Correlation between gene mutation status and selected clinical features
Lung Adenocarcinoma (MOLECULAR_NONSMOKER)
07 February 2013  |  awg_luad__2013_02_07
Maintainer Information
Citation Information
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 selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C12V2D75
Overview
Introduction

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

Summary

Testing the association between mutation status of 15 genes and 8 clinical features across 50 patients, 98 significant findings detected with P value < 1.

  • TP53 mutation correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • EGFR mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • CDKN2A mutation correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • SMAD4 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • KRAS mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • KEAP1 mutation correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • CSMD3 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • BRAF mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • SPTA1 mutation correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • STK11 mutation correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • OR4A5 mutation correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • SETD2 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • CDH10 mutation correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • MGAT4C mutation correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • U2AF2 mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 15 genes and 8 clinical features. Shown in the table are P values from statistical tests. Thresholded by P value < 1, 98 significant findings detected.

Clinical
Features
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test
EGFR 10 (20%) 40 0.317 0.634 1 0.851 0.628 0.174 0.406 0.736
KRAS 4 (8%) 46 0.321 0.492 0.586 0.158 0.16 0.0155 0.913 0.704
CSMD3 10 (20%) 40 0.0169 0.584 0.877 0.217 0.275 1 0.531 0.621
SETD2 5 (10%) 45 0.489 0.172 0.304 0.541 0.594 0.57 0.335 0.216
TP53 17 (34%) 33 0.229 1 1 0.147 0.00103 0.699 0.0625 0.411
CDKN2A 5 (10%) 45 0.307 1 0.804 0.941 0.317 1 0.881 0.538
SMAD4 5 (10%) 45 0.697 0.516 0.586 0.839 1 1 0.509 0.39
KEAP1 6 (12%) 44 0.215 1 0.125 0.163 0.363 0.00033 0.257 0.272
SPTA1 7 (14%) 43 0.473 1 0.139 0.335 0.183 0.0997 0.344 0.136
STK11 3 (6%) 47 0.406 0.15 0.699 0.722 0.00429 0.386 1
OR4A5 3 (6%) 47 0.406 1 5.24e-05 1 1 0.125 0.373
CDH10 4 (8%) 46 1 0.758 0.304 0.431 0.0436 0.56 0.532 1
MGAT4C 3 (6%) 47 1 0.586 0.23 0.494 1 0.874 1
U2AF2 3 (6%) 47 0.588 0.845 1 0.477 0.652
BRAF 5 (10%) 45 1 0.15 1 0.535 1
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.229 (Fisher's exact test)

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 27 12
TP53 MUTATED 6 7 4
TP53 WILD-TYPE 5 20 8

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test)

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 9 13
TP53 MUTATED 5 3 4
TP53 WILD-TYPE 13 6 9

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.147 (Chi-square test)

Table S3.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 7 11 6 9 2
TP53 MUTATED 0 3 2 2 3 2
TP53 WILD-TYPE 5 4 9 4 6 0

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00103 (Fisher's exact test)

Table S4.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 20 16 7
TP53 MUTATED 2 13 1 1
TP53 WILD-TYPE 5 7 15 6

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.699 (Fisher's exact test)

Table S5.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
TP53 MUTATED 2 15
TP53 WILD-TYPE 7 26

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0625 (Chi-square test)

Table S6.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
TP53 MUTATED 5 6 2 1 3
TP53 WILD-TYPE 4 8 5 14 2

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test)

Table S7.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 26 21
TP53 MUTATED 1 11 5
TP53 WILD-TYPE 2 15 16

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.317 (Fisher's exact test)

Table S8.  Gene #2: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 27 12
EGFR MUTATED 4 4 2
EGFR WILD-TYPE 7 23 10

Figure S8.  Get High-res Image Gene #2: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.634 (Fisher's exact test)

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 12 10
EGFR MUTATED 1 2 3
EGFR WILD-TYPE 9 10 7

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

'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test)

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 9 13
EGFR MUTATED 4 2 2
EGFR WILD-TYPE 14 7 11

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

'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.851 (Chi-square test)

