Correlation between gene mutation status and molecular subtypes
Cholangiocarcinoma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C12806M0
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/C12806M0
Overview
Introduction

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

Summary

Testing the association between mutation status of 16 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 16 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
BAP1 | 8 (23%) | 27 | 0.424 (1.00) | 0.874 (1.00) | 0.622 (1.00) | 0.719 (1.00) | 0.347 (1.00) | 0.607 (1.00) | 0.714 (1.00) | 0.852 (1.00) | 0.7 (1.00) | 0.818 (1.00)
PBRM1 | 8 (23%) | 27 | 0.105 (0.868) | 0.0126 (0.267) | 0.362 (1.00) | 0.232 (1.00) | 0.307 (1.00) | 0.319 (1.00) | 0.851 (1.00) | 0.226 (1.00) | 1 (1.00) | 0.358 (1.00)
MLL3 | 7 (20%) | 28 | 0.207 (1.00) | 0.326 (1.00) | 0.362 (1.00) | 1 (1.00) | 0.871 (1.00) | 0.979 (1.00) | 0.243 (1.00) | 0.738 (1.00) | 0.43 (1.00) | 0.615 (1.00)
TP53 | 5 (14%) | 30 | 0.642 (1.00) | 1 (1.00) | 0.268 (1.00) | 0.755 (1.00) | 1 (1.00) | 0.984 (1.00) | 0.923 (1.00) | 0.855 (1.00) | 1 (1.00) | 0.894 (1.00)
HLA-B | 5 (14%) | 30 | 1 (1.00) | 0.0188 (0.307) | 0.622 (1.00) | 0.437 (1.00) | 0.0133 (0.267) | 0.183 (1.00) | 0.00743 (0.267) | 0.0192 (0.307) | 0.631 (1.00) | 0.442 (1.00)
FTH1 | 3 (9%) | 32 | 0.582 (1.00) | 0.1 (0.868) | 0.268 (1.00) | 0.59 (1.00) | 0.0996 (0.868) | 0.231 (1.00) | 0.849 (1.00) | 0.661 (1.00) | 0.565 (1.00) | 1 (1.00)
ARID1A | 5 (14%) | 30 | 0.642 (1.00) | 0.606 (1.00) | 0.268 (1.00) | 0.207 (1.00) | 0.223 (1.00) | 0.648 (1.00) | 1 (1.00) | 0.15 (1.00) | 0.631 (1.00) | 0.624 (1.00)
DDHD1 | 4 (11%) | 31 | 0.312 (1.00) | 1 (1.00) | 1 (1.00) | 0.465 (1.00) | 0.338 (1.00) | 0.915 (1.00) | 0.595 (1.00) | 0.204 (1.00) | 0.292 (1.00) | 0.642 (1.00)
IDH1 | 4 (11%) | 31 | 1 (1.00) | 0.00249 (0.267) | 0.622 (1.00) | 0.586 (1.00) | 0.0722 (0.739) | 0.45 (1.00) | 0.0054 (0.267) | 0.039 (0.567) | 1 (1.00) | 0.392 (1.00)
MUC2 | 7 (20%) | 28 | 0.415 (1.00) | 0.574 (1.00) | 0.622 (1.00) | 0.398 (1.00) | 0.275 (1.00) | 0.152 (1.00) | 0.684 (1.00) | 0.202 (1.00) | 0.43 (1.00) | 0.744 (1.00)
MUC21 | 3 (9%) | 32 | 1 (1.00) | 0.767 (1.00) | 1 (1.00) |  | 0.602 (1.00) | 0.0442 (0.589) | 1 (1.00) | 0.737 (1.00) | 0.565 (1.00) | 1 (1.00)
PAXIP1 | 4 (11%) | 31 | 0.608 (1.00) | 1 (1.00) | 0.539 (1.00) | 0.775 (1.00) | 0.653 (1.00) | 0.299 (1.00) | 0.598 (1.00) | 0.472 (1.00) | 0.619 (1.00) | 0.108 (0.868)
EPHA2 | 4 (11%) | 31 | 1 (1.00) | 0.071 (0.739) | 0.622 (1.00) | 0.486 (1.00) | 0.653 (1.00) | 0.912 (1.00) | 0.00582 (0.267) | 0.329 (1.00) | 1 (1.00) | 0.975 (1.00)
OTOP1 | 4 (11%) | 31 | 1 (1.00) | 1 (1.00) | 0.539 (1.00) | 0.0739 (0.739) | 1 (1.00) | 0.601 (1.00) | 0.81 (1.00) | 0.533 (1.00) | 0.619 (1.00) | 0.428 (1.00)
CDC27 | 5 (14%) | 30 | 0.347 (1.00) | 0.831 (1.00) | 1 (1.00) | 0.0665 (0.739) | 0.833 (1.00) | 0.427 (1.00) | 0.349 (1.00) | 0.147 (1.00) | 0.00925 (0.267) | 0.232 (1.00)
FAM35A | 3 (9%) | 32 | 0.582 (1.00) | 1 (1.00) | 1 (1.00) |  | 1 (1.00) | 0.797 (1.00) | 0.68 (1.00) | 0.692 (1.00) | 1 (1.00) | 0.0107 (0.267)

