Correlation between gene mutation status and molecular subtypes
Cholangiocarcinoma (Primary solid tumor)
21 August 2015 | analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1CJ8CN3
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1CJ8CN3
Overview
Introduction

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

Summary

Testing the association between mutation status of 15 genes and 10 molecular subtypes across 35 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

- No gene mutations related to molecuar subtypes.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 15 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE 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 | Fisher's exact test
PBRM1 | 8 (23%) | 27 | 0.105 (0.92) | 0.0126 (0.281) | 0.856 (1.00) | 0.232 (1.00) | 0.305 (1.00) | 0.314 (1.00) | 0.846 (1.00) | 0.223 (1.00) | 1 (1.00) | 0.359 (1.00)
HLA-B | 5 (14%) | 30 | 1 (1.00) | 0.0186 (0.31) | 0.583 (1.00) | 0.436 (1.00) | 0.0131 (0.281) | 0.185 (1.00) | 0.00707 (0.281) | 0.0183 (0.31) | 0.631 (1.00) | 0.443 (1.00)
MLL3 | 7 (20%) | 28 | 0.207 (1.00) | 0.326 (1.00) | 0.321 (1.00) | 1 (1.00) | 0.872 (1.00) | 0.978 (1.00) | 0.244 (1.00) | 0.737 (1.00) | 0.43 (1.00) | 0.616 (1.00)
FTH1 | 3 (9%) | 32 | 0.582 (1.00) | 0.1 (0.92) | 0.0949 (0.92) | 0.588 (1.00) | 0.102 (0.92) | 0.23 (1.00) | 0.851 (1.00) | 0.659 (1.00) | 0.565 (1.00) | 1 (1.00)
TP53 | 5 (14%) | 30 | 0.642 (1.00) | 1 (1.00) | 0.519 (1.00) | 0.756 (1.00) | 1 (1.00) | 0.983 (1.00) | 0.923 (1.00) | 0.853 (1.00) | 1 (1.00) | 0.894 (1.00)
ARID1A | 5 (14%) | 30 | 0.642 (1.00) | 0.608 (1.00) | 0.518 (1.00) | 0.208 (1.00) | 0.225 (1.00) | 0.648 (1.00) | 1 (1.00) | 0.148 (1.00) | 0.631 (1.00) | 0.624 (1.00)
DDHD1 | 4 (11%) | 31 | 0.312 (1.00) | 1 (1.00) | 0.469 (1.00) | 0.465 (1.00) | 0.34 (1.00) | 0.914 (1.00) | 0.598 (1.00) | 0.205 (1.00) | 0.292 (1.00) | 0.638 (1.00)
MUC2 | 7 (20%) | 28 | 0.415 (1.00) | 0.575 (1.00) | 0.281 (1.00) | 0.401 (1.00) | 0.275 (1.00) | 0.15 (1.00) | 0.686 (1.00) | 0.202 (1.00) | 0.43 (1.00) | 0.743 (1.00)
IDH1 | 4 (11%) | 31 | 1 (1.00) | 0.00232 (0.281) | 1 (1.00) | 0.584 (1.00) | 0.072 (0.831) | 0.446 (1.00) | 0.00527 (0.281) | 0.04 (0.596) | 1 (1.00) | 0.39 (1.00)
MUC21 | 3 (9%) | 32 | 1 (1.00) | 0.771 (1.00) |  |  | 0.604 (1.00) | 0.0437 (0.596) | 1 (1.00) | 0.736 (1.00) | 0.565 (1.00) | 1 (1.00)
CLIP4 | 4 (11%) | 31 | 1 (1.00) | 0.652 (1.00) | 0.65 (1.00) | 0.888 (1.00) | 0.655 (1.00) | 0.916 (1.00) | 0.811 (1.00) | 0.152 (1.00) | 1 (1.00) | 0.893 (1.00)
BAP1 | 6 (17%) | 29 | 1 (1.00) | 0.195 (1.00) | 0.759 (1.00) | 0.588 (1.00) | 0.623 (1.00) | 0.411 (1.00) | 0.713 (1.00) | 0.444 (1.00) | 1 (1.00) | 0.406 (1.00)
CDC27 | 5 (14%) | 30 | 0.347 (1.00) | 0.832 (1.00) | 0.322 (1.00) | 0.0666 (0.831) | 0.834 (1.00) | 0.428 (1.00) | 0.348 (1.00) | 0.151 (1.00) | 0.00925 (0.281) | 0.231 (1.00)
FAM35A | 3 (9%) | 32 | 0.582 (1.00) | 1 (1.00) |  |  | 1 (1.00) | 0.793 (1.00) | 0.681 (1.00) | 0.695 (1.00) | 1 (1.00) | 0.0104 (0.281)
PAXIP1 | 4 (11%) | 31 | 0.608 (1.00) | 1 (1.00) | 1 (1.00) | 0.772 (1.00) | 0.651 (1.00) | 0.298 (1.00) | 0.598 (1.00) | 0.473 (1.00) | 0.619 (1.00) | 0.11 (0.92)