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 7 11 6 9 2
EGFR MUTATED 2 1 2 1 2 0
EGFR WILD-TYPE 3 6 9 5 7 2

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

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.628 (Fisher's exact test)

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 20 16 7
EGFR MUTATED 0 5 4 1
EGFR WILD-TYPE 7 15 12 6

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

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.174 (Fisher's exact test)

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

nPatients CLUS_1 CLUS_2
ALL 9 41
EGFR MUTATED 0 10
EGFR WILD-TYPE 9 31

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

'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.406 (Chi-square test)

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
EGFR MUTATED 1 5 1 3 0
EGFR WILD-TYPE 8 9 6 12 5

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

'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.736 (Fisher's exact test)

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 26 21
EGFR MUTATED 1 5 4
EGFR WILD-TYPE 2 21 17

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

'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.307 (Fisher's exact test)

Table S16.  Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 27 12
CDKN2A MUTATED 2 3 0
CDKN2A WILD-TYPE 9 24 12

Figure S16.  Get High-res Image Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.804 (Fisher's exact test)

Table S17.  Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 9 13
CDKN2A MUTATED 1 1 2
CDKN2A WILD-TYPE 17 8 11

Figure S17.  Get High-res Image Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.941 (Chi-square test)

Table S18.  Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 7 11 6 9 2
CDKN2A MUTATED 0 1 1 1 1 0
CDKN2A WILD-TYPE 5 6 10 5 8 2

Figure S18.  Get High-res Image Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.317 (Fisher's exact test)

Table S19.  Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 20 16 7
CDKN2A MUTATED 1 3 0 1
CDKN2A WILD-TYPE 6 17 16 6

Figure S19.  Get High-res Image Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test)

Table S20.  Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
CDKN2A MUTATED 1 4
CDKN2A WILD-TYPE 8 37

Figure S20.  Get High-res Image Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.881 (Chi-square test)

Table S21.  Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
CDKN2A MUTATED 1 2 1 1 0
CDKN2A WILD-TYPE 8 12 6 14 5

Figure S21.  Get High-res Image Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.538 (Fisher's exact test)

Table S22.  Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 26 21
CDKN2A MUTATED 0 4 1
CDKN2A WILD-TYPE 3 22 20

Figure S22.  Get High-res Image Gene #3: 'CDKN2A MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.697 (Fisher's exact test)

Table S23.  Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 27 12
SMAD4 MUTATED 2 2 1
SMAD4 WILD-TYPE 9 25 11

Figure S23.  Get High-res Image Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'SMAD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.516 (Fisher's exact test)

Table S24.  Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 12 10
SMAD4 MUTATED 2 2 0
SMAD4 WILD-TYPE 8 10 10

Figure S24.  Get High-res Image Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.586 (Fisher's exact test)

Table S25.  Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 9 13
SMAD4 MUTATED 1 0 2
SMAD4 WILD-TYPE 17 9 11

Figure S25.  Get High-res Image Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.839 (Chi-square test)

Table S26.  Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 7 11 6 9 2
SMAD4 MUTATED 0 0 1 1 1 0
SMAD4 WILD-TYPE 5 7 10 5 8 2

Figure S26.  Get High-res Image Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test)

Table S27.  Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
SMAD4 MUTATED 1 4
SMAD4 WILD-TYPE 8 37

Figure S27.  Get High-res Image Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.509 (Chi-square test)

Table S28.  Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
SMAD4 MUTATED 2 2 0 1 0
SMAD4 WILD-TYPE 7 12 7 14 5

Figure S28.  Get High-res Image Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test)

Table S29.  Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 26 21
SMAD4 MUTATED 1 2 2
SMAD4 WILD-TYPE 2 24 19

Figure S29.  Get High-res Image Gene #4: 'SMAD4 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.321 (Fisher's exact test)

Table S30.  Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 27 12
KRAS MUTATED 2 2 0
KRAS WILD-TYPE 9 25 12

Figure S30.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.492 (Fisher's exact test)

Table S31.  Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 12 10
KRAS MUTATED 2 1 0
KRAS WILD-TYPE 8 11 10

Figure S31.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.586 (Fisher's exact test)