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 1

Table S1. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
BAP1 MUTATED | 3 | 5
BAP1 WILD-TYPE | 16 | 11

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.874 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
BAP1 MUTATED | 2 | 2 | 4
BAP1 WILD-TYPE | 11 | 7 | 9

'BAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
BAP1 MUTATED | 1 | 4
BAP1 WILD-TYPE | 10 | 14

'BAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S4. Gene #1: '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 | 1 | 2 | 2
BAP1 WILD-TYPE | 6 | 6 | 6 | 6

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S5. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
BAP1 MUTATED | 1 | 4 | 3
BAP1 WILD-TYPE | 11 | 10 | 6

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.607 (Fisher's exact test), Q value = 1

Table S6. Gene #1: '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 | 3 | 1 | 0 | 1
BAP1 WILD-TYPE | 4 | 4 | 3 | 6 | 4 | 5 | 1

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S7. Gene #1: '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 | 1 | 2 | 4
BAP1 WILD-TYPE | 8 | 4 | 8 | 7

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S8. Gene #1: '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 | 1 | 1 | 1
BAP1 WILD-TYPE | 7 | 8 | 2 | 3 | 4 | 3

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 1

Table S9. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
BAP1 MUTATED | 4 | 4
BAP1 WILD-TYPE | 11 | 16

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S10. Gene #1: '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 | 1 | 1
BAP1 WILD-TYPE | 6 | 2 | 2 | 6 | 4 | 4 | 3

'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 0.87

Table S11. Gene #2: '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 = 0.27

Table S12. Gene #2: '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 #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.362 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
PBRM1 MUTATED | 1 | 5
PBRM1 WILD-TYPE | 10 | 13

'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S14. Gene #2: '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 = 0.307 (Fisher's exact test), Q value = 1

Table S15. Gene #2: '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 = 0.319 (Fisher's exact test), Q value = 1

Table S16. Gene #2: '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 = 0.851 (Fisher's exact test), Q value = 1

Table S17. Gene #2: '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 = 0.226 (Fisher's exact test), Q value = 1

Table S18. Gene #2: '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 S19. Gene #2: '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 = 0.358 (Fisher's exact test), Q value = 1

Table S20. Gene #2: '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

'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 = 0.362 (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
--- | --- | ---
ALL | 11 | 18
MLL3 MUTATED | 1 | 5
MLL3 WILD-TYPE | 10 | 13

'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 = 0.871 (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 = 0.979 (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 = 0.243 (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 = 0.738 (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 = 0.615 (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

'TP53 MUTATION STATUS' versus 'CN_CNMF'

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

Table S31. Gene #4: '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 S32. Gene #4: '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 = 0.268 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
TP53 MUTATED | 0 | 4
TP53 WILD-TYPE | 11 | 14

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S34. Gene #4: '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 S35. Gene #4: '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 = 0.984 (Fisher's exact test), Q value = 1