'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 0.92

Table S1. Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
PBRM1 MUTATED | 2 | 6
PBRM1 WILD-TYPE | 17 | 10

'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.28

Table S2. Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
PBRM1 MUTATED | 0 | 2 | 6
PBRM1 WILD-TYPE | 13 | 7 | 7

Figure S1. Get High-res Image Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 10 | 8 | 11
PBRM1 MUTATED | 2 | 1 | 3
PBRM1 WILD-TYPE | 8 | 7 | 8

'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 1

Table S4. Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
PBRM1 MUTATED | 2 | 1 | 3 | 0
PBRM1 WILD-TYPE | 4 | 6 | 5 | 8

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
PBRM1 MUTATED | 1 | 5 | 2
PBRM1 WILD-TYPE | 11 | 9 | 7

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S6. Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
PBRM1 MUTATED | 0 | 0 | 3 | 2 | 2 | 1 | 0
PBRM1 WILD-TYPE | 4 | 5 | 2 | 7 | 3 | 4 | 2

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.846 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
PBRM1 MUTATED | 1 | 1 | 3 | 3
PBRM1 WILD-TYPE | 8 | 4 | 7 | 8

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.223 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
PBRM1 MUTATED | 0 | 3 | 2 | 1 | 2 | 0
PBRM1 WILD-TYPE | 8 | 7 | 2 | 3 | 3 | 4

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S9. Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
PBRM1 MUTATED | 3 | 5
PBRM1 WILD-TYPE | 12 | 15

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.359 (Fisher's exact test), Q value = 1

Table S10. Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
PBRM1 MUTATED | 0 | 1 | 0 | 2 | 3 | 1 | 1
PBRM1 WILD-TYPE | 6 | 2 | 3 | 7 | 2 | 4 | 3

'HLA-B MUTATION STATUS' versus 'CN_CNMF'

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

Table S11. Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
HLA-B MUTATED | 3 | 2
HLA-B WILD-TYPE | 16 | 14

'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.31

Table S12. Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
HLA-B MUTATED | 1 | 4 | 0
HLA-B WILD-TYPE | 12 | 5 | 13

Figure S2. Get High-res Image Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 10 | 8 | 11
HLA-B MUTATED | 1 | 1 | 3
HLA-B WILD-TYPE | 9 | 7 | 8

'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
HLA-B MUTATED | 0 | 1 | 1 | 3
HLA-B WILD-TYPE | 6 | 6 | 7 | 5

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.28

Table S15. Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
HLA-B MUTATED | 0 | 1 | 4
HLA-B WILD-TYPE | 12 | 13 | 5

Figure S3. Get High-res Image Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
HLA-B MUTATED | 0 | 0 | 0 | 4 | 1 | 0 | 0
HLA-B WILD-TYPE | 4 | 5 | 5 | 5 | 4 | 5 | 2

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00707 (Fisher's exact test), Q value = 0.28

Table S17. Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
HLA-B MUTATED | 0 | 3 | 0 | 2
HLA-B WILD-TYPE | 9 | 2 | 10 | 9

Figure S4. Get High-res Image Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.31

