Correlation between gene mutation status and selected clinical features
Pancreatic Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1SX6BNF
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1SX6BNF
Overview
Introduction

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

Summary

Testing the association between mutation status of 102 genes and 12 clinical features across 44 patients, 5 significant findings detected with Q value < 0.25.

  • FYN mutation correlated to 'Time to Death'.

  • FADS2 mutation correlated to 'NEOPLASM.DISEASESTAGE'.

  • CEL mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • ECSIT mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • PLCZ1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 102 genes and 12 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 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		NUMBERPACKYEARSSMOKED YEAROFTOBACCOSMOKINGONSET COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES
nMutated (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test t-test t-test Fisher's exact test t-test
FYN 5 (11%) 39 0
(0) 		0.731
(1.00) 		0.0354
(1.00) 		0.394
(1.00) 		0.317
(1.00) 		0.0472
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.0482
(1.00) 		0.0909
(1.00)
FADS2 5 (11%) 39 0.627
(1.00) 		0.789
(1.00) 		7.36e-05
(0.0754) 		0.0575
(1.00) 		0.00681
(1.00) 		1
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.0974
(1.00)
CEL 4 (9%) 40 0.000604
(0.617) 		0.468
(1.00) 		0.00547
(1.00) 		0.327
(1.00) 		0.0316
(1.00) 		0.45
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.306
(1.00) 		6.35e-06
(0.00651)
ECSIT 4 (9%) 40 0.000604
(0.617) 		0.468
(1.00) 		0.00547
(1.00) 		0.327
(1.00) 		0.0316
(1.00) 		0.45
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.306
(1.00) 		6.35e-06
(0.00651)
PLCZ1 3 (7%) 41 0.983
(1.00) 		0.264
(1.00) 		0.000858
(0.875) 		0.254
(1.00) 		0.125
(1.00) 		0.651
(1.00) 		1
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.000227
(0.232)
C15ORF24 6 (14%) 38 0.908
(1.00) 		0.281
(1.00) 		0.081
(1.00) 		0.456
(1.00) 		0.12
(1.00) 		0.554
(1.00) 		0.0211
(1.00) 		1
(1.00) 		0.0702
(1.00) 		0.509
(1.00)
IRS1 4 (9%) 40 0.418
(1.00) 		0.00806
(1.00) 		0.422
(1.00) 		1
(1.00) 		1
(1.00) 		0.265
(1.00) 		1
(1.00) 		1
(1.00) 		0.612
(1.00) 		0.568
(1.00)
C14ORF49 8 (18%) 36 0.584
(1.00) 		0.332
(1.00) 		0.614
(1.00) 		0.566
(1.00) 		0.659
(1.00) 		0.8
(1.00) 		0.24
(1.00) 		1
(1.00) 		0.182
(1.00) 		0.166
(1.00)
FGF10 6 (14%) 38 0.607
(1.00) 		0.626
(1.00) 		0.0779
(1.00) 		0.456
(1.00) 		0.606
(1.00) 		0.751
(1.00) 		0.664
(1.00) 		1
(1.00) 		0.547
(1.00) 		0.541
(1.00)
CCR3 5 (11%) 39 0.997
(1.00) 		0.875
(1.00) 		0.949
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.742
(1.00)
OR10A2 6 (14%) 38 0.707
(1.00) 		0.352
(1.00) 		0.589
(1.00) 		0.456
(1.00) 		1
(1.00) 		0.751
(1.00) 		0.664
(1.00) 		1
(1.00) 		0.547
(1.00) 		0.139
(1.00)
OR10A7 9 (20%) 35 0.431
(1.00) 		0.877
