Correlation between gene mutation status and selected clinical features
Prostate Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C15H7FB9
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C15H7FB9
Overview
Introduction

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

Summary

Testing the association between mutation status of 62 genes and 14 clinical features across 420 patients, 5 significant findings detected with Q value < 0.25.

  • TP53 mutation correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.

  • ZMYM3 mutation correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE_SECONDARY'.

  • L1CAM mutation correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 62 genes and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 5 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		HISTOLOGICAL
TYPE 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		GLEASON
SCORE
COMBINED 		GLEASON
SCORE
PRIMARY 		GLEASON
SCORE
SECONDARY 		GLEASON
SCORE 		PSA
RESULT
PREOP 		PSA
VALUE 		RACE
nMutated (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Wilcoxon-test Wilcoxon-test Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test
TP53 42 (10%) 378 0.339
(1.00) 		0.312
(1.00) 		0.0593
(0.943) 		0.18
(1.00) 		0.654
(1.00) 		0.291
(1.00) 		0.0966
(0.965) 		0.000137
(0.0397) 		0.00343
(0.372) 		0.00909
(0.563) 		1.11e-06
(0.000963) 		0.901
(1.00) 		0.0835
(0.943) 		1
(1.00)
ZMYM3 9 (2%) 411 0.46
(1.00) 		0.698
(1.00) 		0.199
(1.00) 		0.166
(1.00) 		1
(1.00) 		0.231
(1.00) 		0.211
(1.00) 		0.000938
(0.163) 		0.0791
(0.943) 		0.000717
(0.156) 		0.0142
(0.626) 		0.234
(1.00) 		0.727
(1.00) 		1
(1.00)
L1CAM 6 (1%) 414 0.000132
(0.0397) 		0.255
(1.00) 		0.724
(1.00) 		0.595
(1.00) 		1
(1.00) 		1
(1.00) 		0.268
(1.00) 		0.421
(1.00) 		0.674
(1.00) 		0.565
(1.00) 		0.721
(1.00) 		0.136
(0.984) 		0.938
(1.00)
SPOP 48 (11%) 372 0.879
(1.00) 		0.0847
(0.943) 		0.551
(1.00) 		0.269
(1.00) 		0.685
(1.00) 		0.107
(0.965) 		0.229
(1.00) 		0.444
(1.00) 		0.154
(1.00) 		0.678
(1.00) 		0.617
(1.00) 		0.694
(1.00) 		0.369
(1.00) 		0.551
(1.00)
PTEN 14 (3%) 406 0.75
(1.00) 		0.744
(1.00) 		1
(1.00) 		1
(1.00) 		0.404
(1.00) 		0.495
(1.00) 		0.928
(1.00) 		0.434
(1.00) 		0.785
(1.00) 		0.402
(1.00) 		0.582
(1.00) 		0.295
(1.00) 		0.00224
(0.324) 		1
(1.00)
CTNNB1 11 (3%) 409 0.46
(1.00) 		0.964
(1.00) 		0.607
(1.00) 		0.377
(1.00) 		0.333
(1.00) 		0.207
