.0757
(1.00) 		0.0293
(1.00) 		1
(1.00)
SOX1 6 (5%) 126 0.361
(1.00) 		0.444
(1.00) 		1
(1.00) 		0.935
(1.00) 		0.187
(1.00) 		0.0865
(1.00) 		1
(1.00) 		0.526
(1.00) 		0.318
(1.00)
POTEG 6 (5%) 126 0.221
(1.00) 		0.00963
(1.00) 		0.684
(1.00) 		0.558
(1.00) 		0.629
(1.00) 		0.589
(1.00) 		1
(1.00) 		0.803
(1.00) 		1
(1.00)
TPTE 16 (12%) 116 0.382
(1.00) 		0.587
(1.00) 		0.424
(1.00) 		0.00416
(1.00) 		0.288
(1.00) 		0.685
(1.00) 		0.508
(1.00) 		1
(1.00) 		1
(1.00)
FSHR 14 (11%) 118 0.55
(1.00) 		0.0322
(1.00) 		0.566
(1.00) 		0.123
(1.00) 		0.048
(1.00) 		0.637
(1.00) 		0.768
(1.00) 		0.566
(1.00) 		1
(1.00)
UNC93B1 3 (2%) 129 0.00167
(1.00) 		0.564
(1.00) 		0.599
(1.00) 		0.2
(1.00) 		1
(1.00) 		1
(1.00)
EDNRB 12 (9%) 120 0.877
(1.00) 		0.762
(1.00) 		0.543
(1.00) 		0.295
(1.00) 		0.253
(1.00) 		0.426
(1.00) 		0.392
(1.00) 		0.859
(1.00) 		1
(1.00)
RASA1 10 (8%) 122 0.307
(1.00) 		0.231
(1.00) 		1
(1.00) 		0.199
(1.00) 		0.0195
(1.00) 		0.723
(1.00) 		0.0878
(1.00) 		0.371
(1.00) 		0.477
(1.00)
KDM4B 11 (8%) 121 0.81
(1.00) 		0.0336
(1.00) 		0.0273
(1.00) 		0.432
(1.00) 		0.158
(1.00) 		0.825
(1.00) 		0.356
(1.00) 		0.533
(1.00) 		1
(1.00)
LHCGR 7 (5%) 125 0.863
(1.00) 		0.403
(1.00) 		1
(1.00) 		0.701
(1.00) 		0.0866
(1.00) 		0.39
(1.00) 		0.216
(1.00) 		1
(1.00) 		0.361
(1.00)
TM7SF4 8 (6%) 124 0.915
(1.00) 		0.321
(1.00) 		1
(1.00) 		0.86
(1.00) 		0.771
(1.00) 		0.825
(1.00) 		1
(1.00) 		0.679
(1.00) 		1
(1.00)
IL2RG 3 (2%) 129 0.448
(1.00) 		0.0625
(1.00) 		0.953
(1.00) 		1
(1.00) 		0.114
(1.00) 		1
(1.00)
TLR4 13 (10%) 119 0.295
(1.00) 		0.946
(1.00) 		0.561
(1.00) 		0.384
(1.00) 		0.393
(1.00) 		0.702
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.179
(1.00)
TSHZ2 7 (5%) 125 0.205
(1.00) 		0.619
(1.00) 		0.438
(1.00) 		0.538
(1.00) 		0.603
(1.00) 		0.021
(1.00) 		0.318
(1.00) 		0.0482
(1.00) 		1
(1.00)
PDZRN4 12 (9%) 120 0.699
(1.00) 		0.994
(1.00) 		0.36
(1.00) 		0.935
(1.00) 		0.136
(1.00) 		0.827
(1.00) 		0.0591
(1.00) 		0.909
(1.00) 		0.544
(1.00)
POM121L12 8 (6%) 124 0.943
(1.00) 		0.502
(1.00) 		0.713
(1.00) 		0.577
(1.00) 		0.118
(1.00) 		0.817
(1.00) 		0.155
(1.00) 		0.295
(1.00) 		1
(1.00)
WBSCR17 12 (9%) 120 0.116
(1.00) 		0.165
(1.00) 		0.543
(1.00) 		0.239
(1.00) 		0.521
(1.00) 		1
(1.00) 		0.199
(1.00) 		0.744
(1.00) 		1
(1.00)
ZC4H2 6 (5%) 126 0.303
(1.00) 		0.874
(1.00) 		1
(1.00) 		0.81
(1.00) 		0.273
(1.00) 		0.151
(1.00) 		0.172
(1.00) 		0.0554
(1.00) 		1
(1.00)
CNBD1 6 (5%) 126 0.0498
(1.00) 		0.684
(1.00) 		0.776
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.338
(1.00) 		0.318
(1.00)
CPS1 14 (11%) 118 0.862
(1.00) 		0.773
(1.00) 		0.158
(1.00) 		0.535
(1.00) 		0.626
(1.00) 		0.539
(1.00) 		0.19
(1.00) 		0.973