Table S32.  Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 9 13
KRAS MUTATED 1 0 2
KRAS WILD-TYPE 17 9 11

Figure S32.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.158 (Chi-square test)

Table S33.  Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 7 11 6 9 2
KRAS MUTATED 0 0 0 1 1 1
KRAS WILD-TYPE 5 7 11 5 8 1

Figure S33.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.16 (Fisher's exact test)

Table S34.  Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 20 16 7
KRAS MUTATED 2 2 0 0
KRAS WILD-TYPE 5 18 16 7

Figure S34.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test)

Table S35.  Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
KRAS MUTATED 3 1
KRAS WILD-TYPE 6 40

Figure S35.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.913 (Chi-square test)

Table S36.  Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
KRAS MUTATED 1 1 1 1 0
KRAS WILD-TYPE 8 13 6 14 5

Figure S36.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.704 (Fisher's exact test)

Table S37.  Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 26 21
KRAS MUTATED 0 3 1
KRAS WILD-TYPE 3 23 20

Figure S37.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.215 (Fisher's exact test)

Table S38.  Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 27 12
KEAP1 MUTATED 3 2 1
KEAP1 WILD-TYPE 8 25 11

Figure S38.  Get High-res Image Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'KEAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.125 (Fisher's exact test)

Table S39.  Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 9 13
KEAP1 MUTATED 1 3 1
KEAP1 WILD-TYPE 17 6 12

Figure S39.  Get High-res Image Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'KEAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.163 (Chi-square test)

Table S40.  Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 7 11 6 9 2
KEAP1 MUTATED 0 3 1 0 1 0
KEAP1 WILD-TYPE 5 4 10 6 8 2

Figure S40.  Get High-res Image Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.363 (Fisher's exact test)

Table S41.  Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 20 16 7
KEAP1 MUTATED 2 3 1 0
KEAP1 WILD-TYPE 5 17 15 7

Figure S41.  Get High-res Image Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test)

Table S42.  Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
KEAP1 MUTATED 5 1
KEAP1 WILD-TYPE 4 40

Figure S42.  Get High-res Image Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.257 (Chi-square test)

Table S43.  Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
KEAP1 MUTATED 0 1 1 2 2
KEAP1 WILD-TYPE 9 13 6 13 3

Figure S43.  Get High-res Image Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.272 (Fisher's exact test)

Table S44.  Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 26 21
KEAP1 MUTATED 1 2 3
KEAP1 WILD-TYPE 2 24 18

Figure S44.  Get High-res Image Gene #6: 'KEAP1 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'CSMD3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0169 (Fisher's exact test)

Table S45.  Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 27 12
CSMD3 MUTATED 5 2 3
CSMD3 WILD-TYPE 6 25 9

Figure S45.  Get High-res Image Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'CSMD3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.584 (Fisher's exact test)

Table S46.  Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 12 10
CSMD3 MUTATED 1 3 1
CSMD3 WILD-TYPE 9 9 9

Figure S46.  Get High-res Image Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'CSMD3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.877 (Fisher's exact test)

Table S47.  Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 9 13
CSMD3 MUTATED 4 1 2
CSMD3 WILD-TYPE 14 8 11

Figure S47.  Get High-res Image Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'CSMD3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.217 (Chi-square test)

Table S48.  Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 7 11 6 9 2
CSMD3 MUTATED 1 3 1 2 0 0
CSMD3 WILD-TYPE 4 4 10 4 9 2

Figure S48.  Get High-res Image Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'CSMD3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.275 (Fisher's exact test)

Table S49.  Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 20 16 7
CSMD3 MUTATED 2 6 1 1
CSMD3 WILD-TYPE 5 14 15 6

Figure S49.  Get High-res Image Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'CSMD3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test)

Table S50.  Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
CSMD3 MUTATED 2 8
CSMD3 WILD-TYPE 7 33

Figure S50.  Get High-res Image Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'CSMD3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.531 (Chi-square test)

Table S51.  Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
CSMD3 MUTATED 1 5 1 2 1
CSMD3 WILD-TYPE 8 9 6 13 4

Figure S51.  Get High-res Image Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'CSMD3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.621 (Fisher's exact test)