Table S18. Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
HLA-B MUTATED | 0 | 0 | 0 | 2 | 1 | 2
HLA-B WILD-TYPE | 8 | 10 | 4 | 2 | 4 | 2

Figure S5. Get High-res Image Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S19. Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
HLA-B MUTATED | 3 | 2
HLA-B WILD-TYPE | 12 | 18

'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.443 (Fisher's exact test), Q value = 1

Table S20. Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
HLA-B MUTATED | 0 | 0 | 0 | 2 | 0 | 2 | 1
HLA-B WILD-TYPE | 6 | 3 | 3 | 7 | 5 | 3 | 3

'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 1

Table S21. Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
MLL3 MUTATED | 2 | 5
MLL3 WILD-TYPE | 17 | 11

'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 1

Table S22. Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
MLL3 MUTATED | 1 | 3 | 3
MLL3 WILD-TYPE | 12 | 6 | 10

'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 1

Table S23. Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 10 | 8 | 11
MLL3 MUTATED | 1 | 1 | 4
MLL3 WILD-TYPE | 9 | 7 | 7

'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S24. Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
MLL3 MUTATED | 1 | 1 | 2 | 2
MLL3 WILD-TYPE | 5 | 6 | 6 | 6

'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S25. Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
MLL3 MUTATED | 3 | 3 | 1
MLL3 WILD-TYPE | 9 | 11 | 8

'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.978 (Fisher's exact test), Q value = 1

Table S26. Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
MLL3 MUTATED | 1 | 1 | 1 | 1 | 2 | 1 | 0
MLL3 WILD-TYPE | 3 | 4 | 4 | 8 | 3 | 4 | 2

'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 1

Table S27. Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
MLL3 MUTATED | 3 | 1 | 0 | 3
MLL3 WILD-TYPE | 6 | 4 | 10 | 8

'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.737 (Fisher's exact test), Q value = 1

Table S28. Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
MLL3 MUTATED | 2 | 1 | 1 | 1 | 2 | 0
MLL3 WILD-TYPE | 6 | 9 | 3 | 3 | 3 | 4

'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.43 (Fisher's exact test), Q value = 1

Table S29. Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
MLL3 MUTATED | 4 | 3
MLL3 WILD-TYPE | 11 | 17

'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.616 (Fisher's exact test), Q value = 1

Table S30. Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
MLL3 MUTATED | 3 | 0 | 0 | 1 | 1 | 1 | 1
MLL3 WILD-TYPE | 3 | 3 | 3 | 8 | 4 | 4 | 3

'FTH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
FTH1 MUTATED | 1 | 2
FTH1 WILD-TYPE | 18 | 14

'FTH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.1 (Fisher's exact test), Q value = 0.92

Table S32. Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
FTH1 MUTATED | 0 | 0 | 3
FTH1 WILD-TYPE | 13 | 9 | 10

'FTH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0949 (Fisher's exact test), Q value = 0.92

Table S33. Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 10 | 8 | 11
FTH1 MUTATED | 0 | 0 | 3
FTH1 WILD-TYPE | 10 | 8 | 8

'FTH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S34. Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
FTH1 MUTATED | 0 | 0 | 1 | 2
FTH1 WILD-TYPE | 6 | 7 | 7 | 6

'FTH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.92

Table S35. Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
FTH1 MUTATED | 0 | 3 | 0
FTH1 WILD-TYPE | 12 | 11 | 9

'FTH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 1

Table S36. Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
FTH1 MUTATED | 0 | 0 | 1 | 0 | 0 | 1 | 1
FTH1 WILD-TYPE | 4 | 5 | 4 | 9 | 5 | 4 | 1

'FTH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.851 (Fisher's exact test), Q value = 1

Table S37. Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
FTH1 MUTATED | 0 | 0 | 1 | 2
FTH1 WILD-TYPE | 9 | 5 | 9 | 9

'FTH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.659 (Fisher's exact test), Q value = 1

Table S38. Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
FTH1 MUTATED | 0 | 1 | 1 | 0 | 1 | 0
FTH1 WILD-TYPE | 8 | 9 | 3 | 4 | 4 | 4

'FTH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 1

Table S39. Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
FTH1 MUTATED | 2 | 1
FTH1 WILD-TYPE | 13 | 19

