Correlation between gene mutation status and molecular subtypes
Uterine Carcinosarcoma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1GT5M92
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/C1GT5M92
Overview
Introduction

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

Summary

Testing the association between mutation status of 13 genes and 10 molecular subtypes across 57 patients, 8 significant findings detected with P value < 0.05 and Q value < 0.25.

- PTEN mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

- CHD4 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 13 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, 8 significant findings 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
PTEN | 11 (19%) | 46 | 0.0935 (0.539) | 6e-05 (0.0078) | 1 (1.00) | 0.0181 (0.262) | 0.00216 (0.14) | 0.0467 (0.506) | 0.0952 (0.539) | 0.0598 (0.539) | 0.00343 (0.149) | 0.0136 (0.241)
KRAS | 7 (12%) | 50 | 0.104 (0.539) | 0.0148 (0.241) | 1 (1.00) | 0.203 (0.645) | 0.033 (0.427) | 0.00677 (0.176) | 0.466 (0.89) | 0.0905 (0.539) | 0.308 (0.79) | 0.0585 (0.539)
CHD4 | 10 (18%) | 47 | 0.346 (0.79) | 0.0102 (0.222) | 0.712 (0.98) | 0.161 (0.62) | 0.184 (0.627) | 0.00525 (0.171) | 0.478 (0.89) | 0.41 (0.82) | 0.0887 (0.539) | 0.217 (0.671)
TP53 | 51 (89%) | 6 | 0.566 (0.953) | 0.629 (0.98) | 0.641 (0.98) | 0.138 (0.618) | 0.878 (1.00) | 0.51 (0.909) | 1 (1.00) | 0.912 (1.00) | 1 (1.00) | 1 (1.00)
FBXW7 | 22 (39%) | 35 | 0.264 (0.762) | 0.724 (0.98) | 0.144 (0.618) | 0.168 (0.624) | 0.632 (0.98) | 0.103 (0.539) | 0.469 (0.89) | 0.931 (1.00) | 1 (1.00) | 0.773 (0.999)
PPP2R1A | 16 (28%) | 41 | 0.762 (0.999) | 0.709 (0.98) | 0.192 (0.627) | 0.501 (0.909) | 0.59 (0.972) | 0.673 (0.98) | 0.568 (0.953) | 0.319 (0.79) | 0.697 (0.98) | 0.234 (0.693)
ZBTB7B | 6 (11%) | 51 | 0.72 (0.98) | 0.939 (1.00) | 0.641 (0.98) | 0.377 (0.79) | 1 (1.00) | 0.914 (1.00) | 0.0963 (0.539) | 0.148 (0.618) | 0.479 (0.89) | 0.162 (0.62)
PIK3R1 | 6 (11%) | 51 | 1 (1.00) | 0.939 (1.00) | 0.383 (0.79) | 0.776 (0.999) | 0.544 (0.953) | 0.706 (0.98) | 0.424 (0.835) | 0.506 (0.909) | 1 (1.00) | 0.307 (0.79)
ARHGAP35 | 6 (11%) | 51 | 0.572 (0.953) | 0.333 (0.79) | 1 (1.00) | 0.343 (0.79) | 1 (1.00) | 0.4 (0.813) | 1 (1.00) | 0.191 (0.627) | 1 (1.00) | 0.176 (0.627)
PIK3CA | 20 (35%) | 37 | 0.638 (0.98) | 0.901 (1.00) | 0.133 (0.618) | 0.295 (0.79) | 0.362 (0.79) | 0.369 (0.79) | 0.112 (0.561) | 0.339 (0.79) | 0.193 (0.627) | 0.27 (0.763)
MAMLD1 | 4 (7%) | 53 | 1 (1.00) | 0.903 (1.00) | 0.121 (0.582) | 0.0362 (0.427) | 0.688 (0.98) | 0.768 (0.999) | 0.0645 (0.539) | 0.678 (0.98) | 0.152 (0.618) | 0.354 (0.79)
RB1 | 6 (11%) | 51 | 0.227 (0.686) | 0.0906 (0.539) | 0.369 (0.79) | 0.313 (0.79) | 0.0787 (0.539) | 0.0981 (0.539) | 0.837 (1.00) | 0.86 (1.00) | 0.866 (1.00) | 1 (1.00)
LYPLA2 | 3 (5%) | 54 | 0.767 (0.999) | 0.617 (0.98) | 1 (1.00) | 0.838 (1.00) | 0.678 (0.98) | 0.348 (0.79) | 0.378 (0.79) | 0.564 (0.953) | 1 (1.00) | 0.693 (0.98)