Table S36. Gene #4: '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 S37. Gene #4: '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 = 0.855 (Fisher's exact test), Q value = 1

Table S38. Gene #4: '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 S39. Gene #4: '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 S40. Gene #4: '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

'HLA-B MUTATION STATUS' versus 'CN_CNMF'

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

Table S41. Gene #5: '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 = 0.0188 (Fisher's exact test), Q value = 0.31

Table S42. Gene #5: '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 #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S43. Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
HLA-B MUTATED | 1 | 4
HLA-B WILD-TYPE | 10 | 14

'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.437 (Fisher's exact test), Q value = 1

Table S44. Gene #5: '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 = 0.0133 (Fisher's exact test), Q value = 0.27

Table S45. Gene #5: '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 #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.183 (Fisher's exact test), Q value = 1

Table S46. Gene #5: '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 = 0.00743 (Fisher's exact test), Q value = 0.27

Table S47. Gene #5: '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 #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.31

Table S48. Gene #5: '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 #5: '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 S49. Gene #5: '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 = 0.442 (Fisher's exact test), Q value = 1

Table S50. Gene #5: '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

'FTH1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S51. Gene #6: '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 = 0.87

Table S52. Gene #6: '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 = 0.268 (Fisher's exact test), Q value = 1

Table S53. Gene #6: 'FTH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
FTH1 MUTATED | 0 | 3
FTH1 WILD-TYPE | 11 | 15

'FTH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S54. Gene #6: '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 = 0.0996 (Fisher's exact test), Q value = 0.87

Table S55. Gene #6: '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 = 0.231 (Fisher's exact test), Q value = 1

Table S56. Gene #6: '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 = 0.849 (Fisher's exact test), Q value = 1

Table S57. Gene #6: '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 = 0.661 (Fisher's exact test), Q value = 1

Table S58. Gene #6: '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 S59. Gene #6: '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 S60. Gene #6: '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

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S61. Gene #7: '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 = 0.606 (Fisher's exact test), Q value = 1

Table S62. Gene #7: '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 = 0.268 (Fisher's exact test), Q value = 1

Table S63. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
ARID1A MUTATED | 0 | 4
ARID1A WILD-TYPE | 11 | 14

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S64. Gene #7: '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 = 0.223 (Fisher's exact test), Q value = 1

Table S65. Gene #7: '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 S66. Gene #7: '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 S67. Gene #7: '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 = 0.15 (Fisher's exact test), Q value = 1

Table S68. Gene #7: '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 S69. Gene #7: '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 S70. Gene #7: '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 S71. Gene #8: '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 S72. Gene #8: '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 = 1 (Fisher's exact test), Q value = 1

Table S73. Gene #8: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
DDHD1 MUTATED | 1 | 2
DDHD1 WILD-TYPE | 10 | 16

'DDHD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S74. Gene #8: '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 = 0.338 (Fisher's exact test), Q value = 1

Table S75. Gene #8: '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 = 0.915 (Fisher's exact test), Q value = 1

Table S76. Gene #8: '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 = 0.595 (Fisher's exact test), Q value = 1

Table S77. Gene #8: '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 = 0.204 (Fisher's exact test), Q value = 1

Table S78. Gene #8: '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 S79. Gene #8: '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 = 0.642 (Fisher's exact test), Q value = 1

Table S80. Gene #8: '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

'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 = 0.00249 (Fisher's exact test), Q value = 0.27

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 = 0.622 (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
--- | --- | ---
ALL | 11 | 18
IDH1 MUTATED | 2 | 2
IDH1 WILD-TYPE | 9 | 16

'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.586 (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 = 0.0722 (Fisher's exact test), Q value = 0.74

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 = 0.45 (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 = 0.0054 (Fisher's exact test), Q value = 0.27

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 = 0.039 (Fisher's exact test), Q value = 0.57

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 = 0.392 (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

'MUC2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S91. Gene #10: '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 = 0.574 (Fisher's exact test), Q value = 1

Table S92. Gene #10: '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 = 0.622 (Fisher's exact test), Q value = 1