'FTH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S40. Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
FTH1 MUTATED | 1 | 0 | 0 | 1 | 1 | 0 | 0
FTH1 WILD-TYPE | 5 | 3 | 3 | 8 | 4 | 5 | 4

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S41. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
TP53 MUTATED | 2 | 3
TP53 WILD-TYPE | 17 | 13

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S42. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
TP53 MUTATED | 2 | 1 | 2
TP53 WILD-TYPE | 11 | 8 | 11

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 1

Table S43. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 10 | 8 | 11
TP53 MUTATED | 2 | 0 | 2
TP53 WILD-TYPE | 8 | 8 | 9

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.756 (Fisher's exact test), Q value = 1

Table S44. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
TP53 MUTATED | 1 | 0 | 1 | 2
TP53 WILD-TYPE | 5 | 7 | 7 | 6

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S45. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
TP53 MUTATED | 2 | 2 | 1
TP53 WILD-TYPE | 10 | 12 | 8

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.983 (Fisher's exact test), Q value = 1

Table S46. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.923 (Fisher's exact test), Q value = 1

Table S47. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
TP53 MUTATED | 1 | 1 | 2 | 1
TP53 WILD-TYPE | 8 | 4 | 8 | 10

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.853 (Fisher's exact test), Q value = 1

Table S48. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
TP53 MUTATED | 1 | 2 | 1 | 1 | 0 | 0
TP53 WILD-TYPE | 7 | 8 | 3 | 3 | 5 | 4

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S49. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
TP53 MUTATED | 2 | 3
TP53 WILD-TYPE | 13 | 17

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.894 (Fisher's exact test), Q value = 1

Table S50. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S51. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
ARID1A MUTATED | 2 | 3
ARID1A WILD-TYPE | 17 | 13

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S52. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
ARID1A MUTATED | 1 | 1 | 3
ARID1A WILD-TYPE | 12 | 8 | 10

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S53. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 10 | 8 | 11
ARID1A MUTATED | 2 | 0 | 2
ARID1A WILD-TYPE | 8 | 8 | 9

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.208 (Fisher's exact test), Q value = 1

Table S54. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
ARID1A MUTATED | 0 | 0 | 3 | 1
ARID1A WILD-TYPE | 6 | 7 | 5 | 7

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 1

Table S55. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
ARID1A MUTATED | 0 | 3 | 2
ARID1A WILD-TYPE | 12 | 11 | 7

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S56. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
ARID1A MUTATED | 0 | 0 | 2 | 2 | 1 | 0 | 0
ARID1A WILD-TYPE | 4 | 5 | 3 | 7 | 4 | 5 | 2

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S57. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
ARID1A MUTATED | 1 | 1 | 1 | 2
ARID1A WILD-TYPE | 8 | 4 | 9 | 9

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 1

Table S58. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
ARID1A MUTATED | 0 | 1 | 2 | 1 | 0 | 1
ARID1A WILD-TYPE | 8 | 9 | 2 | 3 | 5 | 3

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S59. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
ARID1A MUTATED | 3 | 2
ARID1A WILD-TYPE | 12 | 18

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S60. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
ARID1A MUTATED | 0 | 0 | 0 | 3 | 1 | 1 | 0
ARID1A WILD-TYPE | 6 | 3 | 3 | 6 | 4 | 4 | 4

'DDHD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 1

Table S61. Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
DDHD1 MUTATED | 1 | 3
DDHD1 WILD-TYPE | 18 | 13

'DDHD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S62. Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
DDHD1 MUTATED | 1 | 1 | 2
DDHD1 WILD-TYPE | 12 | 8 | 11

'DDHD1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S63. Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 10 | 8 | 11
DDHD1 MUTATED | 0 | 1 | 2
DDHD1 WILD-TYPE | 10 | 7 | 9

'DDHD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.465 (Fisher's exact test), Q value = 1

Table S64. Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
DDHD1 MUTATED | 0 | 1 | 0 | 2
DDHD1 WILD-TYPE | 6 | 6 | 8 | 6