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 0.95

Table S1. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
TP53 MUTATED | 17 | 19 | 14
TP53 WILD-TYPE | 1 | 2 | 3

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 0.98

Table S2. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
TP53 MUTATED | 12 | 8 | 8 | 12 | 11
TP53 WILD-TYPE | 0 | 1 | 2 | 1 | 2

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 0.98

Table S3. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 27 | 21
TP53 MUTATED | 25 | 18
TP53 WILD-TYPE | 2 | 3

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.62

Table S4. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 9 | 8 | 7 | 7 | 7 | 5 | 5
TP53 MUTATED | 9 | 8 | 7 | 6 | 6 | 4 | 3
TP53 WILD-TYPE | 0 | 0 | 0 | 1 | 1 | 1 | 2

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
TP53 MUTATED | 14 | 18 | 10 | 9
TP53 WILD-TYPE | 1 | 2 | 2 | 1

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.51 (Fisher's exact test), Q value = 0.91

Table S6. Gene #1: '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 | 11 | 4 | 8 | 6 | 8 | 6 | 14
TP53 MUTATED | 11 | 3 | 8 | 5 | 7 | 5 | 12
TP53 WILD-TYPE | 0 | 1 | 0 | 1 | 1 | 1 | 2

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S7. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
TP53 MUTATED | 10 | 20 | 4 | 17
TP53 WILD-TYPE | 1 | 2 | 0 | 2

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S8. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
TP53 MUTATED | 21 | 8 | 16 | 6
TP53 WILD-TYPE | 3 | 0 | 2 | 0

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S9. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
TP53 MUTATED | 12 | 21 | 18
TP53 WILD-TYPE | 1 | 2 | 2

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S10. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
TP53 MUTATED | 22 | 7 | 15 | 7
TP53 WILD-TYPE | 3 | 0 | 2 | 0

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.264 (Fisher's exact test), Q value = 0.76

Table S11. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
FBXW7 MUTATED | 9 | 9 | 4
FBXW7 WILD-TYPE | 9 | 12 | 13

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 0.98

Table S12. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
FBXW7 MUTATED | 6 | 4 | 4 | 3 | 5
FBXW7 WILD-TYPE | 6 | 5 | 6 | 10 | 8

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.62

Table S13. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 27 | 21
FBXW7 MUTATED | 14 | 6
FBXW7 WILD-TYPE | 13 | 15

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 0.62

Table S14. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 9 | 8 | 7 | 7 | 7 | 5 | 5
FBXW7 MUTATED | 4 | 4 | 1 | 3 | 5 | 3 | 0
FBXW7 WILD-TYPE | 5 | 4 | 6 | 4 | 2 | 2 | 5

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 0.98

Table S15. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
FBXW7 MUTATED | 7 | 8 | 5 | 2
FBXW7 WILD-TYPE | 8 | 12 | 7 | 8

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.54

Table S16. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
FBXW7 MUTATED | 4 | 4 | 5 | 2 | 2 | 2 | 3
FBXW7 WILD-TYPE | 7 | 0 | 3 | 4 | 6 | 4 | 11

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 0.89

Table S17. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
FBXW7 MUTATED | 5 | 8 | 3 | 6
FBXW7 WILD-TYPE | 6 | 14 | 1 | 13

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.931 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
FBXW7 MUTATED | 9 | 4 | 7 | 2
FBXW7 WILD-TYPE | 15 | 4 | 11 | 4

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S19. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
FBXW7 MUTATED | 5 | 9 | 8
FBXW7 WILD-TYPE | 8 | 14 | 12

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.773 (Fisher's exact test), Q value = 1

Table S20. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
FBXW7 MUTATED | 9 | 4 | 6 | 3
FBXW7 WILD-TYPE | 16 | 3 | 11 | 4

'PPP2R1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S21. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
PPP2R1A MUTATED | 4 | 7 | 5
PPP2R1A WILD-TYPE | 14 | 14 | 12