(1.00) 		0.15
(1.00) 		0.742
(1.00) 		0.865
(1.00) 		0.709
(1.00) 		0.277
(1.00) 		0.114
(0.965) 		0.707
(1.00) 		1
(1.00)
FOXA1 25 (6%) 395 0.414
(1.00) 		0.415
(1.00) 		1
(1.00) 		0.221
(1.00) 		0.608
(1.00) 		0.948
(1.00) 		0.199
(1.00) 		0.678
(1.00) 		0.22
(1.00) 		0.314
(1.00) 		0.639
(1.00) 		0.573
(1.00) 		0.873
(1.00) 		0.0538
(0.943)
ATM 19 (5%) 401 0.0991
(0.965) 		0.881
(1.00) 		0.0696
(0.943) 		1
(1.00) 		1
(1.00) 		0.117
(0.979) 		0.763
(1.00) 		0.62
(1.00) 		0.007
(0.506) 		0.0314
(0.806) 		0.508
(1.00) 		0.00628
(0.495) 		0.785
(1.00) 		0.346
(1.00)
PIK3CA 11 (3%) 409 0.445
(1.00) 		0.0751
(0.943) 		0.464
(1.00) 		1
(1.00) 		0.333
(1.00) 		0.00562
(0.488) 		0.69
(1.00) 		0.266
(1.00) 		0.343
(1.00) 		0.493
(1.00) 		0.0353
(0.806) 		0.469
(1.00) 		0.338
(1.00) 		1
(1.00)
BRAF 8 (2%) 412 0.707
(1.00) 		0.622
(1.00) 		0.534
(1.00) 		0.318
(1.00) 		0.254
(1.00) 		0.414
(1.00) 		0.494
(1.00) 		0.72
(1.00) 		0.188
(1.00) 		0.484
(1.00) 		0.954
(1.00) 		0.994
(1.00) 		0.201
(1.00)
HRAS 5 (1%) 415 0.783
(1.00) 		0.547
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.368
(1.00) 		0.637
(1.00) 		0.35
(1.00) 		0.839
(1.00) 		0.748
(1.00) 		0.471
(1.00) 		0.937
(1.00)
KDM6A 9 (2%) 411 0.736
(1.00) 		0.159
(1.00) 		0.0132
(0.626) 		0.365
(1.00) 		1
(1.00) 		0.0501
(0.943) 		0.173
(1.00) 		0.957
(1.00) 		0.0509
(0.943) 		0.0844
(0.943) 		0.831
(1.00) 		0.602
(1.00) 		0.471
(1.00) 		1
(1.00)
IDH1 5 (1%) 415 0.747
(1.00) 		0.0691
(0.943) 		0.445
(1.00) 		0.59
(1.00) 		1
(1.00) 		0.0599
(0.943) 		0.922
(1.00) 		0.0143
(0.626) 		0.0594
(0.943) 		0.072
(0.943) 		0.0207
(0.781) 		0.0843
(0.943) 		0.49
(1.00)
SMG7 7 (2%) 413 0.741
(1.00) 		0.184
(1.00) 		0.32
(1.00) 		0.604
(1.00) 		1
(1.00) 		0.776
(1.00) 		0.231
(1.00) 		0.569
(1.00) 		0.994
(1.00) 		0.522
(1.00) 		0.905
(1.00) 		0.0696
(0.943) 		0.223
(1.00) 		1
(1.00)
EHHADH 5 (1%) 415 0.76
(1.00) 		0.352
(1.00) 		0.447
(1.00) 		0.59
(1.00) 		1
(1.00) 		0.699
(1.00) 		0.922
(1.00) 		0.277
(1.00) 		0.159
(1.00) 		0.938
(1.00) 		0.36
(1.00) 		0.618
(1.00) 		0.768
(1.00)
TP53BP1 7 (2%) 413 0.731
(1.00) 		0.285
(1.00) 		0.317
(1.00) 		0.59
(1.00) 		1
(1.00) 		1
(1.00) 		0.727
(1.00) 		0.0197
(0.777) 		0.0282
(0.806) 		0.304
(1.00) 		0.0312
(0.806) 		0.488
(1.00) 		0.467
(1.00)
CNTNAP1 7 (2%) 413 0.885
(1.00) 		0.595
(1.00) 		1
(1.00) 		0.59
(1.00) 		0.226
(1.00) 		0.412
(1.00) 		0.802