Table S52.  Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 26 21
CSMD3 MUTATED 1 6 3
CSMD3 WILD-TYPE 2 20 18

Figure S52.  Get High-res Image Gene #7: 'CSMD3 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.15 (Fisher's exact test)

Table S53.  Gene #8: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 20 16 7
BRAF MUTATED 2 2 0 1
BRAF WILD-TYPE 5 18 16 6

Figure S53.  Get High-res Image Gene #8: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test)

Table S54.  Gene #8: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
BRAF MUTATED 1 4
BRAF WILD-TYPE 8 37

Figure S54.  Get High-res Image Gene #8: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.535 (Chi-square test)

Table S55.  Gene #8: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
BRAF MUTATED 2 1 0 2 0
BRAF WILD-TYPE 7 13 7 13 5

Figure S55.  Get High-res Image Gene #8: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'SPTA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.473 (Fisher's exact test)

Table S56.  Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 27 12
SPTA1 MUTATED 3 3 1
SPTA1 WILD-TYPE 8 24 11

Figure S56.  Get High-res Image Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'SPTA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.139 (Fisher's exact test)

Table S57.  Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 9 13
SPTA1 MUTATED 4 2 0
SPTA1 WILD-TYPE 14 7 13

Figure S57.  Get High-res Image Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'SPTA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.335 (Chi-square test)

Table S58.  Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 7 11 6 9 2
SPTA1 MUTATED 2 2 1 1 0 0
SPTA1 WILD-TYPE 3 5 10 5 9 2

Figure S58.  Get High-res Image Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'SPTA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.183 (Fisher's exact test)

Table S59.  Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 20 16 7
SPTA1 MUTATED 3 2 2 0
SPTA1 WILD-TYPE 4 18 14 7

Figure S59.  Get High-res Image Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'SPTA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0997 (Fisher's exact test)

Table S60.  Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
SPTA1 MUTATED 3 4
SPTA1 WILD-TYPE 6 37

Figure S60.  Get High-res Image Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'SPTA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.344 (Chi-square test)

Table S61.  Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
SPTA1 MUTATED 1 4 0 2 0
SPTA1 WILD-TYPE 8 10 7 13 5

Figure S61.  Get High-res Image Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'SPTA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test)

Table S62.  Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 26 21
SPTA1 MUTATED 1 5 1
SPTA1 WILD-TYPE 2 21 20

Figure S62.  Get High-res Image Gene #9: 'SPTA1 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'STK11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.406 (Fisher's exact test)

Table S63.  Gene #10: 'STK11 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 27 12
STK11 MUTATED 0 3 0
STK11 WILD-TYPE 11 24 12

Figure S63.  Get High-res Image Gene #10: 'STK11 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'STK11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.15 (Fisher's exact test)

Table S64.  Gene #10: 'STK11 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 9 13
STK11 MUTATED 1 2 0
STK11 WILD-TYPE 17 7 13

Figure S64.  Get High-res Image Gene #10: 'STK11 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'STK11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.699 (Chi-square test)

Table S65.  Gene #10: 'STK11 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 7 11 6 9 2
STK11 MUTATED 1 1 1 0 0 0
STK11 WILD-TYPE 4 6 10 6 9 2

Figure S65.  Get High-res Image Gene #10: 'STK11 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'STK11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.722 (Fisher's exact test)

Table S66.  Gene #10: 'STK11 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 20 16 7
STK11 MUTATED 1 1 1 0
STK11 WILD-TYPE 6 19 15 7

Figure S66.  Get High-res Image Gene #10: 'STK11 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'STK11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00429 (Fisher's exact test)

Table S67.  Gene #10: 'STK11 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
STK11 MUTATED 3 0
STK11 WILD-TYPE 6 41

Figure S67.  Get High-res Image Gene #10: 'STK11 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'STK11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.386 (Chi-square test)

Table S68.  Gene #10: 'STK11 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
STK11 MUTATED 0 1 1 0 1
STK11 WILD-TYPE 9 13 6 15 4

Figure S68.  Get High-res Image Gene #10: 'STK11 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'OR4A5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.406 (Fisher's exact test)