(1.00) 		0.0233
(1.00) 		0.18
(1.00) 		0.175
(1.00) 		0.82
(1.00) 		0.132
(1.00) 		1
(1.00) 		0.156
(1.00) 		0.612
(1.00)
POP5 5 (11%) 39 0.344
(1.00) 		0.522
(1.00) 		0.0354
(1.00) 		0.394
(1.00) 		0.317
(1.00) 		0.353
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.696
(1.00)
SRP14 7 (16%) 37 0.602
(1.00) 		0.29
(1.00) 		0.932
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.364
(1.00) 		0.841
(1.00)
WRN 4 (9%) 40 0.908
(1.00) 		0.387
(1.00) 		0.354
(1.00) 		0.327
(1.00) 		0.218
(1.00) 		1
(1.00) 		0.108
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.916
(1.00)
TMEM40 8 (18%) 36 0.54
(1.00) 		0.752
(1.00) 		0.614
(1.00) 		0.566
(1.00) 		0.659
(1.00) 		0.8
(1.00) 		0.698
(1.00) 		1
(1.00) 		0.785
(1.00) 		0.458
(1.00)
KRAS 23 (52%) 21 0.351
(1.00) 		0.731
(1.00) 		0.483
(1.00) 		0.335
(1.00) 		0.155
(1.00) 		0.674
(1.00) 		1
(1.00) 		0.41
(1.00) 		0.251
(1.00) 		0.981
(1.00) 		0.653
(1.00) 		0.465
(1.00)
TP53 27 (61%) 17 0.32
(1.00) 		0.34
(1.00) 		0.464
(1.00) 		0.634
(1.00) 		0.473
(1.00) 		0.728
(1.00) 		1
(1.00) 		0.731
(1.00) 		0.604
(1.00) 		0.686
(1.00) 		0.0169
(1.00) 		0.441
(1.00)
QRICH1 7 (16%) 37 0.743
(1.00) 		0.953
(1.00) 		0.932
(1.00) 		1
(1.00) 		1
(1.00) 		0.782
(1.00) 		1
(1.00) 		0.523
(1.00) 		0.181
(1.00) 		0.0241
(1.00) 		0.0482
(1.00) 		0.568
(1.00)
ST6GALNAC5 5 (11%) 39 0.797
(1.00) 		0.517
(1.00) 		0.865
(1.00) 		1
(1.00) 		0.573
(1.00) 		0.731
(1.00) 		1
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.646
(1.00)
TNFSF9 6 (14%) 38 0.664
(1.00) 		0.0667
(1.00) 		0.555
(1.00) 		1
(1.00) 		0.606
(1.00) 		0.554
(1.00) 		0.664
(1.00) 		1
(1.00) 		0.227
(1.00) 		0.0737
(1.00)
CDKN2A 10 (23%) 34 0.155
(1.00) 		0.368
(1.00) 		0.505
(1.00) 		1
(1.00) 		0.0853
(1.00) 		0.835
(1.00) 		0.721
(1.00) 		1
(1.00) 		0.139
(1.00) 		0.479
(1.00) 		0.191
(1.00) 		0.0626
(1.00)
SEH1L 8 (18%) 36 0.993
(1.00) 		0.212
(1.00) 		0.812
(1.00) 		0.566
(1.00) 		1
(1.00) 		0.8
(1.00) 		0.698
(1.00) 		1
(1.00) 		0.0244
(1.00) 		0.794
(1.00)
SCD 8 (18%) 36 0.997
(1.00) 		0.483
(1.00) 		0.0104
(1.00) 		0.145
(1.00) 		0.0641
(1.00) 		0.8
(1.00) 		0.698
(1.00) 		1
(1.00) 		0.0321
(1.00) 		0.139
(1.00)
TMC4 7 (16%) 37 0.976
(1.00) 		0.438
(1.00) 		0.932
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.227
(1.00) 		0.578
(1.00)
MED15 9 (20%) 35 0.922
(1.00) 		0.658
(1.00) 		0.642
(1.00) 		1
(1.00) 		0.402
(1.00) 		1
(1.00) 		0.457
(1.00) 		1
(1.00) 		0.156
(1.00) 		0.068
(1.00)
TNFRSF9 6 (14%) 38 0.784
(1.00) 		0.254
(1.00) 		0.946
(1.00) 		1
(1.00) 		1
(1.00) 		0.751
(1.00) 		1
(1.00) 		1
(1.00) 		0.547
(1.00) 		0.494
(1.00)
BRDT 8 (18%) 36 0.422
(1.00) 		0.23
(1.00) 		0.907
(1.00) 		1
(1.00) 		0.659
(1.00) 		0.318
(1.00) 		1
(1.00) 		1
(1.00) 		0.646
(1.00) 		0.378
(1.00)
CXXC4 4 (9%) 40 0.233
(1.00) 		0.555
(1.00) 		0.933
(1.00) 		1
(1.00) 		1
(1.00) 		0.45
(1.00) 		1
(1.00) 		0.334
(1.00) 		0.502
(1.00) 		0.173
(1.00)
MBD3 6 (14%) 38 0.762
(1.00) 		0.633