(1.00) 		0.183
(1.00) 		0.761
(1.00) 		0.0822
(0.943) 		0.506
(1.00) 		0.878
(1.00) 		0.281
(1.00)
BMP2K 6 (1%) 414 0.799
(1.00) 		0.49
(1.00) 		0.0609
(0.943) 		0.51
(1.00) 		1
(1.00) 		0.0325
(0.806) 		0.738
(1.00) 		0.0939
(0.965) 		0.278
(1.00) 		0.209
(1.00) 		0.212
(1.00) 		0.781
(1.00) 		0.407
(1.00)
RPTN 6 (1%) 414 0.732
(1.00) 		0.329
(1.00) 		0.305
(1.00) 		1
(1.00) 		1
(1.00) 		0.176
(1.00) 		0.313
(1.00) 		0.421
(1.00) 		0.674
(1.00) 		0.565
(1.00) 		0.368
(1.00) 		0.487
(1.00) 		0.131
(0.984) 		0.164
(1.00)
TCEB3 4 (1%) 416 0.883
(1.00) 		0.467
(1.00) 		0.663
(1.00) 		0.413
(1.00) 		1
(1.00) 		1
(1.00) 		0.518
(1.00) 		0.282
(1.00) 		0.238
(1.00) 		0.674
(1.00) 		0.339
(1.00) 		0.447
(1.00) 		0.861
(1.00)
NTM 5 (1%) 415 0.78
(1.00) 		0.353
(1.00) 		0.445
(1.00) 		1
(1.00) 		1
(1.00) 		0.699
(1.00) 		0.313
(1.00) 		0.866
(1.00) 		0.914
(1.00) 		0.706
(1.00) 		0.951
(1.00) 		0.227
(1.00) 		0.263
(1.00) 		1
(1.00)
MED12 7 (2%) 413 0.793
(1.00) 		0.616
(1.00) 		0.509
(1.00) 		1
(1.00) 		1
(1.00) 		0.104
(0.965) 		0.929
(1.00) 		0.218
(1.00) 		0.48
(1.00) 		0.291
(1.00) 		0.167
(1.00) 		0.706
(1.00) 		0.424
(1.00) 		1
(1.00)
MED15 6 (1%) 414 0.803
(1.00) 		0.413
(1.00) 		0.724
(1.00) 		0.595
(1.00) 		1
(1.00) 		0.749
(1.00) 		0.268
(1.00) 		0.22
(1.00) 		0.107
(0.965) 		0.646
(1.00) 		0.279
(1.00) 		0.312
(1.00) 		0.0999
(0.965) 		0.164
(1.00)
ERN1 3 (1%) 417 0.828
(1.00) 		0.722
(1.00) 		0.592
(1.00) 		0.413
(1.00) 		1
(1.00) 		0.294
(1.00) 		0.518
(1.00) 		0.423
(1.00) 		0.446
(1.00) 		0.671
(1.00) 		0.369
(1.00) 		0.744
(1.00) 		0.336
(1.00)
LMOD2 5 (1%) 415 0.875
(1.00) 		0.304
(1.00) 		0.676
(1.00) 		0.51
(1.00) 		1
(1.00) 		1
(1.00) 		0.738
(1.00) 		0.912
(1.00) 		0.559
(1.00) 		0.43
(1.00) 		0.814
(1.00) 		0.0677
(0.943) 		0.16
(1.00)
FAM111A 3 (1%) 417 0.0837
(0.943) 		0.765
(1.00) 		0.299
(1.00) 		0.413
(1.00) 		0.104
(0.965) 		0.629
(1.00) 		0.253
(1.00) 		0.768
(1.00) 		0.216
(1.00) 		0.31
(1.00) 		0.519
(1.00) 		0.0144
(0.626)
ZNF709 5 (1%) 415 0.737
(1.00) 		0.501
(1.00) 		0.144
(1.00) 		1
(1.00) 		1
(1.00) 		0.239
(1.00) 		0.313
(1.00) 		0.17
(1.00) 		0.0254
(0.806) 		0.839
(1.00) 		0.129
(0.984) 		0.655
(1.00) 		0.517
(1.00)
MLLT10 4 (1%) 416 0.827
(1.00) 		0.134
(0.984) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.657
(1.00) 		0.368
(1.00) 		0.943
(1.00) 		0.51
(1.00) 		0.574
(1.00) 		0.969
(1.00) 		0.602
(1.00) 		0.13