Table S69.  Gene #11: 'OR4A5 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 27 12
OR4A5 MUTATED 0 3 0
OR4A5 WILD-TYPE 11 24 12

Figure S69.  Get High-res Image Gene #11: 'OR4A5 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'OR4A5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test)

Table S70.  Gene #11: 'OR4A5 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 9 13
OR4A5 MUTATED 1 1 1
OR4A5 WILD-TYPE 17 8 12

Figure S70.  Get High-res Image Gene #11: 'OR4A5 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'OR4A5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 5.24e-05 (Chi-square test)

Table S71.  Gene #11: 'OR4A5 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 7 11 6 9 2
OR4A5 MUTATED 0 0 0 0 1 2
OR4A5 WILD-TYPE 5 7 11 6 8 0

Figure S71.  Get High-res Image Gene #11: 'OR4A5 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'OR4A5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test)

Table S72.  Gene #11: 'OR4A5 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
OR4A5 MUTATED 0 3
OR4A5 WILD-TYPE 9 38

Figure S72.  Get High-res Image Gene #11: 'OR4A5 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'OR4A5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.125 (Chi-square test)

Table S73.  Gene #11: 'OR4A5 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
OR4A5 MUTATED 2 0 1 0 0
OR4A5 WILD-TYPE 7 14 6 15 5

Figure S73.  Get High-res Image Gene #11: 'OR4A5 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'OR4A5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.373 (Fisher's exact test)

Table S74.  Gene #11: 'OR4A5 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 26 21
OR4A5 MUTATED 0 3 0
OR4A5 WILD-TYPE 3 23 21

Figure S74.  Get High-res Image Gene #11: 'OR4A5 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.489 (Fisher's exact test)

Table S75.  Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 27 12
SETD2 MUTATED 0 3 2
SETD2 WILD-TYPE 11 24 10

Figure S75.  Get High-res Image Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.172 (Fisher's exact test)

Table S76.  Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 12 10
SETD2 MUTATED 3 1 0
SETD2 WILD-TYPE 7 11 10

Figure S76.  Get High-res Image Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.304 (Fisher's exact test)

Table S77.  Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 9 13
SETD2 MUTATED 3 0 0
SETD2 WILD-TYPE 15 9 13

Figure S77.  Get High-res Image Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.541 (Chi-square test)

Table S78.  Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 7 11 6 9 2
SETD2 MUTATED 0 1 2 0 0 0
SETD2 WILD-TYPE 5 6 9 6 9 2

Figure S78.  Get High-res Image Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.594 (Fisher's exact test)

Table S79.  Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 20 16 7
SETD2 MUTATED 1 1 2 1
SETD2 WILD-TYPE 6 19 14 6

Figure S79.  Get High-res Image Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.57 (Fisher's exact test)

Table S80.  Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
SETD2 MUTATED 0 5
SETD2 WILD-TYPE 9 36

Figure S80.  Get High-res Image Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.335 (Chi-square test)

Table S81.  Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
SETD2 MUTATED 2 0 0 2 1
SETD2 WILD-TYPE 7 14 7 13 4

Figure S81.  Get High-res Image Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.216 (Fisher's exact test)

Table S82.  Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 26 21
SETD2 MUTATED 0 1 4
SETD2 WILD-TYPE 3 25 17

Figure S82.  Get High-res Image Gene #12: 'SETD2 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'CDH10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.758 (Fisher's exact test)

Table S83.  Gene #13: 'CDH10 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 12 10
CDH10 MUTATED 0 2 1
CDH10 WILD-TYPE 10 10 9

Figure S83.  Get High-res Image Gene #13: 'CDH10 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'CDH10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.304 (Fisher's exact test)

Table S84.  Gene #13: 'CDH10 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 9 13
CDH10 MUTATED 3 0 0
CDH10 WILD-TYPE 15 9 13

Figure S84.  Get High-res Image Gene #13: 'CDH10 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'CDH10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.431 (Chi-square test)

Table S85.  Gene #13: 'CDH10 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 7 11 6 9 2
CDH10 MUTATED 1 0 2 0 0 0
CDH10 WILD-TYPE 4 7 9 6 9 2