'DDHD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 1

Table S65. Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
DDHD1 MUTATED | 0 | 2 | 2
DDHD1 WILD-TYPE | 12 | 12 | 7

'DDHD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.914 (Fisher's exact test), Q value = 1

Table S66. Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
DDHD1 MUTATED | 0 | 0 | 1 | 2 | 0 | 1 | 0
DDHD1 WILD-TYPE | 4 | 5 | 4 | 7 | 5 | 4 | 2

'DDHD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S67. Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
DDHD1 MUTATED | 1 | 1 | 0 | 2
DDHD1 WILD-TYPE | 8 | 4 | 10 | 9

'DDHD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.205 (Fisher's exact test), Q value = 1

Table S68. Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
DDHD1 MUTATED | 0 | 0 | 1 | 1 | 1 | 1
DDHD1 WILD-TYPE | 8 | 10 | 3 | 3 | 4 | 3

'DDHD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S69. Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
DDHD1 MUTATED | 3 | 1
DDHD1 WILD-TYPE | 12 | 19

'DDHD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S70. Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
DDHD1 MUTATED | 1 | 0 | 0 | 1 | 0 | 2 | 0
DDHD1 WILD-TYPE | 5 | 3 | 3 | 8 | 5 | 3 | 4

'MUC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.415 (Fisher's exact test), Q value = 1

Table S71. Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
MUC2 MUTATED | 5 | 2
MUC2 WILD-TYPE | 14 | 14

'MUC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 1

Table S72. Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
MUC2 MUTATED | 4 | 1 | 2
MUC2 WILD-TYPE | 9 | 8 | 11

'MUC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 1

Table S73. Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 10 | 8 | 11
MUC2 MUTATED | 3 | 0 | 1
MUC2 WILD-TYPE | 7 | 8 | 10

'MUC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 1

Table S74. Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
MUC2 MUTATED | 2 | 0 | 1 | 1
MUC2 WILD-TYPE | 4 | 7 | 7 | 7

'MUC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 1

Table S75. Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
MUC2 MUTATED | 4 | 1 | 2
MUC2 WILD-TYPE | 8 | 13 | 7

'MUC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S76. Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
MUC2 MUTATED | 3 | 1 | 0 | 2 | 1 | 0 | 0
MUC2 WILD-TYPE | 1 | 4 | 5 | 7 | 4 | 5 | 2

'MUC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 1

Table S77. Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
MUC2 MUTATED | 3 | 1 | 1 | 2
MUC2 WILD-TYPE | 6 | 4 | 9 | 9

'MUC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 1

Table S78. Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
MUC2 MUTATED | 4 | 1 | 1 | 1 | 0 | 0
MUC2 WILD-TYPE | 4 | 9 | 3 | 3 | 5 | 4

'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.43 (Fisher's exact test), Q value = 1

Table S79. Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
MUC2 MUTATED | 4 | 3
MUC2 WILD-TYPE | 11 | 17

'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.743 (Fisher's exact test), Q value = 1

Table S80. Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
MUC2 MUTATED | 2 | 1 | 1 | 2 | 0 | 1 | 0
MUC2 WILD-TYPE | 4 | 2 | 2 | 7 | 5 | 4 | 4

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S81. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
IDH1 MUTATED | 2 | 2
IDH1 WILD-TYPE | 17 | 14

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.28

Table S82. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
IDH1 MUTATED | 0 | 4 | 0
IDH1 WILD-TYPE | 13 | 5 | 13

Figure S6. Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S83. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 10 | 8 | 11
IDH1 MUTATED | 1 | 1 | 2
IDH1 WILD-TYPE | 9 | 7 | 9

'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S84. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
IDH1 MUTATED | 1 | 1 | 0 | 2
IDH1 WILD-TYPE | 5 | 6 | 8 | 6

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.072 (Fisher's exact test), Q value = 0.83

Table S85. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
IDH1 MUTATED | 0 | 1 | 3
IDH1 WILD-TYPE | 12 | 13 | 6

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.446 (Fisher's exact test), Q value = 1

Table S86. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
IDH1 MUTATED | 0 | 0 | 0 | 3 | 0 | 1 | 0
IDH1 WILD-TYPE | 4 | 5 | 5 | 6 | 5 | 4 | 2