(0.984) 		1
(1.00)
TNRC18 4 (1%) 416 0.49
(1.00) 		0.941
(1.00) 		0.66
(1.00) 		0.51
(1.00) 		1
(1.00) 		0.177
(1.00) 		0.533
(1.00) 		0.943
(1.00) 		0.789
(1.00) 		0.674
(1.00) 		0.969
(1.00) 		0.702
(1.00) 		0.706
(1.00)
GAGE2D 3 (1%) 417 0.883
(1.00) 		0.347
(1.00) 		0.111
(0.965) 		1
(1.00) 		1
(1.00) 		0.629
(1.00) 		0.12
(0.982) 		0.0678
(0.943) 		0.671
(1.00) 		0.105
(0.965) 		0.13
(0.984)
EMG1 4 (1%) 416 0.714
(1.00) 		0.813
(1.00) 		1
(1.00) 		1
(1.00) 		0.136
(0.984) 		0.654
(1.00) 		0.368
(1.00) 		0.114
(0.965) 		0.0347
(0.806) 		0.82
(1.00) 		0.777
(1.00) 		0.758
(1.00) 		0.245
(1.00)
LAMA3 7 (2%) 413 0.796
(1.00) 		0.919
(1.00) 		0.218
(1.00) 		1
(1.00) 		1
(1.00) 		0.155
(1.00) 		0.929
(1.00) 		0.294
(1.00) 		0.48
(1.00) 		0.0255
(0.806) 		0.373
(1.00) 		0.555
(1.00) 		0.457
(1.00)
RPL11 4 (1%) 416 0.863
(1.00) 		0.536
(1.00) 		0.192
(1.00) 		1
(1.00) 		0.136
(0.984) 		0.0274
(0.806) 		0.268
(1.00) 		0.516
(1.00) 		0.283
(1.00) 		0.321
(1.00) 		0.863
(1.00)
ZFHX3 13 (3%) 407 0.726
(1.00) 		0.29
(1.00) 		1
(1.00) 		0.211
(1.00) 		0.381
(1.00) 		0.41
(1.00) 		0.231
(1.00) 		0.0801
(0.943) 		0.424
(1.00) 		0.109
(0.965) 		0.0257
(0.806) 		0.894
(1.00) 		0.905
(1.00) 		0.259
(1.00)
MUC17 23 (5%) 397 0.295
(1.00) 		0.241
(1.00) 		0.762
(1.00) 		0.547
(1.00) 		0.577
(1.00) 		0.078
(0.943) 		0.67
(1.00) 		0.142
(1.00) 		0.0738
(0.943) 		0.685
(1.00) 		0.00263
(0.326) 		0.832
(1.00) 		0.701
(1.00) 		0.0269
(0.806)
CDKN1B 5 (1%) 415 0.754
(1.00) 		0.439
(1.00) 		0.0575
(0.943) 		0.59
(1.00) 		1
(1.00) 		0.0955
(0.965) 		0.922
(1.00) 		0.637
(1.00) 		0.914
(1.00) 		0.615
(1.00) 		0.223
(1.00) 		0.505
(1.00) 		0.788
(1.00) 		1
(1.00)
POM121 3 (1%) 417 0.952
(1.00) 		0.0288
(0.806) 		0.594
(1.00) 		1
(1.00) 		0.104
(0.965) 		1
(1.00) 		0.437
(1.00) 		0.726
(1.00) 		0.446
(1.00) 		0.216
(1.00) 		0.803
(1.00) 		0.275
(1.00) 		0.102
(0.965)
ESCO1 4 (1%) 416 0.875
(1.00) 		0.257
(1.00) 		0.663
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.368
(1.00) 		0.943
(1.00) 		0.234
(1.00) 		0.224
(1.00) 		0.969
(1.00) 		0.609
(1.00) 		0.367
(1.00) 		1
(1.00)
MYOT 4 (1%) 416 0.802
(1.00) 		0.0615
(0.943) 		0.192
(1.00) 		0.413
(1.00) 		0.136
(0.984) 		0.177
(1.00) 		0.518
(1.00) 		0.0376
(0.815) 		0.238
(1.00) 		0.0618
(0.943) 		0.0504
(0.943) 		0.927
(1.00) 		0.377
(1.00)
FAM47C 9 (2%) 411 0.714
(1.00) 		0.601
(1.00) 		0.559
(1.00) 		0.604
(1.00) 		1