'PPP2R1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.709 (Fisher's exact test), Q value = 0.98

Table S22. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
PPP2R1A MUTATED | 4 | 3 | 4 | 3 | 2
PPP2R1A WILD-TYPE | 8 | 6 | 6 | 10 | 11

'PPP2R1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.63

Table S23. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 27 | 21
PPP2R1A MUTATED | 5 | 8
PPP2R1A WILD-TYPE | 22 | 13

'PPP2R1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.501 (Fisher's exact test), Q value = 0.91

Table S24. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 9 | 8 | 7 | 7 | 7 | 5 | 5
PPP2R1A MUTATED | 3 | 1 | 3 | 3 | 1 | 2 | 0
PPP2R1A WILD-TYPE | 6 | 7 | 4 | 4 | 6 | 3 | 5

'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 0.97

Table S25. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
PPP2R1A MUTATED | 6 | 5 | 2 | 3
PPP2R1A WILD-TYPE | 9 | 15 | 10 | 7

'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.673 (Fisher's exact test), Q value = 0.98

Table S26. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
PPP2R1A MUTATED | 4 | 1 | 4 | 1 | 2 | 2 | 2
PPP2R1A WILD-TYPE | 7 | 3 | 4 | 5 | 6 | 4 | 12

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 0.95

Table S27. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
PPP2R1A MUTATED | 5 | 5 | 1 | 5
PPP2R1A WILD-TYPE | 6 | 17 | 3 | 14

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 0.79

Table S28. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
PPP2R1A MUTATED | 8 | 4 | 3 | 1
PPP2R1A WILD-TYPE | 16 | 4 | 15 | 5

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 0.98

Table S29. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
PPP2R1A MUTATED | 5 | 6 | 5
PPP2R1A WILD-TYPE | 8 | 17 | 15

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.234 (Fisher's exact test), Q value = 0.69

Table S30. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
PPP2R1A MUTATED | 8 | 4 | 3 | 1
PPP2R1A WILD-TYPE | 17 | 3 | 14 | 6

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0935 (Fisher's exact test), Q value = 0.54

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
PTEN MUTATED | 1 | 7 | 3
PTEN WILD-TYPE | 17 | 14 | 14

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0078

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
PTEN MUTATED | 0 | 0 | 6 | 5 | 0
PTEN WILD-TYPE | 12 | 9 | 4 | 8 | 13

Figure S1. Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 27 | 21
PTEN MUTATED | 5 | 3
PTEN WILD-TYPE | 22 | 18

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.26

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 9 | 8 | 7 | 7 | 7 | 5 | 5
PTEN MUTATED | 0 | 2 | 0 | 1 | 0 | 3 | 2
PTEN WILD-TYPE | 9 | 6 | 7 | 6 | 7 | 2 | 3

Figure S2. Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.14

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
PTEN MUTATED | 0 | 8 | 0 | 3
PTEN WILD-TYPE | 15 | 12 | 12 | 7

Figure S3. Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0467 (Fisher's exact test), Q value = 0.51

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
PTEN MUTATED | 0 | 0 | 3 | 0 | 3 | 0 | 5
PTEN WILD-TYPE | 11 | 4 | 5 | 6 | 5 | 6 | 9

Figure S4. Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0952 (Fisher's exact test), Q value = 0.54

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
PTEN MUTATED | 2 | 1 | 1 | 6
PTEN WILD-TYPE | 9 | 21 | 3 | 13

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0598 (Fisher's exact test), Q value = 0.54

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
PTEN MUTATED | 8 | 0 | 1 | 1
PTEN WILD-TYPE | 16 | 8 | 17 | 5

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00343 (Fisher's exact test), Q value = 0.15

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
PTEN MUTATED | 3 | 0 | 7
PTEN WILD-TYPE | 10 | 23 | 13

Figure S5. Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.24

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
PTEN MUTATED | 8 | 0 | 0 | 2
PTEN WILD-TYPE | 17 | 7 | 17 | 5

Figure S6. Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 0.54

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
KRAS MUTATED | 2 | 5 | 0
KRAS WILD-TYPE | 16 | 16 | 17

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.24

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
KRAS MUTATED | 0 | 1 | 1 | 0 | 5
KRAS WILD-TYPE | 12 | 8 | 9 | 13 | 8