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00527 (Fisher's exact test), Q value = 0.28

Table S87. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
IDH1 MUTATED | 0 | 3 | 0 | 1
IDH1 WILD-TYPE | 9 | 2 | 10 | 10

Figure S7. Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.6

Table S88. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
IDH1 MUTATED | 0 | 0 | 0 | 2 | 1 | 1
IDH1 WILD-TYPE | 8 | 10 | 4 | 2 | 4 | 3

Figure S8. Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S89. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
IDH1 MUTATED | 2 | 2
IDH1 WILD-TYPE | 13 | 18

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 1

Table S90. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
IDH1 MUTATED | 0 | 0 | 0 | 2 | 0 | 2 | 0
IDH1 WILD-TYPE | 6 | 3 | 3 | 7 | 5 | 3 | 4

'MUC21 MUTATION STATUS' versus 'CN_CNMF'

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

Table S91. Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
MUC21 MUTATED | 2 | 1
MUC21 WILD-TYPE | 17 | 15

'MUC21 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.771 (Fisher's exact test), Q value = 1

Table S92. Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
MUC21 MUTATED | 2 | 0 | 1
MUC21 WILD-TYPE | 11 | 9 | 12

'MUC21 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.604 (Fisher's exact test), Q value = 1

Table S93. Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
MUC21 MUTATED | 2 | 1 | 0
MUC21 WILD-TYPE | 10 | 13 | 9

'MUC21 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.6

Table S94. Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
MUC21 MUTATED | 2 | 0 | 1 | 0 | 0 | 0 | 0
MUC21 WILD-TYPE | 2 | 5 | 4 | 9 | 5 | 5 | 2

Figure S9. Get High-res Image Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MUC21 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S95. Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
MUC21 MUTATED | 1 | 0 | 1 | 1
MUC21 WILD-TYPE | 8 | 5 | 9 | 10

'MUC21 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.736 (Fisher's exact test), Q value = 1

Table S96. Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
MUC21 MUTATED | 2 | 1 | 0 | 0 | 0 | 0
MUC21 WILD-TYPE | 6 | 9 | 4 | 4 | 5 | 4

'MUC21 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 1

Table S97. Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
MUC21 MUTATED | 2 | 1
MUC21 WILD-TYPE | 13 | 19

'MUC21 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S98. Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
MUC21 MUTATED | 1 | 0 | 0 | 1 | 1 | 0 | 0
MUC21 WILD-TYPE | 5 | 3 | 3 | 8 | 4 | 5 | 4

'CLIP4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S99. Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
CLIP4 MUTATED | 2 | 2
CLIP4 WILD-TYPE | 17 | 14

'CLIP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S100. Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
CLIP4 MUTATED | 2 | 0 | 2
CLIP4 WILD-TYPE | 11 | 9 | 11

'CLIP4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.65 (Fisher's exact test), Q value = 1

Table S101. Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 10 | 8 | 11
CLIP4 MUTATED | 1 | 2 | 1
CLIP4 WILD-TYPE | 9 | 6 | 10

'CLIP4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.888 (Fisher's exact test), Q value = 1

Table S102. Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
CLIP4 MUTATED | 0 | 1 | 1 | 2
CLIP4 WILD-TYPE | 6 | 6 | 7 | 6

'CLIP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S103. Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
CLIP4 MUTATED | 1 | 1 | 2
CLIP4 WILD-TYPE | 11 | 13 | 7

'CLIP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S104. Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
CLIP4 MUTATED | 0 | 0 | 1 | 2 | 0 | 1 | 0
CLIP4 WILD-TYPE | 4 | 5 | 4 | 7 | 5 | 4 | 2

'CLIP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.811 (Fisher's exact test), Q value = 1

Table S105. Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
CLIP4 MUTATED | 1 | 0 | 2 | 1
CLIP4 WILD-TYPE | 8 | 5 | 8 | 10

'CLIP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.152 (Fisher's exact test), Q value = 1

Table S106. Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
CLIP4 MUTATED | 0 | 2 | 0 | 0 | 0 | 2
CLIP4 WILD-TYPE | 8 | 8 | 4 | 4 | 5 | 2