(1.00) 		0.946
(1.00) 		1
(1.00) 		1
(1.00) 		0.313
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.409
(1.00)
TULP1 6 (14%) 38 0.812
(1.00) 		0.315
(1.00) 		0.0183
(1.00) 		0.456
(1.00) 		0.0179
(1.00) 		1
(1.00) 		0.185
(1.00) 		1
(1.00) 		0.1
(1.00) 		0.227
(1.00)
PHF13 4 (9%) 40 0.919
(1.00) 		0.821
(1.00) 		0.933
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.607
(1.00) 		0.334
(1.00) 		0.855
(1.00) 		1
(1.00) 		0.85
(1.00)
BHLHB9 4 (9%) 40 0.0191
(1.00) 		0.173
(1.00) 		0.422
(1.00) 		1
(1.00) 		1
(1.00) 		0.265
(1.00) 		1
(1.00) 		1
(1.00) 		0.0298
(1.00) 		0.632
(1.00)
PRDM8 6 (14%) 38 0.63
(1.00) 		0.479
(1.00) 		0.946
(1.00) 		1
(1.00) 		1
(1.00) 		0.751
(1.00) 		1
(1.00) 		1
(1.00) 		0.1
(1.00) 		0.212
(1.00)
SMAD4 7 (16%) 37 0.648
(1.00) 		0.902
(1.00) 		0.766
(1.00) 		1
(1.00) 		1
(1.00) 		0.272
(1.00) 		1
(1.00) 		1
(1.00) 		0.694
(1.00) 		0.149
(1.00) 		1
(1.00) 		0.798
(1.00)
C14ORF43 7 (16%) 37 0.148
(1.00) 		0.374
(1.00) 		0.0709
(1.00) 		0.513
(1.00) 		0.322
(1.00) 		0.272
(1.00) 		1
(1.00) 		1
(1.00) 		0.193
(1.00) 		0.183
(1.00)
MEPCE 7 (16%) 37 0.794
(1.00) 		0.68
(1.00) 		0.766
(1.00) 		0.513
(1.00) 		0.649
(1.00) 		0.588
(1.00) 		0.412
(1.00) 		1
(1.00) 		0.0655
(1.00) 		0.224
(1.00)
HVCN1 4 (9%) 40 0.222
(1.00) 		0.753
(1.00) 		0.00547
(1.00) 		0.327
(1.00) 		0.0316
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.00295
(1.00)
FOXP2 7 (16%) 37 0.547
(1.00) 		0.385
(1.00) 		0.766
(1.00) 		0.513
(1.00) 		0.649
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.785
(1.00) 		0.837
(1.00)
GRIN1 5 (11%) 39 0.544
(1.00) 		0.631
(1.00) 		0.0292
(1.00) 		0.394
(1.00) 		0.0688
(1.00) 		0.731
(1.00) 		1
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.00922
(1.00)
MAGEA10 4 (9%) 40 0.583
(1.00) 		0.155
(1.00) 		0.0514
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.836
(1.00)
C16ORF79 4 (9%) 40 0.36
(1.00) 		0.957
(1.00) 		0.354
(1.00) 		0.327
(1.00) 		0.218
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.146
(1.00)
ERF 6 (14%) 38 0.357
(1.00) 		0.825
(1.00) 		0.589
(1.00) 		0.456
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.93
(1.00)
IFNGR2 4 (9%) 40 0.417
(1.00) 		0.544
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.559
(1.00) 		0.677
(1.00) 		1
(1.00) 		1
(1.00) 		0.201
(1.00) 		0.292
(1.00)
OLIG3 5 (11%) 39 0.673
(1.00) 		0.737
(1.00) 		0.415
(1.00) 		1
(1.00) 		0.317
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.716
(1.00) 		0.216
(1.00)
NDEL1 4 (9%) 40 0.222
(1.00) 		0.456
(1.00) 		0.0409
(1.00) 		1
(1.00) 		0.218
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.00461
(1.00)
EGR1 8 (18%) 36 0.62
(1.00) 		0.725
(1.00) 		0.812
(1.00) 		0.566
(1.00) 		1
(1.00) 		0.318
(1.00) 		0.698
(1.00) 		1
(1.00) 		0.646
(1.00) 		0.541
(1.00)
CDH3 4 (9%) 40 0.288
(1.00) 		0.263
(1.00) 		0.933
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00) 		1
(1.00) 		0.632
(1.00)
PCDHAC2 7 (16%) 37 0.908