(1.00) 		0.655
(1.00) 		0.231
(1.00) 		0.168
(1.00) 		0.923
(1.00) 		0.0703
(0.943) 		0.271
(1.00) 		0.449
(1.00) 		0.861
(1.00) 		1
(1.00)
CR1L 5 (1%) 415 0.816
(1.00) 		0.964
(1.00) 		0.448
(1.00) 		0.59
(1.00) 		1
(1.00) 		1
(1.00) 		0.753
(1.00) 		0.0884
(0.965) 		0.159
(1.00) 		0.529
(1.00) 		0.131
(0.984) 		0.297
(1.00) 		0.00857
(0.563) 		1
(1.00)
FAM120B 3 (1%) 417 0.816
(1.00) 		0.932
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.628
(1.00) 		0.423
(1.00) 		0.768
(1.00) 		0.18
(1.00) 		0.369
(1.00) 		0.565
(1.00) 		0.706
(1.00) 		1
(1.00)
EDC4 3 (1%) 417 0.816
(1.00) 		0.339
(1.00) 		1
(1.00) 		0.413
(1.00) 		1
(1.00) 		0.629
(1.00) 		0.518
(1.00) 		0.423
(1.00) 		0.446
(1.00) 		0.671
(1.00) 		0.369
(1.00) 		0.186
(1.00) 		0.587
(1.00) 		0.164
(1.00)
KIRREL 5 (1%) 415 0.738
(1.00) 		0.797
(1.00) 		1
(1.00) 		0.51
(1.00) 		1
(1.00) 		1
(1.00) 		0.564
(1.00) 		0.85
(1.00) 		0.914
(1.00) 		0.938
(1.00) 		0.984
(1.00) 		0.307
(1.00) 		0.381
(1.00) 		1
(1.00)
TCERG1 4 (1%) 416 0.723
(1.00) 		0.88
(1.00) 		1
(1.00) 		1
(1.00) 		0.136
(0.984) 		1
(1.00) 		0.437
(1.00) 		0.114
(0.965) 		0.234
(1.00) 		0.307
(1.00) 		0.707
(1.00) 		0.319
(1.00) 		0.718
(1.00)
SLC16A6 4 (1%) 416 0.772
(1.00) 		0.56
(1.00) 		0.663
(1.00) 		0.0698
(0.943) 		1
(1.00) 		0.103
(0.965) 		0.0106
(0.613) 		0.447
(1.00) 		0.789
(1.00) 		0.224
(1.00) 		0.535
(1.00) 		0.386
(1.00) 		0.549
(1.00)
NKX3-1 5 (1%) 415 0.812
(1.00) 		0.395
(1.00) 		0.226
(1.00) 		1
(1.00) 		1
(1.00) 		0.482
(1.00) 		0.313
(1.00) 		0.299
(1.00) 		0.914
(1.00) 		0.134
(0.984) 		0.0845
(0.943) 		0.857
(1.00) 		0.991
(1.00) 		1
(1.00)
RNF17 3 (1%) 417 0.873
(1.00) 		0.393
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.625
(1.00) 		0.437
(1.00) 		0.423
(1.00) 		0.0678
(0.943) 		0.627
(1.00) 		0.369
(1.00) 		0.444
(1.00) 		1
(1.00)
KYNU 3 (1%) 417 0.872
(1.00) 		0.816
(1.00) 		1
(1.00) 		0.413
(1.00) 		1
(1.00) 		1
(1.00) 		0.518
(1.00) 		0.994
(1.00) 		0.446
(1.00) 		0.627
(1.00) 		0.894
(1.00) 		0.467
(1.00) 		0.12
(0.982)
LARP1 4 (1%) 416 0.796
(1.00) 		0.522
(1.00) 		0.664
(1.00) 		0.51
(1.00) 		1
(1.00) 		0.155
(1.00) 		0.564
(1.00) 		0.121
(0.983) 		0.234
(1.00) 		0.307
(1.00) 		0.316
(1.00) 		0.866
(1.00) 		0.464
(1.00)
CDK12 8 (2%) 412 0.732
(1.00) 		0.397
(1.00) 		1
(1.00) 		0.318
(1.00) 		0.254
(1.00) 		0.477
(1.00) 		0.345
(1.00) 		0.0727
(0.943) 		0.193
(1.00) 		0.287
(1.00) 		0.111