'CLIP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S107. Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
CLIP4 MUTATED | 2 | 2
CLIP4 WILD-TYPE | 13 | 18

'CLIP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S108. Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
CLIP4 MUTATED | 0 | 0 | 0 | 1 | 1 | 1 | 1
CLIP4 WILD-TYPE | 6 | 3 | 3 | 8 | 4 | 4 | 3

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S109. Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
BAP1 MUTATED | 3 | 3
BAP1 WILD-TYPE | 16 | 13

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 1

Table S110. Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
BAP1 MUTATED | 2 | 0 | 4
BAP1 WILD-TYPE | 11 | 9 | 9

'BAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S111. Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 10 | 8 | 11
BAP1 MUTATED | 1 | 0 | 2
BAP1 WILD-TYPE | 9 | 8 | 9

'BAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S112. Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
BAP1 MUTATED | 0 | 0 | 1 | 2
BAP1 WILD-TYPE | 6 | 7 | 7 | 6

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.623 (Fisher's exact test), Q value = 1

Table S113. Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
BAP1 MUTATED | 1 | 3 | 2
BAP1 WILD-TYPE | 11 | 11 | 7

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 1

Table S114. Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
BAP1 MUTATED | 0 | 1 | 2 | 2 | 0 | 0 | 1
BAP1 WILD-TYPE | 4 | 4 | 3 | 7 | 5 | 5 | 1

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.713 (Fisher's exact test), Q value = 1

Table S115. Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
BAP1 MUTATED | 1 | 0 | 2 | 3
BAP1 WILD-TYPE | 8 | 5 | 8 | 8

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S116. Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
BAP1 MUTATED | 1 | 2 | 2 | 0 | 0 | 1
BAP1 WILD-TYPE | 7 | 8 | 2 | 4 | 5 | 3

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S117. Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
BAP1 MUTATED | 3 | 3
BAP1 WILD-TYPE | 12 | 17

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.406 (Fisher's exact test), Q value = 1

Table S118. Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
BAP1 MUTATED | 0 | 1 | 1 | 3 | 1 | 0 | 0
BAP1 WILD-TYPE | 6 | 2 | 2 | 6 | 4 | 5 | 4

'CDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 1

Table S119. Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
CDC27 MUTATED | 4 | 1
CDC27 WILD-TYPE | 15 | 15

'CDC27 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S120. Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
CDC27 MUTATED | 2 | 2 | 1
CDC27 WILD-TYPE | 11 | 7 | 12

'CDC27 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 1

Table S121. Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 10 | 8 | 11
CDC27 MUTATED | 3 | 0 | 2
CDC27 WILD-TYPE | 7 | 8 | 9

'CDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0666 (Fisher's exact test), Q value = 0.83

Table S122. Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
CDC27 MUTATED | 2 | 0 | 0 | 3
CDC27 WILD-TYPE | 4 | 7 | 8 | 5

'CDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S123. Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
CDC27 MUTATED | 1 | 2 | 2
CDC27 WILD-TYPE | 11 | 12 | 7

'CDC27 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.428 (Fisher's exact test), Q value = 1

Table S124. Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
CDC27 MUTATED | 1 | 0 | 0 | 2 | 0 | 1 | 1
CDC27 WILD-TYPE | 3 | 5 | 5 | 7 | 5 | 4 | 1

'CDC27 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 1

Table S125. Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
CDC27 MUTATED | 1 | 1 | 0 | 3
CDC27 WILD-TYPE | 8 | 4 | 10 | 8

'CDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 1

Table S126. Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
CDC27 MUTATED | 1 | 0 | 1 | 0 | 1 | 2
CDC27 WILD-TYPE | 7 | 10 | 3 | 4 | 4 | 2

'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00925 (Fisher's exact test), Q value = 0.28

Table S127. Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
CDC27 MUTATED | 5 | 0
CDC27 WILD-TYPE | 10 | 20

Figure S10. Get High-res Image Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.231 (Fisher's exact test), Q value = 1