Figure S85.  Get High-res Image Gene #13: 'CDH10 MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'CDH10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0436 (Fisher's exact test)

Table S86.  Gene #13: 'CDH10 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 20 16 7
CDH10 MUTATED 1 0 1 2
CDH10 WILD-TYPE 6 20 15 5

Figure S86.  Get High-res Image Gene #13: 'CDH10 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'CDH10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.56 (Fisher's exact test)

Table S87.  Gene #13: 'CDH10 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
CDH10 MUTATED 1 3
CDH10 WILD-TYPE 8 38

Figure S87.  Get High-res Image Gene #13: 'CDH10 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'CDH10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.532 (Chi-square test)

Table S88.  Gene #13: 'CDH10 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
CDH10 MUTATED 0 2 0 2 0
CDH10 WILD-TYPE 9 12 7 13 5

Figure S88.  Get High-res Image Gene #13: 'CDH10 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'MGAT4C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.586 (Fisher's exact test)

Table S89.  Gene #14: 'MGAT4C MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 9 13
MGAT4C MUTATED 1 0 2
MGAT4C WILD-TYPE 17 9 11

Figure S89.  Get High-res Image Gene #14: 'MGAT4C MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'MGAT4C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.23 (Chi-square test)

Table S90.  Gene #14: 'MGAT4C MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 7 11 6 9 2
MGAT4C MUTATED 0 0 1 0 1 1
MGAT4C WILD-TYPE 5 7 10 6 8 1

Figure S90.  Get High-res Image Gene #14: 'MGAT4C MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'MGAT4C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.494 (Fisher's exact test)

Table S91.  Gene #14: 'MGAT4C MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 20 16 7
MGAT4C MUTATED 0 2 0 1
MGAT4C WILD-TYPE 7 18 16 6

Figure S91.  Get High-res Image Gene #14: 'MGAT4C MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'MGAT4C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test)

Table S92.  Gene #14: 'MGAT4C MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
MGAT4C MUTATED 0 3
MGAT4C WILD-TYPE 9 38

Figure S92.  Get High-res Image Gene #14: 'MGAT4C MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'MGAT4C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.874 (Chi-square test)

Table S93.  Gene #14: 'MGAT4C MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
MGAT4C MUTATED 1 1 0 1 0
MGAT4C WILD-TYPE 8 13 7 14 5

Figure S93.  Get High-res Image Gene #14: 'MGAT4C MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'U2AF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.588 (Fisher's exact test)

Table S94.  Gene #15: 'U2AF2 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 27 12
U2AF2 MUTATED 1 1 1
U2AF2 WILD-TYPE 10 26 11

Figure S94.  Get High-res Image Gene #15: 'U2AF2 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'U2AF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.845 (Fisher's exact test)

Table S95.  Gene #15: 'U2AF2 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 20 16 7
U2AF2 MUTATED 0 1 2 0
U2AF2 WILD-TYPE 7 19 14 7

Figure S95.  Get High-res Image Gene #15: 'U2AF2 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'U2AF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test)

Table S96.  Gene #15: 'U2AF2 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 41
U2AF2 MUTATED 0 3
U2AF2 WILD-TYPE 9 38

Figure S96.  Get High-res Image Gene #15: 'U2AF2 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'U2AF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.477 (Chi-square test)

Table S97.  Gene #15: 'U2AF2 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 14 7 15 5
U2AF2 MUTATED 1 0 0 2 0
U2AF2 WILD-TYPE 8 14 7 13 5

Figure S97.  Get High-res Image Gene #15: 'U2AF2 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'U2AF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.652 (Fisher's exact test)

Table S98.  Gene #15: 'U2AF2 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 26 21
U2AF2 MUTATED 0 1 2
U2AF2 WILD-TYPE 3 25 19

Figure S98.  Get High-res Image Gene #15: 'U2AF2 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input
  • Mutation data file = MOLECULAR_NONSMOKER.mutsig.cluster.txt

  • Clinical data file = MOLECULAR_NONSMOKER.transferedmergedcluster.txt

  • Number of patients = 50

  • Number of significantly mutated genes = 15

  • Number of selected clinical features = 8

  • 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

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)