(1.00) 		0.561
(1.00) 		0.766
(1.00) 		1
(1.00) 		1
(1.00) 		0.272
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.841
(1.00)
ZFP36 4 (9%) 40 0.00545
(1.00) 		0.649
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.559
(1.00) 		0.45
(1.00) 		0.607
(1.00) 		1
(1.00) 		1
(1.00) 		0.225
(1.00)
NR4A3 5 (11%) 39 0.775
(1.00) 		0.541
(1.00) 		0.0354
(1.00) 		1
(1.00) 		0.317
(1.00) 		0.255
(1.00) 		1
(1.00) 		1
(1.00) 		0.716
(1.00) 		0.109
(1.00)
RAB11FIP5 5 (11%) 39 0.411
(1.00) 		0.833
(1.00) 		0.53
(1.00) 		0.394
(1.00) 		1
(1.00) 		0.731
(1.00) 		1
(1.00) 		1
(1.00) 		0.716
(1.00) 		0.961
(1.00)
OTUD4 7 (16%) 37 0.594
(1.00) 		0.776
(1.00) 		0.277
(1.00) 		1
(1.00) 		0.649
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.364
(1.00) 		0.156
(1.00)
PPARGC1B 6 (14%) 38 0.552
(1.00) 		0.578
(1.00) 		0.195
(1.00) 		1
(1.00) 		0.606
(1.00) 		0.554
(1.00) 		1
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.87
(1.00)
PDZD2 9 (20%) 35 0.288
(1.00) 		0.679
(1.00) 		0.394
(1.00) 		0.566
(1.00) 		1
(1.00) 		0.204
(1.00) 		1
(1.00) 		1
(1.00) 		0.272
(1.00) 		0.861
(1.00)
MED9 3 (7%) 41 0.337
(1.00) 		0.0312
(1.00) 		0.256
(1.00) 		0.254
(1.00) 		0.548
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.77
(1.00)
BCL2L1 3 (7%) 41 0.502
(1.00) 		0.0651
(1.00) 		0.0796
(1.00) 		1
(1.00) 		0.125
(1.00) 		0.651
(1.00) 		1
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.326
(1.00)
CPLX3 3 (7%) 41 0.684
(1.00) 		0.567
(1.00) 		0.956
(1.00) 		1
(1.00) 		1
(1.00) 		0.651
(1.00) 		1
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.795
(1.00)
NFAT5 8 (18%) 36 0.237
(1.00) 		0.146
(1.00) 		0.0402
(1.00) 		0.145
(1.00) 		0.0641
(1.00) 		0.8
(1.00) 		1
(1.00) 		0.258
(1.00) 		0.182
(1.00) 		0.526
(1.00)
WASF3 5 (11%) 39 0.444
(1.00) 		0.871
(1.00) 		0.547
(1.00) 		0.394
(1.00) 		0.317
(1.00) 		0.731
(1.00) 		1
(1.00) 		1
(1.00) 		0.716
(1.00) 		0.933
(1.00)
ABCC2 5 (11%) 39 0.945
(1.00) 		0.32
(1.00) 		0.53
(1.00) 		0.0575
(1.00) 		1
(1.00) 		0.731
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.716
(1.00) 		0.127
(1.00)
ATP13A3 4 (9%) 40 0.972
(1.00) 		0.838
(1.00) 		0.422
(1.00) 		0.327
(1.00) 		1
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00) 		1
(1.00) 		0.611
(1.00)
ARHGAP18 4 (9%) 40 0.797
(1.00) 		0.0982
(1.00) 		0.0514
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.108
(1.00) 		1
(1.00) 		1
(1.00) 		0.909
(1.00)
CIR1 3 (7%) 41 0.893
(1.00) 		0.952
(1.00) 		0.871
(1.00) 		1
(1.00) 		0.548
(1.00) 		1
(1.00) 		0.233
(1.00) 		1
(1.00) 		1
(1.00) 		0.472
(1.00)
KIAA0020 4 (9%) 40 0.00795
(1.00) 		0.466
(1.00) 		0.0514
(1.00) 		1
(1.00) 		1
(1.00) 		0.0815
(1.00) 		0.607
(1.00) 		1
(1.00) 		1
(1.00) 		0.861
(1.00)
ZNF608 6 (14%) 38 0.213
(1.00) 		0.408
(1.00) 		0.158
(1.00) 		1
(1.00) 		1
(1.00) 		0.313
(1.00) 		0.664
(1.00) 		1
(1.00) 		0.1
(1.00) 		0.688
(1.00)
NEDD4L 5 (11%) 39 0.615
(1.00) 		0.502
(1.00) 		0.53
(1.00) 		0.0575
(1.00) 		1