(0.965) 		0.274
(1.00) 		0.625
(1.00)
ACPT 3 (1%) 417 0.875
(1.00) 		0.558
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.157
(1.00) 		0.423
(1.00) 		0.768
(1.00) 		0.18
(1.00) 		0.369
(1.00) 		0.396
(1.00)
AP4B1 5 (1%) 415 0.753
(1.00) 		0.637
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.368
(1.00) 		0.111
(0.965) 		0.265
(1.00) 		0.43
(1.00) 		0.0906
(0.965) 		0.61
(1.00) 		0.403
(1.00)
RAG1 9 (2%) 411 0.793
(1.00) 		0.924
(1.00) 		1
(1.00) 		0.604
(1.00) 		1
(1.00) 		0.791
(1.00) 		0.231
(1.00) 		0.168
(1.00) 		0.102
(0.965) 		0.832
(1.00) 		0.187
(1.00) 		0.82
(1.00) 		0.196
(1.00) 		1
(1.00)
APC 8 (2%) 412 0.589
(1.00) 		0.229
(1.00) 		0.533
(1.00) 		1
(1.00) 		1
(1.00) 		0.166
(1.00) 		0.799
(1.00) 		0.0395
(0.837) 		0.114
(0.965) 		0.244
(1.00) 		0.0669
(0.943) 		0.423
(1.00) 		0.359
(1.00)
MSLNL 4 (1%) 416 0.00451
(0.435) 		0.356
(1.00) 		1
(1.00) 		0.413
(1.00) 		1
(1.00) 		1
(1.00) 		0.518
(1.00) 		0.811
(1.00) 		0.234
(1.00) 		0.574
(1.00) 		0.707
(1.00) 		0.0141
(0.626) 		0.822
(1.00)
GAB2 5 (1%) 415 0.885
(1.00) 		0.785
(1.00) 		0.447
(1.00) 		0.0698
(0.943) 		1
(1.00) 		1
(1.00) 		0.0376
(0.815) 		0.0232
(0.806) 		0.35
(1.00) 		0.0171
(0.709) 		0.0346
(0.806) 		0.17
(1.00) 		0.204
(1.00)
DNMT3B 4 (1%) 416 0.796
(1.00) 		0.853
(1.00) 		0.662
(1.00) 		1
(1.00) 		1
(1.00) 		0.0845
(0.943) 		0.437
(1.00) 		0.0327
(0.806) 		0.516
(1.00) 		0.0618
(0.943) 		0.199
(1.00) 		0.313
(1.00) 		0.787
(1.00)
NCKAP1L 5 (1%) 415 0.483
(1.00) 		0.444
(1.00) 		0.679
(1.00) 		0.187
(1.00) 		1
(1.00) 		0.0947
(0.965) 		0.14
(1.00) 		0.299
(1.00) 		0.124
(0.984) 		0.938
(1.00) 		0.244
(1.00) 		0.634
(1.00) 		0.943
(1.00)
PRTFDC1 3 (1%) 417 0.816
(1.00) 		0.584
(1.00) 		0.591
(1.00) 		1
(1.00) 		1
(1.00) 		0.437
(1.00) 		0.423
(1.00) 		0.446
(1.00) 		0.671
(1.00) 		0.369
(1.00) 		0.941
(1.00) 		0.69
(1.00)
PCSK5 6 (1%) 414 0.803
(1.00) 		0.895
(1.00) 		0.459
(1.00) 		1
(1.00) 		1
(1.00) 		0.701
(1.00) 		0.368
(1.00) 		0.288
(1.00) 		0.392
(1.00) 		0.646
(1.00) 		0.368
(1.00) 		0.591
(1.00) 		0.356
(1.00) 		0.214
(1.00)
ITGA2B 4 (1%) 416 0.772
(1.00) 		0.375
(1.00) 		0.664
(1.00) 		0.51
(1.00) 		1
(1.00) 		0.629
(1.00) 		0.738
(1.00) 		0.282
(1.00) 		0.796
(1.00) 		0.224
(1.00) 		0.339
(1.00) 		0.227
(1.00) 		0.973
(1.00)
'TP53 MUTATION STATUS' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000137 (Wilcoxon-test), Q value = 0.04