Table S128. Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
CDC27 MUTATED | 1 | 0 | 0 | 4 | 0 | 0 | 0
CDC27 WILD-TYPE | 5 | 3 | 3 | 5 | 5 | 5 | 4

'FAM35A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 1

Table S129. Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
FAM35A MUTATED | 1 | 2
FAM35A WILD-TYPE | 18 | 14

'FAM35A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S130. Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
FAM35A MUTATED | 1 | 1 | 1
FAM35A WILD-TYPE | 12 | 8 | 12

'FAM35A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S131. Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
FAM35A MUTATED | 1 | 1 | 1
FAM35A WILD-TYPE | 11 | 13 | 8

'FAM35A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S132. Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
FAM35A MUTATED | 1 | 0 | 0 | 1 | 1 | 0 | 0
FAM35A WILD-TYPE | 3 | 5 | 5 | 8 | 4 | 5 | 2

'FAM35A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 1

Table S133. Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
FAM35A MUTATED | 0 | 0 | 2 | 1
FAM35A WILD-TYPE | 9 | 5 | 8 | 10

'FAM35A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.695 (Fisher's exact test), Q value = 1

Table S134. Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
FAM35A MUTATED | 0 | 2 | 0 | 0 | 1 | 0
FAM35A WILD-TYPE | 8 | 8 | 4 | 4 | 4 | 4

'FAM35A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S135. Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
FAM35A MUTATED | 1 | 2
FAM35A WILD-TYPE | 14 | 18

'FAM35A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.28

Table S136. Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
FAM35A MUTATED | 0 | 2 | 0 | 0 | 0 | 0 | 1
FAM35A WILD-TYPE | 6 | 1 | 3 | 9 | 5 | 5 | 3

Figure S11. Get High-res Image Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PAXIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S137. Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
PAXIP1 MUTATED | 3 | 1
PAXIP1 WILD-TYPE | 16 | 15

'PAXIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S138. Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
PAXIP1 MUTATED | 1 | 1 | 2
PAXIP1 WILD-TYPE | 12 | 8 | 11

'PAXIP1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S139. Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 10 | 8 | 11
PAXIP1 MUTATED | 1 | 1 | 1
PAXIP1 WILD-TYPE | 9 | 7 | 10

'PAXIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.772 (Fisher's exact test), Q value = 1

Table S140. Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
PAXIP1 MUTATED | 1 | 1 | 0 | 1
PAXIP1 WILD-TYPE | 5 | 6 | 8 | 7

'PAXIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.651 (Fisher's exact test), Q value = 1

Table S141. Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
PAXIP1 MUTATED | 1 | 1 | 2
PAXIP1 WILD-TYPE | 11 | 13 | 7

'PAXIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.298 (Fisher's exact test), Q value = 1

Table S142. Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 4 | 5 | 5 | 9 | 5 | 5 | 2
PAXIP1 MUTATED | 1 | 0 | 0 | 2 | 0 | 0 | 1
PAXIP1 WILD-TYPE | 3 | 5 | 5 | 7 | 5 | 5 | 1

'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S143. Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
PAXIP1 MUTATED | 0 | 1 | 2 | 1
PAXIP1 WILD-TYPE | 9 | 4 | 8 | 10

'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 1

Table S144. Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 10 | 4 | 4 | 5 | 4
PAXIP1 MUTATED | 0 | 2 | 1 | 1 | 0 | 0
PAXIP1 WILD-TYPE | 8 | 8 | 3 | 3 | 5 | 4

'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 1

Table S145. Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
PAXIP1 MUTATED | 1 | 3
PAXIP1 WILD-TYPE | 14 | 17

'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.11 (Fisher's exact test), Q value = 0.92

Table S146. Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 6 | 3 | 3 | 9 | 5 | 5 | 4
PAXIP1 MUTATED | 0 | 2 | 0 | 1 | 0 | 1 | 0
PAXIP1 WILD-TYPE | 6 | 1 | 3 | 8 | 5 | 4 | 4

Methods & Data
Input

- Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

- Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CHOL-TP/19893431/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CHOL-TP/20125181/CHOL-TP.transferedmergedcluster.txt

- Number of patients = 35

- Number of significantly mutated genes = 15

- Number of Molecular subtypes = 10

- 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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