(1.00) 		0.488
(1.00) 		1
(1.00) 		1
(1.00) 		0.716
(1.00) 		0.648
(1.00)
THBS4 6 (14%) 38 0.702
(1.00) 		0.859
(1.00) 		0.0779
(1.00) 		0.456
(1.00) 		0.606
(1.00) 		1
(1.00) 		0.185
(1.00) 		1
(1.00) 		0.547
(1.00) 		0.331
(1.00)
MMRN1 6 (14%) 38 0.555
(1.00) 		0.424
(1.00) 		0.946
(1.00) 		1
(1.00) 		1
(1.00) 		0.751
(1.00) 		0.664
(1.00) 		1
(1.00) 		0.547
(1.00) 		0.386
(1.00)
GPR25 3 (7%) 41 0.796
(1.00) 		0.272
(1.00) 		0.956
(1.00) 		1
(1.00) 		1
(1.00) 		0.651
(1.00) 		1
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.795
(1.00)
SORBS2 5 (11%) 39 0.199
(1.00) 		0.269
(1.00) 		0.865
(1.00) 		1
(1.00) 		0.573
(1.00) 		0.488
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.34
(1.00)
ZNF326 4 (9%) 40 0.554
(1.00) 		0.978
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.559
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00) 		1
(1.00) 		0.723
(1.00)
C15ORF52 3 (7%) 41 0.249
(1.00) 		0.947
(1.00) 		0.956
(1.00) 		1
(1.00) 		1
(1.00) 		0.651
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.403
(1.00)
SLC39A5 3 (7%) 41 0.648
(1.00) 		0.358
(1.00) 		0.956
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.233
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.251
(1.00)
SLC24A1 4 (9%) 40 0.796
(1.00) 		0.895
(1.00) 		0.422
(1.00) 		0.327
(1.00) 		1
(1.00) 		0.45
(1.00) 		1
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.37
(1.00)
PUM2 5 (11%) 39 0.993
(1.00) 		0.167
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.317
(1.00) 		0.488
(1.00) 		1
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.681
(1.00)
SYT2 5 (11%) 39 0.147
(1.00) 		0.0255
(1.00) 		0.865
(1.00) 		1
(1.00) 		0.573
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.439
(1.00)
SLITRK5 6 (14%) 38 0.993
(1.00) 		0.156
(1.00) 		0.195
(1.00) 		1
(1.00) 		0.606
(1.00) 		0.751
(1.00) 		1
(1.00) 		1
(1.00) 		0.1
(1.00) 		0.48
(1.00)
NAP1L3 3 (7%) 41 0.897
(1.00) 		0.256
(1.00) 		0.254
(1.00) 		0.548
(1.00) 		0.651
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.177
(1.00)
PHF14 3 (7%) 41 0.222
(1.00) 		0.161
(1.00) 		0.871
(1.00) 		1
(1.00) 		0.548
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.488
(1.00)
CCDC28B 4 (9%) 40 0.715
(1.00) 		0.887
(1.00) 		0.00547
(1.00) 		0.327
(1.00) 		0.0316
(1.00) 		0.45
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.764
(1.00)
PDE12 3 (7%) 41 0.00795
(1.00) 		0.898
(1.00) 		0.956
(1.00) 		1
(1.00) 		1
(1.00) 		0.219
(1.00) 		1
(1.00) 		1
(1.00) 		0.872
(1.00)
FLAD1 3 (7%) 41 0.982
(1.00) 		0.256
(1.00) 		0.254
(1.00) 		0.548
(1.00) 		0.219
(1.00) 		1
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.38
(1.00)
ENG 3 (7%) 41 0.335
(1.00) 		0.256
(1.00) 		0.254
(1.00) 		0.548
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.976
(1.00)
PABPC1 4 (9%) 40 0.158
(1.00) 		0.0459
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.559
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00) 		1
(1.00) 		0.494
(1.00)