Figure S7. Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 27 | 21
KRAS MUTATED | 3 | 2
KRAS WILD-TYPE | 24 | 19

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 0.65

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 9 | 8 | 7 | 7 | 7 | 5 | 5
KRAS MUTATED | 0 | 0 | 2 | 1 | 2 | 0 | 0
KRAS WILD-TYPE | 9 | 8 | 5 | 6 | 5 | 5 | 5

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.43

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
KRAS MUTATED | 0 | 3 | 4 | 0
KRAS WILD-TYPE | 15 | 17 | 8 | 10

Figure S8. Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00677 (Fisher's exact test), Q value = 0.18

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
KRAS MUTATED | 0 | 0 | 1 | 0 | 0 | 4 | 2
KRAS WILD-TYPE | 11 | 4 | 7 | 6 | 8 | 2 | 12

Figure S9. Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 0.89

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
KRAS MUTATED | 1 | 4 | 1 | 1
KRAS WILD-TYPE | 10 | 18 | 3 | 18

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0905 (Fisher's exact test), Q value = 0.54

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
KRAS MUTATED | 1 | 0 | 5 | 1
KRAS WILD-TYPE | 23 | 8 | 13 | 5

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.308 (Fisher's exact test), Q value = 0.79

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
KRAS MUTATED | 1 | 5 | 1
KRAS WILD-TYPE | 12 | 18 | 19

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0585 (Fisher's exact test), Q value = 0.54

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
KRAS MUTATED | 1 | 0 | 5 | 1
KRAS WILD-TYPE | 24 | 7 | 12 | 6

'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.72 (Fisher's exact test), Q value = 0.98

Table S51. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
ZBTB7B MUTATED | 2 | 1 | 2
ZBTB7B WILD-TYPE | 16 | 20 | 15

'ZBTB7B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.939 (Fisher's exact test), Q value = 1

Table S52. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
ZBTB7B MUTATED | 2 | 1 | 1 | 1 | 1
ZBTB7B WILD-TYPE | 10 | 8 | 9 | 12 | 12

'ZBTB7B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 0.98

Table S53. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 27 | 21
ZBTB7B MUTATED | 2 | 3
ZBTB7B WILD-TYPE | 25 | 18

'ZBTB7B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 0.79

Table S54. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 9 | 8 | 7 | 7 | 7 | 5 | 5
ZBTB7B MUTATED | 2 | 2 | 0 | 0 | 0 | 0 | 1
ZBTB7B WILD-TYPE | 7 | 6 | 7 | 7 | 7 | 5 | 4

'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S55. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
ZBTB7B MUTATED | 2 | 2 | 1 | 1
ZBTB7B WILD-TYPE | 13 | 18 | 11 | 9

'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S56. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
ZBTB7B MUTATED | 2 | 0 | 0 | 0 | 1 | 1 | 2
ZBTB7B WILD-TYPE | 9 | 4 | 8 | 6 | 7 | 5 | 12

'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0963 (Fisher's exact test), Q value = 0.54

Table S57. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
ZBTB7B MUTATED | 1 | 1 | 2 | 2
ZBTB7B WILD-TYPE | 10 | 21 | 2 | 17

'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.62

Table S58. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
ZBTB7B MUTATED | 5 | 1 | 0 | 0
ZBTB7B WILD-TYPE | 19 | 7 | 18 | 6

'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 0.89

Table S59. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
ZBTB7B MUTATED | 2 | 1 | 3
ZBTB7B WILD-TYPE | 11 | 22 | 17

'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 0.62

Table S60. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
ZBTB7B MUTATED | 5 | 1 | 0 | 0
ZBTB7B WILD-TYPE | 20 | 6 | 17 | 7

'CHD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.79

Table S61. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
CHD4 MUTATED | 2 | 6 | 2
CHD4 WILD-TYPE | 16 | 15 | 15

'CHD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.22

Table S62. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
CHD4 MUTATED | 0 | 4 | 4 | 1 | 1
CHD4 WILD-TYPE | 12 | 5 | 6 | 12 | 12

Figure S10. Get High-res Image Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CHD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.712 (Fisher's exact test), Q value = 0.98

Table S63. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 27 | 21
CHD4 MUTATED | 6 | 3
CHD4 WILD-TYPE | 21 | 18

