Correlation between gene mutation status and molecular subtypes
Rectum Adenocarcinoma (Primary solid tumor)
15 July 2014 | analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1MC8XTD
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 molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1MC8XTD
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 12 genes and 9 molecular subtypes across 69 patients, 3 significant findings detected with P value < 0.05 and Q value < 0.25.

- TP53 mutation correlated to 'MRNA_CNMF'.

- KRAS mutation correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 12 genes and 9 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 3 significant findings detected.

|  | Clinical Features | MRNA CNMF | MRNA CHIERARCHICAL | CN 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
KRAS | 38 (55%) | 31 | 0.249 (1.00) | 0.00752 (0.729) | 0.00131 (0.13) | 0.833 (1.00) | 0.852 (1.00) | 0.0465 (1.00) | 0.00019 (0.019) | 0.291 (1.00) | 0.00564 (0.553)
TP53 | 44 (64%) | 25 | 0.00015 (0.0151) | 0.015 (1.00) | 0.532 (1.00) | 0.162 (1.00) | 0.839 (1.00) | 0.487 (1.00) | 0.652 (1.00) | 1 (1.00) | 0.146 (1.00)
APC | 56 (81%) | 13 | 0.925 (1.00) | 0.916 (1.00) | 0.405 (1.00) | 0.361 (1.00) | 0.384 (1.00) | 0.242 (1.00) | 1 (1.00) | 0.452 (1.00) | 0.624 (1.00)
SMAD4 | 8 (12%) | 61 | 0.078 (1.00) | 0.777 (1.00) | 0.893 (1.00) | 0.156 (1.00) | 0.055 (1.00) | 0.186 (1.00) | 0.228 (1.00) | 0.311 (1.00) | 0.263 (1.00)
FBXW7 | 9 (13%) | 60 | 0.19 (1.00) | 0.409 (1.00) | 0.434 (1.00) | 0.689 (1.00) | 0.633 (1.00) | 1 (1.00) | 0.119 (1.00) | 0.806 (1.00) | 0.577 (1.00)
NRAS | 5 (7%) | 64 | 1 (1.00) | 0.839 (1.00) | 0.111 (1.00) |  |  | 1 (1.00) | 1 (1.00) | 0.0977 (1.00) | 1 (1.00)
ARID1A | 5 (7%) | 64 | 0.364 (1.00) | 0.393 (1.00) | 0.525 (1.00) | 0.171 (1.00) | 0.532 (1.00) | 1 (1.00) | 1 (1.00) | 0.314 (1.00) | 0.256 (1.00)
RBM10 | 4 (6%) | 65 | 1 (1.00) | 0.789 (1.00) | 0.469 (1.00) | 1 (1.00) | 0.78 (1.00) | 0.0164 (1.00) | 0.0443 (1.00) | 0.533 (1.00) | 0.566 (1.00)
TCF7L2 | 7 (10%) | 62 | 0.78 (1.00) | 0.204 (1.00) | 0.227 (1.00) | 0.15 (1.00) | 0.292 (1.00) | 1 (1.00) | 0.306 (1.00) | 1 (1.00) | 0.69 (1.00)
ERBB2 | 4 (6%) | 65 | 1 (1.00) | 0.877 (1.00) | 0.469 (1.00) | 0.675 (1.00) | 0.409 (1.00) | 0.0308 (1.00) | 0.0349 (1.00) | 1 (1.00) | 1 (1.00)
KIAA1804 | 9 (13%) | 60 | 0.512 (1.00) | 0.837 (1.00) | 0.474 (1.00) | 1 (1.00) | 0.599 (1.00) | 1 (1.00) | 0.758 (1.00) | 0.804 (1.00) | 0.574 (1.00)
CCDC88C | 3 (4%) | 66 |  |  |  |  |  | 1 (1.00) | 0.593 (1.00) | 0.432 (1.00) | 0.466 (1.00)

'APC MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.925 (Fisher's exact test), Q value = 1

Table S1. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 24 | 21 | 19
APC MUTATED | 19 | 16 | 16
APC WILD-TYPE | 5 | 5 | 3

'APC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2
APC MUTATED | 4 | 10 | 8 | 8 | 5 | 7 | 7 | 2
APC WILD-TYPE | 2 | 2 | 4 | 1 | 1 | 2 | 1 | 0

'APC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.405 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | ---
ALL | 17 | 18 | 17 | 11 | 5
APC MUTATED | 11 | 16 | 15 | 9 | 4
APC WILD-TYPE | 6 | 2 | 2 | 2 | 1