ATG16L2 3 (7%) 41 0.278
(1.00) 		0.836
(1.00) 		0.0131
(1.00) 		1
(1.00) 		0.548
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.488
(1.00)
LRCH1 7 (16%) 37 0.592
(1.00) 		0.829
(1.00) 		0.00344
(1.00) 		0.113
(1.00) 		0.0367
(1.00) 		1
(1.00) 		0.412
(1.00) 		1
(1.00) 		0.0655
(1.00) 		0.032
(1.00)
TAOK2 4 (9%) 40 0.841
(1.00) 		0.676
(1.00) 		0.354
(1.00) 		0.327
(1.00) 		0.218
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00) 		1
(1.00) 		0.481
(1.00)
ZMIZ1 5 (11%) 39 0.774
(1.00) 		0.293
(1.00) 		0.949
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.0482
(1.00) 		0.0145
(1.00)
SYT15 6 (14%) 38 0.316
(1.00) 		0.569
(1.00) 		0.0779
(1.00) 		1
(1.00) 		0.606
(1.00) 		0.115
(1.00) 		1
(1.00) 		1
(1.00) 		0.752
(1.00) 		0.333
(1.00)
LRTM1 3 (7%) 41 0.0182
(1.00) 		0.646
(1.00) 		0.871
(1.00) 		1
(1.00) 		0.548
(1.00) 		1
(1.00) 		0.233
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.867
(1.00)
TIMM50 3 (7%) 41 0.531
(1.00) 		0.259
(1.00) 		0.871
(1.00) 		1
(1.00) 		0.548
(1.00) 		0.336
(1.00) 		1
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.261
(1.00)
CCNK 4 (9%) 40 0.531
(1.00) 		0.23
(1.00) 		0.933
(1.00) 		1
(1.00) 		1
(1.00) 		0.677
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.0926
(1.00)
TTK 5 (11%) 39 0.495
(1.00) 		0.0517
(1.00) 		0.949
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.716
(1.00) 		0.488
(1.00)
TMEM175 4 (9%) 40 0.484
(1.00) 		0.976
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.559
(1.00) 		0.677
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.145
(1.00)
CD93 5 (11%) 39 0.641
(1.00) 		0.949
(1.00) 		0.0292
(1.00) 		0.394
(1.00) 		0.0688
(1.00) 		1
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.0482
(1.00) 		0.0221
(1.00)
C19ORF55 4 (9%) 40 0.15
(1.00) 		0.26
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.559
(1.00) 		0.677
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.7
(1.00) 		0.341
(1.00)
MRPL48 3 (7%) 41 0.796
(1.00) 		0.646
(1.00) 		0.956
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.544
(1.00)
PVRL1 5 (11%) 39 0.985
(1.00) 		0.84
(1.00) 		0.53
(1.00) 		0.394
(1.00) 		1
(1.00) 		0.731
(1.00) 		1
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.965
(1.00)
ACIN1 3 (7%) 41 0.575
(1.00) 		0.654
(1.00) 		0.956
(1.00) 		1
(1.00) 		1
(1.00) 		0.651
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.28
(1.00)
MAML3 6 (14%) 38 0.229
(1.00) 		0.497
(1.00) 		0.158
(1.00) 		1
(1.00) 		1
(1.00) 		0.313
(1.00) 		0.664
(1.00) 		1
(1.00) 		0.752
(1.00) 		0.535
(1.00)
EDC4 4 (9%) 40 0.402
(1.00) 		0.914
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.559
(1.00) 		0.677
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.413
(1.00)
'FYN MUTATION STATUS' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S1.  Gene #3: 'FYN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 43 16 0.0 - 49.4 (5.0)
FYN MUTATED 4 0 0.3 - 1.0 (0.7)
FYN WILD-TYPE 39 16 0.0 - 49.4 (6.0)