(1.00) 		0.599
(1.00)
KIAA0748 8 (6%) 124 0.337
(1.00) 		0.237
(1.00) 		1
(1.00) 		0.755
(1.00) 		0.69
(1.00) 		0.516
(1.00) 		1
(1.00) 		0.14
(1.00) 		1
(1.00)
OR2T6 7 (5%) 125 0.996
(1.00) 		0.962
(1.00) 		1
(1.00) 		0.558
(1.00) 		0.0689
(1.00) 		0.39
(1.00) 		0.628
(1.00) 		0.0837
(1.00) 		0.361
(1.00)
CHRM2 7 (5%) 125 0.607
(1.00) 		0.241
(1.00) 		0.104
(1.00) 		0.466
(1.00) 		0.912
(1.00) 		1
(1.00) 		0.118
(1.00) 		0.361
(1.00)
NDN 8 (6%) 124 0.148
(1.00) 		0.827
(1.00) 		0.266
(1.00) 		0.726
(1.00) 		0.603
(1.00) 		0.719
(1.00) 		1
(1.00) 		0.952
(1.00) 		1
(1.00)
TCEB3C 5 (4%) 127 0.945
(1.00) 		0.68
(1.00) 		1
(1.00) 		0.846
(1.00) 		0.875
(1.00) 		0.172
(1.00) 		0.504
(1.00) 		0.339
(1.00) 		0.272
(1.00)
IL13RA2 7 (5%) 125 0.161
(1.00) 		0.32
(1.00) 		0.438
(1.00) 		0.561
(1.00) 		0.187
(1.00) 		0.39
(1.00) 		0.628
(1.00) 		0.658
(1.00) 		0.0581
(1.00)
ASTN2 16 (12%) 116 0.525
(1.00) 		0.0817
(1.00) 		0.182
(1.00) 		0.172
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.228
(1.00) 		0.85
(1.00) 		1
(1.00)
FCRL3 9 (7%) 123 0.515
(1.00) 		0.963
(1.00) 		0.483
(1.00) 		0.913
(1.00) 		0.332
(1.00) 		0.421
(1.00) 		1
(1.00) 		0.882
(1.00) 		1
(1.00)
PARK2 9 (7%) 123 0.73
(1.00) 		0.00798
(1.00) 		0.74
(1.00) 		0.12
(1.00) 		0.238
(1.00) 		0.472
(1.00) 		0.192
(1.00) 		0.14
(1.00) 		0.441
(1.00)
POU3F2 4 (3%) 128 0.461
(1.00) 		0.149
(1.00) 		0.81
(1.00) 		0.571
(1.00) 		0.418
(1.00) 		0.162
(1.00) 		1
(1.00) 		1
(1.00)
FAM9A 6 (5%) 126 0.677
(1.00) 		0.249
(1.00) 		0.684
(1.00) 		0.81
(1.00) 		0.00697
(1.00) 		0.175
(1.00) 		0.00559
(1.00) 		0.122
(1.00) 		1
(1.00)
CSNK2A1 4 (3%) 128 0.465
(1.00) 		0.684
(1.00) 		0.649
(1.00) 		0.348
(1.00) 		0.821
(1.00) 		1
(1.00) 		1
(1.00) 		0.207
(1.00) 		0.224
(1.00)
CAPN6 7 (5%) 125 0.399
(1.00) 		1
(1.00) 		0.919
(1.00) 		0.097
(1.00) 		0.558
(1.00) 		0.121
(1.00) 		1
(1.00) 		1
(1.00)
ELF3 6 (5%) 126 0.541
(1.00) 		0.391
(1.00) 		0.218
(1.00) 		0.444
(1.00) 		0.441
(1.00) 		0.366
(1.00) 		1
(1.00) 		0.935
(1.00) 		1
(1.00)
FBXW7 10 (8%) 122 0.876
(1.00) 		0.0737
(1.00) 		0.522
(1.00) 		0.619
(1.00) 		1
(1.00) 		0.313
(1.00) 		0.222
(1.00) 		0.768
(1.00) 		1
(1.00)
TP53TG5 4 (3%) 128 0.739
(1.00) 		0.735
(1.00) 		0.649
(1.00) 		0.0217
(1.00) 		0.0607
(1.00) 		0.395
(1.00) 		1
(1.00) 		0.526
(1.00) 		1
(1.00)
ZNF559 7 (5%) 125 0.184
(1.00) 		0.542
(1.00) 		0.116
(1.00) 		0.459
(1.00) 		0.0368
(1.00) 		0.65
(1.00) 		0.628
(1.00) 		0.0999
(1.00) 		1
(1.00)
CHRM3 6 (5%) 126 0.497
(1.00) 		0.0592
(1.00) 		0.684
(1.00) 		0.459
(1.00) 		0.271
(1.00) 		0.466
(1.00) 		0.266
(1.00) 		0.695
(1.00) 		1
(1.00)
ELL2 8 (6%) 124 0.567
(1.00) 		0.396
(1.00) 		1
(1.00) 		0.755
(1.00) 		0.157
(1.00) 		0.439
(1.00) 		0.25
(1.00) 		0.859