'APC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 1

Table S4. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 16 | 14 | 23
APC MUTATED | 11 | 12 | 20
APC WILD-TYPE | 5 | 2 | 3

'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.384 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 20 | 9 | 14 | 2 | 8
APC MUTATED | 15 | 7 | 12 | 1 | 8
APC WILD-TYPE | 5 | 2 | 2 | 1 | 0

'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 1 | 4 | 2 | 61
APC MUTATED | 0 | 4 | 2 | 50
APC WILD-TYPE | 1 | 0 | 0 | 11

'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | ---
ALL | 1 | 38 | 29
APC MUTATED | 1 | 31 | 24
APC WILD-TYPE | 0 | 7 | 5

'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | ---
ALL | 2 | 3 | 6 | 54
APC MUTATED | 1 | 3 | 5 | 45
APC WILD-TYPE | 1 | 0 | 1 | 9

'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.624 (Fisher's exact test), Q value = 1

Table S9. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 9 | 3 | 53
APC MUTATED | 8 | 2 | 44
APC WILD-TYPE | 1 | 1 | 9

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.015

Table S10. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 24 | 21 | 19
TP53 MUTATED | 7 | 15 | 17
TP53 WILD-TYPE | 17 | 6 | 2

Figure S1. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2
TP53 MUTATED | 2 | 8 | 4 | 9 | 5 | 6 | 5 | 0
TP53 WILD-TYPE | 4 | 4 | 8 | 0 | 1 | 3 | 3 | 2

Figure S2. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.532 (Fisher's exact test), Q value = 1

Table S12. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | ---
ALL | 17 | 18 | 17 | 11 | 5
TP53 MUTATED | 13 | 9 | 10 | 8 | 3
TP53 WILD-TYPE | 4 | 9 | 7 | 3 | 2

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 16 | 14 | 23
TP53 MUTATED | 10 | 12 | 13
TP53 WILD-TYPE | 6 | 2 | 10

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 20 | 9 | 14 | 2 | 8
TP53 MUTATED | 12 | 7 | 9 | 1 | 6
TP53 WILD-TYPE | 8 | 2 | 5 | 1 | 2

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.487 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 1 | 4 | 2 | 61
TP53 MUTATED | 0 | 2 | 1 | 40
TP53 WILD-TYPE | 1 | 2 | 1 | 21

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.652 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | ---
ALL | 1 | 38 | 29
TP53 MUTATED | 1 | 22 | 20
TP53 WILD-TYPE | 0 | 16 | 9

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S17. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | ---
ALL | 2 | 3 | 6 | 54
TP53 MUTATED | 1 | 2 | 4 | 34
TP53 WILD-TYPE | 1 | 1 | 2 | 20

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 9 | 3 | 53
TP53 MUTATED | 8 | 1 | 32
TP53 WILD-TYPE | 1 | 2 | 21

'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.249 (Fisher's exact test), Q value = 1

Table S19. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 24 | 21 | 19
KRAS MUTATED | 16 | 11 | 8
KRAS WILD-TYPE | 8 | 10 | 11

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00752 (Fisher's exact test), Q value = 0.73

Table S20. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2
KRAS MUTATED | 3 | 9 | 9 | 3 | 3 | 6 | 0 | 2
KRAS WILD-TYPE | 3 | 3 | 3 | 6 | 3 | 3 | 8 | 0

Figure S3. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.13

Table S21. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | ---
ALL | 17 | 18 | 17 | 11 | 5
KRAS MUTATED | 3 | 13 | 9 | 8 | 5
KRAS WILD-TYPE | 14 | 5 | 8 | 3 | 0

Figure S4. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S22. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 16 | 14 | 23
KRAS MUTATED | 7 | 8 | 12
KRAS WILD-TYPE | 9 | 6 | 11

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S23. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 20 | 9 | 14 | 2 | 8
KRAS MUTATED | 9 | 4 | 9 | 1 | 4
KRAS WILD-TYPE | 11 | 5 | 5 | 1 | 4

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 1 | 4 | 2 | 61
KRAS MUTATED | 1 | 4 | 0 | 32
KRAS WILD-TYPE | 0 | 0 | 2 | 29

Figure S5. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.019

Table S25. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | ---
ALL | 1 | 38 | 29
KRAS MUTATED | 1 | 28 | 8
KRAS WILD-TYPE | 0 | 10 | 21