Table S93. Gene #10: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
MUC2 MUTATED | 2 | 2
MUC2 WILD-TYPE | 9 | 16

'MUC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.398 (Fisher's exact test), Q value = 1

Table S94. Gene #10: '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 S95. Gene #10: '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 = 0.152 (Fisher's exact test), Q value = 1

Table S96. Gene #10: '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 = 0.684 (Fisher's exact test), Q value = 1

Table S97. Gene #10: '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 S98. Gene #10: '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 S99. Gene #10: '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 = 0.744 (Fisher's exact test), Q value = 1

Table S100. Gene #10: '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

'MUC21 MUTATION STATUS' versus 'CN_CNMF'

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

Table S101. Gene #11: '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 = 0.767 (Fisher's exact test), Q value = 1

Table S102. Gene #11: '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 'RPPA_CNMF'

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

Table S103. Gene #11: 'MUC21 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
MUC21 MUTATED | 1 | 1
MUC21 WILD-TYPE | 10 | 17

'MUC21 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S104. Gene #11: '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 = 0.0442 (Fisher's exact test), Q value = 0.59

Table S105. Gene #11: '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 #11: '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 S106. Gene #11: '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 = 0.737 (Fisher's exact test), Q value = 1

Table S107. Gene #11: '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 S108. Gene #11: '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 S109. Gene #11: '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

'PAXIP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S110. Gene #12: '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 S111. Gene #12: '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 = 0.539 (Fisher's exact test), Q value = 1

Table S112. Gene #12: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
PAXIP1 MUTATED | 2 | 1
PAXIP1 WILD-TYPE | 9 | 17

'PAXIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S113. Gene #12: '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 = 0.653 (Fisher's exact test), Q value = 1

Table S114. Gene #12: '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 = 0.299 (Fisher's exact test), Q value = 1

Table S115. Gene #12: '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 S116. Gene #12: '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 = 0.472 (Fisher's exact test), Q value = 1

Table S117. Gene #12: '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 S118. Gene #12: '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 = 0.108 (Fisher's exact test), Q value = 0.87

Table S119. Gene #12: '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

'EPHA2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S120. Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
EPHA2 MUTATED | 2 | 2
EPHA2 WILD-TYPE | 17 | 14

'EPHA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.071 (Fisher's exact test), Q value = 0.74

Table S121. Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
EPHA2 MUTATED | 0 | 3 | 1
EPHA2 WILD-TYPE | 13 | 6 | 12

'EPHA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S122. Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
EPHA2 MUTATED | 2 | 2
EPHA2 WILD-TYPE | 9 | 16

'EPHA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 1

Table S123. Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
EPHA2 MUTATED | 1 | 2 | 0 | 1
EPHA2 WILD-TYPE | 5 | 5 | 8 | 7

'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.653 (Fisher's exact test), Q value = 1

Table S124. Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
EPHA2 MUTATED | 1 | 1 | 2
EPHA2 WILD-TYPE | 11 | 13 | 7

'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S125. Gene #13: 'EPHA2 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
EPHA2 MUTATED | 0 | 1 | 0 | 2 | 1 | 0 | 0
EPHA2 WILD-TYPE | 4 | 4 | 5 | 7 | 4 | 5 | 2

'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00582 (Fisher's exact test), Q value = 0.27

Table S126. Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
EPHA2 MUTATED | 0 | 3 | 0 | 1
EPHA2 WILD-TYPE | 9 | 2 | 10 | 10

Figure S10. Get High-res Image Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 1

Table S127. Gene #13: 'EPHA2 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
EPHA2 MUTATED | 1 | 0 | 1 | 1 | 0 | 1
EPHA2 WILD-TYPE | 7 | 10 | 3 | 3 | 5 | 3

'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S128. Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
EPHA2 MUTATED | 2 | 2
EPHA2 WILD-TYPE | 13 | 18

'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.975 (Fisher's exact test), Q value = 1

Table S129. Gene #13: 'EPHA2 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
EPHA2 MUTATED | 1 | 0 | 0 | 2 | 0 | 1 | 0
EPHA2 WILD-TYPE | 5 | 3 | 3 | 7 | 5 | 4 | 4