Figure S1.  Get High-res Image Gene #3: 'FYN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'FADS2 MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 7.36e-05 (Chi-square test), Q value = 0.075

Table S2.  Gene #4: 'FADS2 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
ALL 1 2 5 33 1 2
FADS2 MUTATED 0 2 1 1 1 0
FADS2 WILD-TYPE 1 0 4 32 0 2

Figure S2.  Get High-res Image Gene #4: 'FADS2 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'CEL MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.35e-06 (t-test), Q value = 0.0065

Table S3.  Gene #7: 'CEL MUTATION STATUS' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 44 2.9 (3.1)
CEL MUTATED 4 0.2 (0.5)
CEL WILD-TYPE 40 3.2 (3.1)

Figure S3.  Get High-res Image Gene #7: 'CEL MUTATION STATUS' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'ECSIT MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.35e-06 (t-test), Q value = 0.0065

Table S4.  Gene #70: 'ECSIT MUTATION STATUS' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 44 2.9 (3.1)
ECSIT MUTATED 4 0.2 (0.5)
ECSIT WILD-TYPE 40 3.2 (3.1)

Figure S4.  Get High-res Image Gene #70: 'ECSIT MUTATION STATUS' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'PLCZ1 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000227 (t-test), Q value = 0.23

Table S5.  Gene #87: 'PLCZ1 MUTATION STATUS' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 44 2.9 (3.1)
PLCZ1 MUTATED 3 0.3 (0.6)
PLCZ1 WILD-TYPE 41 3.1 (3.1)

Figure S5.  Get High-res Image Gene #87: 'PLCZ1 MUTATION STATUS' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Clinical data file = PAAD-TP.merged_data.txt

  • Number of patients = 44

  • Number of significantly mutated genes = 102

  • Number of selected clinical features = 12

  • 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

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

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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[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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