Figure S6. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 1

Table S26. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | ---
ALL | 2 | 3 | 6 | 54
KRAS MUTATED | 1 | 2 | 1 | 30
KRAS WILD-TYPE | 1 | 1 | 5 | 24

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00564 (Fisher's exact test), Q value = 0.55

Table S27. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 9 | 3 | 53
KRAS MUTATED | 1 | 3 | 30
KRAS WILD-TYPE | 8 | 0 | 23

Figure S7. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

'SMAD4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.078 (Fisher's exact test), Q value = 1

Table S28. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 24 | 21 | 19
SMAD4 MUTATED | 5 | 0 | 2
SMAD4 WILD-TYPE | 19 | 21 | 17

'SMAD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S29. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2
SMAD4 MUTATED | 0 | 3 | 2 | 1 | 0 | 1 | 0 | 0
SMAD4 WILD-TYPE | 6 | 9 | 10 | 8 | 6 | 8 | 8 | 2

'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.893 (Fisher's exact test), Q value = 1

Table S30. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | ---
ALL | 17 | 18 | 17 | 11 | 5
SMAD4 MUTATED | 1 | 3 | 2 | 1 | 1
SMAD4 WILD-TYPE | 16 | 15 | 15 | 10 | 4

'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 16 | 14 | 23
SMAD4 MUTATED | 0 | 3 | 4
SMAD4 WILD-TYPE | 16 | 11 | 19

'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.055 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 20 | 9 | 14 | 2 | 8
SMAD4 MUTATED | 0 | 3 | 3 | 0 | 1
SMAD4 WILD-TYPE | 20 | 6 | 11 | 2 | 7

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 1 | 4 | 2 | 61
SMAD4 MUTATED | 1 | 0 | 0 | 7
SMAD4 WILD-TYPE | 0 | 4 | 2 | 54

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 1

Table S34. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | ---
ALL | 1 | 38 | 29
SMAD4 MUTATED | 0 | 7 | 1
SMAD4 WILD-TYPE | 1 | 31 | 28

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.311 (Fisher's exact test), Q value = 1

Table S35. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | ---
ALL | 2 | 3 | 6 | 54
SMAD4 MUTATED | 1 | 0 | 0 | 7
SMAD4 WILD-TYPE | 1 | 3 | 6 | 47

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 1

Table S36. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 9 | 3 | 53
SMAD4 MUTATED | 0 | 1 | 7
SMAD4 WILD-TYPE | 9 | 2 | 46

'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S37. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 24 | 21 | 19
FBXW7 MUTATED | 2 | 5 | 1
FBXW7 WILD-TYPE | 22 | 16 | 18

'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 1

Table S38. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2
FBXW7 MUTATED | 0 | 3 | 1 | 1 | 0 | 3 | 0 | 0
FBXW7 WILD-TYPE | 6 | 9 | 11 | 8 | 6 | 6 | 8 | 2

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 1

Table S39. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | ---
ALL | 17 | 18 | 17 | 11 | 5
FBXW7 MUTATED | 2 | 3 | 4 | 0 | 0
FBXW7 WILD-TYPE | 15 | 15 | 13 | 11 | 5

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.689 (Fisher's exact test), Q value = 1

Table S40. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 16 | 14 | 23
FBXW7 MUTATED | 3 | 2 | 2
FBXW7 WILD-TYPE | 13 | 12 | 21

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.633 (Fisher's exact test), Q value = 1

Table S41. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 20 | 9 | 14 | 2 | 8
FBXW7 MUTATED | 2 | 2 | 1 | 0 | 2
FBXW7 WILD-TYPE | 18 | 7 | 13 | 2 | 6

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S42. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 1 | 4 | 2 | 61
FBXW7 MUTATED | 0 | 0 | 0 | 9
FBXW7 WILD-TYPE | 1 | 4 | 2 | 52

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 1

Table S43. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | ---
ALL | 1 | 38 | 29
FBXW7 MUTATED | 0 | 8 | 1
FBXW7 WILD-TYPE | 1 | 30 | 28

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.806 (Fisher's exact test), Q value = 1

Table S44. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | ---
ALL | 2 | 3 | 6 | 54
FBXW7 MUTATED | 0 | 0 | 0 | 9
FBXW7 WILD-TYPE | 2 | 3 | 6 | 45

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.577 (Fisher's exact test), Q value = 1

Table S45. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 9 | 3 | 53
FBXW7 MUTATED | 0 | 0 | 9
FBXW7 WILD-TYPE | 9 | 3 | 44