(1.00) 		1
(1.00)
EPHA6 14 (11%) 118 0.322
(1.00) 		0.397
(1.00) 		0.781
(1.00) 		0.302
(1.00) 		0.175
(1.00) 		0.478
(1.00) 		0.462
(1.00) 		0.383
(1.00) 		1
(1.00)
OSGIN2 6 (5%) 126 0.329
(1.00) 		0.639
(1.00) 		0.218
(1.00) 		0.748
(1.00) 		0.349
(1.00) 		0.766
(1.00) 		0.0894
(1.00) 		0.709
(1.00) 		1
(1.00)
KRTAP4-1 3 (2%) 129 0.291
(1.00) 		0.617
(1.00) 		0.564
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.296
(1.00) 		1
(1.00) 		0.878
(1.00) 		1
(1.00)
SMAD2 7 (5%) 125 0.386
(1.00) 		0.238
(1.00) 		0.438
(1.00) 		0.571
(1.00) 		0.69
(1.00) 		0.51
(1.00) 		0.628
(1.00) 		0.709
(1.00) 		1
(1.00)
EDIL3 6 (5%) 126 0.931
(1.00) 		0.877
(1.00) 		0.218
(1.00) 		0.782
(1.00) 		0.349
(1.00) 		0.558
(1.00) 		0.57
(1.00) 		0.333
(1.00) 		1
(1.00)
OR4C13 5 (4%) 127 0.748
(1.00) 		0.713
(1.00) 		0.39
(1.00) 		0.741
(1.00) 		0.821
(1.00) 		1
(1.00) 		1
(1.00) 		0.482
(1.00) 		1
(1.00)
OR4C16 9 (7%) 123 0.614
(1.00) 		0.204
(1.00) 		0.74
(1.00) 		0.257
(1.00) 		0.414
(1.00) 		0.441
(1.00) 		0.697
(1.00) 		0.848
(1.00) 		1
(1.00)
PRR11 4 (3%) 128 0.483
(1.00) 		1
(1.00) 		0.787
(1.00) 		0.0317
(1.00) 		0.79
(1.00) 		0.162
(1.00) 		0.338
(1.00) 		1
(1.00)
AUH 5 (4%) 127 0.00659
(1.00) 		0.39
(1.00) 		0.89
(1.00) 		0.236
(1.00) 		0.887
(1.00) 		0.213
(1.00) 		0.878
(1.00) 		1
(1.00)
AFAP1 5 (4%) 127 0.33
(1.00) 		0.76
(1.00) 		1
(1.00) 		0.946
(1.00) 		0.0573
(1.00) 		0.707
(1.00) 		0.0616
(1.00) 		0.295
(1.00) 		1
(1.00)
LIN7A 6 (5%) 126 0.471
(1.00) 		0.914
(1.00) 		0.684
(1.00) 		0.869
(1.00) 		0.327
(1.00) 		0.912
(1.00) 		1
(1.00) 		0.339
(1.00) 		0.318
(1.00)
OR8B4 3 (2%) 129 0.541
(1.00) 		0.758
(1.00) 		0.564
(1.00) 		0.269
(1.00) 		0.288
(1.00) 		0.098
(1.00) 		1
(1.00) 		0.338
(1.00) 		0.172
(1.00)
PID1 5 (4%) 127 0.361
(1.00) 		0.624
(1.00) 		0.648
(1.00) 		0.161
(1.00) 		0.583
(1.00) 		0.128
(1.00) 		0.213
(1.00) 		0.132
(1.00) 		1
(1.00)
AVP 3 (2%) 129 0.362
(1.00) 		1
(1.00) 		0.953
(1.00) 		1
(1.00) 		1
(1.00) 		0.0196
(1.00) 		1
(1.00) 		1
(1.00)
'ANAPC1 MUTATION STATUS' versus 'AGE'

P value = 0.000135 (t-test), Q value = 0.1

Table S1.  Gene #77: 'ANAPC1 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 130 67.8 (10.8)
ANAPC1 MUTATED 12 79.2 (7.9)
ANAPC1 WILD-TYPE 118 66.7 (10.4)

Figure S1.  Get High-res Image Gene #77: 'ANAPC1 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

Methods & Data
Input

  • Mutation data file = STAD.mutsig.cluster.txt

  • Clinical data file = STAD.clin.merged.picked.txt

  • Number of patients = 132

  • Number of significantly mutated genes = 87

  • Number of selected clinical features = 9

  • 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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