Table S1.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 420 7.4 (0.9)
TP53 MUTATED 42 8.0 (1.0)
TP53 WILD-TYPE 378 7.4 (0.9)

Figure S1.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'TP53 MUTATION STATUS' versus 'GLEASON_SCORE'

P value = 1.11e-06 (Wilcoxon-test), Q value = 0.00096

Table S2.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 420 7.5 (0.9)
TP53 MUTATED 42 8.2 (0.9)
TP53 WILD-TYPE 378 7.4 (0.9)

Figure S2.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'GLEASON_SCORE'

'ZMYM3 MUTATION STATUS' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000938 (Wilcoxon-test), Q value = 0.16

Table S3.  Gene #13: 'ZMYM3 MUTATION STATUS' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 420 7.4 (0.9)
ZMYM3 MUTATED 9 8.6 (0.9)
ZMYM3 WILD-TYPE 411 7.4 (0.9)

Figure S3.  Get High-res Image Gene #13: 'ZMYM3 MUTATION STATUS' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'ZMYM3 MUTATION STATUS' versus 'GLEASON_SCORE_SECONDARY'

P value = 0.000717 (Wilcoxon-test), Q value = 0.16

Table S4.  Gene #13: 'ZMYM3 MUTATION STATUS' versus Clinical Feature #10: 'GLEASON_SCORE_SECONDARY'

nPatients Mean (Std.Dev)
ALL 420 3.9 (0.7)
ZMYM3 MUTATED 9 4.7 (0.7)
ZMYM3 WILD-TYPE 411 3.8 (0.7)

Figure S4.  Get High-res Image Gene #13: 'ZMYM3 MUTATION STATUS' versus Clinical Feature #10: 'GLEASON_SCORE_SECONDARY'

'L1CAM MUTATION STATUS' versus 'Time to Death'

P value = 0.000132 (logrank test), Q value = 0.04

Table S5.  Gene #39: 'L1CAM MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 419 7 0.7 - 165.2 (27.3)
L1CAM MUTATED 6 1 9.0 - 113.1 (23.6)
L1CAM WILD-TYPE 413 6 0.7 - 165.2 (27.3)

Figure S5.  Get High-res Image Gene #39: 'L1CAM 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/PRAD-TP/15170475/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PRAD-TP/15087329/PRAD-TP.merged_data.txt

  • Number of patients = 420

  • Number of significantly mutated genes = 62

  • Number of selected clinical features = 14

  • 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.

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] 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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