'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S46. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 24 | 21 | 19
NRAS MUTATED | 2 | 2 | 1
NRAS WILD-TYPE | 22 | 19 | 18

'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S47. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2
NRAS MUTATED | 1 | 2 | 1 | 1 | 0 | 0 | 0 | 0
NRAS WILD-TYPE | 5 | 10 | 11 | 8 | 6 | 9 | 8 | 2

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 1

Table S48. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | ---
ALL | 17 | 18 | 17 | 11 | 5
NRAS MUTATED | 0 | 3 | 0 | 2 | 0
NRAS WILD-TYPE | 17 | 15 | 17 | 9 | 5

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S49. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 1 | 4 | 2 | 61
NRAS MUTATED | 0 | 0 | 0 | 5
NRAS WILD-TYPE | 1 | 4 | 2 | 56

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S50. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | ---
ALL | 1 | 38 | 29
NRAS MUTATED | 0 | 3 | 2
NRAS WILD-TYPE | 1 | 35 | 27

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0977 (Fisher's exact test), Q value = 1

Table S51. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | ---
ALL | 2 | 3 | 6 | 54
NRAS MUTATED | 1 | 0 | 1 | 3
NRAS WILD-TYPE | 1 | 3 | 5 | 51

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S52. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 9 | 3 | 53
NRAS MUTATED | 0 | 0 | 5
NRAS WILD-TYPE | 9 | 3 | 48

'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.364 (Fisher's exact test), Q value = 1

Table S53. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 24 | 21 | 19
ARID1A MUTATED | 3 | 2 | 0
ARID1A WILD-TYPE | 21 | 19 | 19

'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.393 (Fisher's exact test), Q value = 1

Table S54. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2
ARID1A MUTATED | 1 | 1 | 1 | 0 | 0 | 1 | 0 | 1
ARID1A WILD-TYPE | 5 | 11 | 11 | 9 | 6 | 8 | 8 | 1

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.525 (Fisher's exact test), Q value = 1

Table S55. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | ---
ALL | 17 | 18 | 17 | 11 | 5
ARID1A MUTATED | 1 | 3 | 0 | 1 | 0
ARID1A WILD-TYPE | 16 | 15 | 17 | 10 | 5

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 1

Table S56. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 16 | 14 | 23
ARID1A MUTATED | 2 | 1 | 0
ARID1A WILD-TYPE | 14 | 13 | 23

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 1

Table S57. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 20 | 9 | 14 | 2 | 8
ARID1A MUTATED | 2 | 0 | 0 | 0 | 1
ARID1A WILD-TYPE | 18 | 9 | 14 | 2 | 7

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S58. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 1 | 4 | 2 | 61
ARID1A MUTATED | 0 | 0 | 0 | 5
ARID1A WILD-TYPE | 1 | 4 | 2 | 56

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S59. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | ---
ALL | 1 | 38 | 29
ARID1A MUTATED | 0 | 3 | 2
ARID1A WILD-TYPE | 1 | 35 | 27

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.314 (Fisher's exact test), Q value = 1

Table S60. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | ---
ALL | 2 | 3 | 6 | 54
ARID1A MUTATED | 0 | 1 | 0 | 3
ARID1A WILD-TYPE | 2 | 2 | 6 | 51

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.256 (Fisher's exact test), Q value = 1

Table S61. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 9 | 3 | 53
ARID1A MUTATED | 0 | 1 | 3
ARID1A WILD-TYPE | 9 | 2 | 50

'RBM10 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S62. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 24 | 21 | 19
RBM10 MUTATED | 2 | 1 | 1
RBM10 WILD-TYPE | 22 | 20 | 18

'RBM10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.789 (Fisher's exact test), Q value = 1

Table S63. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2
RBM10 MUTATED | 1 | 1 | 0 | 1 | 0 | 1 | 0 | 0
RBM10 WILD-TYPE | 5 | 11 | 12 | 8 | 6 | 8 | 8 | 2

'RBM10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 1

Table S64. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | ---
ALL | 17 | 18 | 17 | 11 | 5
RBM10 MUTATED | 1 | 1 | 0 | 1 | 1
RBM10 WILD-TYPE | 16 | 17 | 17 | 10 | 4

'RBM10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S65. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 16 | 14 | 23
RBM10 MUTATED | 1 | 1 | 1
RBM10 WILD-TYPE | 15 | 13 | 22