'CHD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.62

Table S64. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 9 | 8 | 7 | 7 | 7 | 5 | 5
CHD4 MUTATED | 0 | 2 | 0 | 3 | 1 | 2 | 1
CHD4 WILD-TYPE | 9 | 6 | 7 | 4 | 6 | 3 | 4

'CHD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.63

Table S65. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
CHD4 MUTATED | 2 | 5 | 0 | 3
CHD4 WILD-TYPE | 13 | 15 | 12 | 7

'CHD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00525 (Fisher's exact test), Q value = 0.17

Table S66. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
CHD4 MUTATED | 0 | 2 | 4 | 0 | 3 | 0 | 1
CHD4 WILD-TYPE | 11 | 2 | 4 | 6 | 5 | 6 | 13

Figure S11. Get High-res Image Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CHD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 0.89

Table S67. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
CHD4 MUTATED | 3 | 2 | 1 | 3
CHD4 WILD-TYPE | 8 | 20 | 3 | 16

'CHD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.41 (Fisher's exact test), Q value = 0.82

Table S68. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
CHD4 MUTATED | 6 | 0 | 2 | 1
CHD4 WILD-TYPE | 18 | 8 | 16 | 5

'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0887 (Fisher's exact test), Q value = 0.54

Table S69. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
CHD4 MUTATED | 4 | 1 | 4
CHD4 WILD-TYPE | 9 | 22 | 16

'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.217 (Fisher's exact test), Q value = 0.67

Table S70. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
CHD4 MUTATED | 6 | 0 | 1 | 2
CHD4 WILD-TYPE | 19 | 7 | 16 | 5

'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S71. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
PIK3R1 MUTATED | 2 | 2 | 2
PIK3R1 WILD-TYPE | 16 | 19 | 15

'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.939 (Fisher's exact test), Q value = 1

Table S72. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
PIK3R1 MUTATED | 2 | 1 | 1 | 1 | 1
PIK3R1 WILD-TYPE | 10 | 8 | 9 | 12 | 12

'PIK3R1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.383 (Fisher's exact test), Q value = 0.79

Table S73. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 27 | 21
PIK3R1 MUTATED | 2 | 4
PIK3R1 WILD-TYPE | 25 | 17

'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.776 (Fisher's exact test), Q value = 1

Table S74. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 9 | 8 | 7 | 7 | 7 | 5 | 5
PIK3R1 MUTATED | 2 | 2 | 0 | 1 | 1 | 0 | 0
PIK3R1 WILD-TYPE | 7 | 6 | 7 | 6 | 6 | 5 | 5

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 0.95

Table S75. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
PIK3R1 MUTATED | 3 | 2 | 1 | 0
PIK3R1 WILD-TYPE | 12 | 18 | 11 | 10

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.706 (Fisher's exact test), Q value = 0.98

Table S76. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
PIK3R1 MUTATED | 2 | 1 | 1 | 0 | 0 | 1 | 1
PIK3R1 WILD-TYPE | 9 | 3 | 7 | 6 | 8 | 5 | 13

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.84

Table S77. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
PIK3R1 MUTATED | 2 | 2 | 1 | 1
PIK3R1 WILD-TYPE | 9 | 20 | 3 | 18

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.506 (Fisher's exact test), Q value = 0.91

Table S78. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
PIK3R1 MUTATED | 2 | 2 | 2 | 0
PIK3R1 WILD-TYPE | 22 | 6 | 16 | 6

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S79. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
PIK3R1 MUTATED | 1 | 3 | 2
PIK3R1 WILD-TYPE | 12 | 20 | 18

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 0.79

Table S80. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
PIK3R1 MUTATED | 2 | 2 | 1 | 1
PIK3R1 WILD-TYPE | 23 | 5 | 16 | 6

'ARHGAP35 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 0.95

Table S81. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
ARHGAP35 MUTATED | 1 | 2 | 3
ARHGAP35 WILD-TYPE | 17 | 19 | 14

'ARHGAP35 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 0.79

Table S82. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
ARHGAP35 MUTATED | 2 | 0 | 2 | 0 | 2
ARHGAP35 WILD-TYPE | 10 | 9 | 8 | 13 | 11

'ARHGAP35 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S83. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 27 | 21
ARHGAP35 MUTATED | 3 | 3
ARHGAP35 WILD-TYPE | 24 | 18