'OTOP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S130. Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 16
OTOP1 MUTATED | 2 | 2
OTOP1 WILD-TYPE | 17 | 14

'OTOP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S131. Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 9 | 13
OTOP1 MUTATED | 1 | 1 | 2
OTOP1 WILD-TYPE | 12 | 8 | 11

'OTOP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 1

Table S132. Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
OTOP1 MUTATED | 2 | 1
OTOP1 WILD-TYPE | 9 | 17

'OTOP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0739 (Fisher's exact test), Q value = 0.74

Table S133. Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 6 | 7 | 8 | 8
OTOP1 MUTATED | 2 | 1 | 0 | 0
OTOP1 WILD-TYPE | 4 | 6 | 8 | 8

'OTOP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S134. Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 14 | 9
OTOP1 MUTATED | 1 | 2 | 1
OTOP1 WILD-TYPE | 11 | 12 | 8

'OTOP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S135. Gene #14: 'OTOP1 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
OTOP1 MUTATED | 0 | 1 | 0 | 1 | 0 | 2 | 0
OTOP1 WILD-TYPE | 4 | 4 | 5 | 8 | 5 | 3 | 2

'OTOP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.81 (Fisher's exact test), Q value = 1

Table S136. Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 9 | 5 | 10 | 11
OTOP1 MUTATED | 1 | 0 | 2 | 1
OTOP1 WILD-TYPE | 8 | 5 | 8 | 10

'OTOP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S137. Gene #14: 'OTOP1 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
OTOP1 MUTATED | 1 | 1 | 0 | 0 | 2 | 0
OTOP1 WILD-TYPE | 7 | 9 | 4 | 4 | 3 | 4

'OTOP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S138. Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 15 | 20
OTOP1 MUTATED | 1 | 3
OTOP1 WILD-TYPE | 14 | 17

'OTOP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S139. Gene #14: 'OTOP1 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
OTOP1 MUTATED | 0 | 1 | 1 | 1 | 1 | 0 | 0
OTOP1 WILD-TYPE | 6 | 2 | 2 | 8 | 4 | 5 | 4

'CDC27 MUTATION STATUS' versus 'CN_CNMF'

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

Table S140. Gene #15: '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 = 0.831 (Fisher's exact test), Q value = 1

Table S141. Gene #15: '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 = 1 (Fisher's exact test), Q value = 1

Table S142. Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
CDC27 MUTATED | 2 | 3
CDC27 WILD-TYPE | 9 | 15

'CDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0665 (Fisher's exact test), Q value = 0.74

Table S143. Gene #15: '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 = 0.833 (Fisher's exact test), Q value = 1

Table S144. Gene #15: '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 = 0.427 (Fisher's exact test), Q value = 1

Table S145. Gene #15: '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 = 0.349 (Fisher's exact test), Q value = 1

Table S146. Gene #15: '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 = 0.147 (Fisher's exact test), Q value = 1

Table S147. Gene #15: '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 = 0.27

Table S148. Gene #15: '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 S11. Get High-res Image Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S149. Gene #15: '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 S150. Gene #16: '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 S151. Gene #16: '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 'RPPA_CNMF'

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

Table S152. Gene #16: 'FAM35A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 11 | 18
FAM35A MUTATED | 1 | 1
FAM35A WILD-TYPE | 10 | 17

'FAM35A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S153. Gene #16: '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 = 0.797 (Fisher's exact test), Q value = 1

Table S154. Gene #16: '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 = 0.68 (Fisher's exact test), Q value = 1

Table S155. Gene #16: '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 = 0.692 (Fisher's exact test), Q value = 1

Table S156. Gene #16: '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 S157. Gene #16: '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 = 0.0107 (Fisher's exact test), Q value = 0.27

Table S158. Gene #16: '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 S12. Get High-res Image Gene #16: 'FAM35A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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/15866307/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CHOL-TP/15087707/CHOL-TP.transferedmergedcluster.txt

- Number of patients = 35

- Number of significantly mutated genes = 16

- 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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