'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.78 (Fisher's exact test), Q value = 1

Table S66. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 20 | 9 | 14 | 2 | 8
RBM10 MUTATED | 1 | 0 | 1 | 0 | 1
RBM10 WILD-TYPE | 19 | 9 | 13 | 2 | 7

'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 1

Table S67. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 1 | 4 | 2 | 61
RBM10 MUTATED | 0 | 2 | 0 | 1
RBM10 WILD-TYPE | 1 | 2 | 2 | 60

Figure S8. Get High-res Image Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0443 (Fisher's exact test), Q value = 1

Table S68. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | ---
ALL | 1 | 38 | 29
RBM10 MUTATED | 1 | 1 | 1
RBM10 WILD-TYPE | 0 | 37 | 28

Figure S9. Get High-res Image Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S69. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | ---
ALL | 2 | 3 | 6 | 54
RBM10 MUTATED | 0 | 0 | 1 | 3
RBM10 WILD-TYPE | 2 | 3 | 5 | 51

'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 1

Table S70. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 9 | 3 | 53
RBM10 MUTATED | 1 | 0 | 3
RBM10 WILD-TYPE | 8 | 3 | 50

'TCF7L2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.78 (Fisher's exact test), Q value = 1

Table S71. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 24 | 21 | 19
TCF7L2 MUTATED | 2 | 2 | 3
TCF7L2 WILD-TYPE | 22 | 19 | 16

'TCF7L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 1

Table S72. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2
TCF7L2 MUTATED | 1 | 0 | 1 | 1 | 1 | 0 | 3 | 0
TCF7L2 WILD-TYPE | 5 | 12 | 11 | 8 | 5 | 9 | 5 | 2

'TCF7L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 1

Table S73. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | ---
ALL | 17 | 18 | 17 | 11 | 5
TCF7L2 MUTATED | 4 | 0 | 2 | 1 | 0
TCF7L2 WILD-TYPE | 13 | 18 | 15 | 10 | 5

'TCF7L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 1

Table S74. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 16 | 14 | 23
TCF7L2 MUTATED | 2 | 2 | 0
TCF7L2 WILD-TYPE | 14 | 12 | 23

'TCF7L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 1

Table S75. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 20 | 9 | 14 | 2 | 8
TCF7L2 MUTATED | 2 | 0 | 0 | 0 | 2
TCF7L2 WILD-TYPE | 18 | 9 | 14 | 2 | 6

'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S76. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 1 | 4 | 2 | 61
TCF7L2 MUTATED | 0 | 0 | 0 | 7
TCF7L2 WILD-TYPE | 1 | 4 | 2 | 54

'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.306 (Fisher's exact test), Q value = 1

Table S77. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | ---
ALL | 1 | 38 | 29
TCF7L2 MUTATED | 0 | 2 | 5
TCF7L2 WILD-TYPE | 1 | 36 | 24

'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S78. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | ---
ALL | 2 | 3 | 6 | 54
TCF7L2 MUTATED | 0 | 0 | 0 | 6
TCF7L2 WILD-TYPE | 2 | 3 | 6 | 48

'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.69 (Fisher's exact test), Q value = 1

Table S79. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 9 | 3 | 53
TCF7L2 MUTATED | 0 | 0 | 6
TCF7L2 WILD-TYPE | 9 | 3 | 47

'ERBB2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S80. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 24 | 21 | 19
ERBB2 MUTATED | 2 | 1 | 1
ERBB2 WILD-TYPE | 22 | 20 | 18

'ERBB2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S81. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2
ERBB2 MUTATED | 0 | 1 | 2 | 1 | 0 | 0 | 0 | 0
ERBB2 WILD-TYPE | 6 | 11 | 10 | 8 | 6 | 9 | 8 | 2

'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 1

Table S82. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | ---
ALL | 17 | 18 | 17 | 11 | 5
ERBB2 MUTATED | 1 | 1 | 0 | 1 | 1
ERBB2 WILD-TYPE | 16 | 17 | 17 | 10 | 4

'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 1

Table S83. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 16 | 14 | 23
ERBB2 MUTATED | 1 | 2 | 1
ERBB2 WILD-TYPE | 15 | 12 | 22

'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 1

Table S84. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 20 | 9 | 14 | 2 | 8
ERBB2 MUTATED | 1 | 0 | 1 | 0 | 2
ERBB2 WILD-TYPE | 19 | 9 | 13 | 2 | 6

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 1

Table S85. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 1 | 4 | 2 | 61
ERBB2 MUTATED | 0 | 2 | 0 | 2
ERBB2 WILD-TYPE | 1 | 2 | 2 | 59

Figure S10. Get High-res Image Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0349 (Fisher's exact test), Q value = 1

Table S86. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | ---
ALL | 1 | 38 | 29
ERBB2 MUTATED | 1 | 1 | 2
ERBB2 WILD-TYPE | 0 | 37 | 27

Figure S11. Get High-res Image Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S87. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | ---
ALL | 2 | 3 | 6 | 54
ERBB2 MUTATED | 0 | 0 | 0 | 3
ERBB2 WILD-TYPE | 2 | 3 | 6 | 51

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S88. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 9 | 3 | 53
ERBB2 MUTATED | 0 | 0 | 3
ERBB2 WILD-TYPE | 9 | 3 | 50

'KIAA1804 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.512 (Fisher's exact test), Q value = 1

Table S89. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 24 | 21 | 19
KIAA1804 MUTATED | 3 | 4 | 1
KIAA1804 WILD-TYPE | 21 | 17 | 18

'KIAA1804 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S90. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 12 | 12 | 9 | 6 | 9 | 8 | 2
KIAA1804 MUTATED | 0 | 1 | 3 | 1 | 0 | 2 | 1 | 0
KIAA1804 WILD-TYPE | 6 | 11 | 9 | 8 | 6 | 7 | 7 | 2

'KIAA1804 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.474 (Fisher's exact test), Q value = 1

Table S91. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | ---
ALL | 17 | 18 | 17 | 11 | 5
KIAA1804 MUTATED | 2 | 4 | 3 | 0 | 0
KIAA1804 WILD-TYPE | 15 | 14 | 14 | 11 | 5

'KIAA1804 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S92. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 16 | 14 | 23
KIAA1804 MUTATED | 2 | 2 | 4
KIAA1804 WILD-TYPE | 14 | 12 | 19

'KIAA1804 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.599 (Fisher's exact test), Q value = 1

Table S93. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 20 | 9 | 14 | 2 | 8
KIAA1804 MUTATED | 3 | 0 | 3 | 0 | 2
KIAA1804 WILD-TYPE | 17 | 9 | 11 | 2 | 6

'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S94. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 1 | 4 | 2 | 61
KIAA1804 MUTATED | 0 | 0 | 0 | 9
KIAA1804 WILD-TYPE | 1 | 4 | 2 | 52

'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.758 (Fisher's exact test), Q value = 1

Table S95. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | ---
ALL | 1 | 38 | 29
KIAA1804 MUTATED | 0 | 6 | 3
KIAA1804 WILD-TYPE | 1 | 32 | 26

'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.804 (Fisher's exact test), Q value = 1

Table S96. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | ---
ALL | 2 | 3 | 6 | 54
KIAA1804 MUTATED | 0 | 0 | 0 | 9
KIAA1804 WILD-TYPE | 2 | 3 | 6 | 45

'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S97. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 9 | 3 | 53
KIAA1804 MUTATED | 0 | 0 | 9
KIAA1804 WILD-TYPE | 9 | 3 | 44

'CCDC88C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S98. Gene #12: 'CCDC88C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 1 | 4 | 2 | 61
CCDC88C MUTATED | 0 | 0 | 0 | 3
CCDC88C WILD-TYPE | 1 | 4 | 2 | 58

'CCDC88C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 1

Table S99. Gene #12: 'CCDC88C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | ---
ALL | 1 | 38 | 29
CCDC88C MUTATED | 0 | 1 | 2
CCDC88C WILD-TYPE | 1 | 37 | 27

'CCDC88C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.432 (Fisher's exact test), Q value = 1

Table S100. Gene #12: 'CCDC88C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | ---
ALL | 2 | 3 | 6 | 54
CCDC88C MUTATED | 0 | 0 | 1 | 2
CCDC88C WILD-TYPE | 2 | 3 | 5 | 52

'CCDC88C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.466 (Fisher's exact test), Q value = 1

Table S101. Gene #12: 'CCDC88C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 9 | 3 | 53
CCDC88C MUTATED | 1 | 0 | 2
CCDC88C WILD-TYPE | 8 | 3 | 51

Methods & Data
Input

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

- Molecular subtypes file = READ-TP.transferedmergedcluster.txt

- Number of patients = 69

- Number of significantly mutated genes = 12

- Number of Molecular subtypes = 9

- 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

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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] 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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