'ARHGAP35 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.343 (Fisher's exact test), Q value = 0.79

Table S84. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 9 | 8 | 7 | 7 | 7 | 5 | 5
ARHGAP35 MUTATED | 2 | 0 | 0 | 0 | 2 | 1 | 1
ARHGAP35 WILD-TYPE | 7 | 8 | 7 | 7 | 5 | 4 | 4

'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S85. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
ARHGAP35 MUTATED | 2 | 2 | 1 | 1
ARHGAP35 WILD-TYPE | 13 | 18 | 11 | 9

'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 0.81

Table S86. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
ARHGAP35 MUTATED | 2 | 0 | 2 | 0 | 1 | 1 | 0
ARHGAP35 WILD-TYPE | 9 | 4 | 6 | 6 | 7 | 5 | 14

'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S87. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
ARHGAP35 MUTATED | 1 | 2 | 0 | 2
ARHGAP35 WILD-TYPE | 10 | 20 | 4 | 17

'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.63

Table S88. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
ARHGAP35 MUTATED | 1 | 2 | 1 | 1
ARHGAP35 WILD-TYPE | 23 | 6 | 17 | 5

'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S89. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
ARHGAP35 MUTATED | 1 | 2 | 2
ARHGAP35 WILD-TYPE | 12 | 21 | 18

'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.176 (Fisher's exact test), Q value = 0.63

Table S90. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
ARHGAP35 MUTATED | 1 | 2 | 1 | 1
ARHGAP35 WILD-TYPE | 24 | 5 | 16 | 6

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.638 (Fisher's exact test), Q value = 0.98

Table S91. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
PIK3CA MUTATED | 5 | 9 | 5
PIK3CA WILD-TYPE | 13 | 12 | 12

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.901 (Fisher's exact test), Q value = 1

Table S92. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
PIK3CA MUTATED | 4 | 3 | 5 | 4 | 4
PIK3CA WILD-TYPE | 8 | 6 | 5 | 9 | 9

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.62

Table S93. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 27 | 21
PIK3CA MUTATED | 13 | 5
PIK3CA WILD-TYPE | 14 | 16

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 0.79

Table S94. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 9 | 8 | 7 | 7 | 7 | 5 | 5
PIK3CA MUTATED | 2 | 3 | 2 | 1 | 3 | 4 | 3
PIK3CA WILD-TYPE | 7 | 5 | 5 | 6 | 4 | 1 | 2

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.362 (Fisher's exact test), Q value = 0.79

Table S95. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
PIK3CA MUTATED | 5 | 10 | 3 | 2
PIK3CA WILD-TYPE | 10 | 10 | 9 | 8

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 0.79

Table S96. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
PIK3CA MUTATED | 3 | 3 | 4 | 2 | 1 | 1 | 6
PIK3CA WILD-TYPE | 8 | 1 | 4 | 4 | 7 | 5 | 8

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.56

Table S97. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
PIK3CA MUTATED | 4 | 4 | 2 | 10
PIK3CA WILD-TYPE | 7 | 18 | 2 | 9

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.339 (Fisher's exact test), Q value = 0.79

Table S98. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
PIK3CA MUTATED | 11 | 2 | 4 | 3
PIK3CA WILD-TYPE | 13 | 6 | 14 | 3

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.193 (Fisher's exact test), Q value = 0.63

Table S99. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
PIK3CA MUTATED | 6 | 5 | 9
PIK3CA WILD-TYPE | 7 | 18 | 11

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.27 (Fisher's exact test), Q value = 0.76

Table S100. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
PIK3CA MUTATED | 12 | 1 | 4 | 3
PIK3CA WILD-TYPE | 13 | 6 | 13 | 4

'MAMLD1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S101. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
MAMLD1 MUTATED | 1 | 2 | 1
MAMLD1 WILD-TYPE | 17 | 19 | 16

'MAMLD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S102. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
MAMLD1 MUTATED | 0 | 1 | 1 | 1 | 1
MAMLD1 WILD-TYPE | 12 | 8 | 9 | 12 | 12

'MAMLD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.58

Table S103. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 27 | 21
MAMLD1 MUTATED | 4 | 0
MAMLD1 WILD-TYPE | 23 | 21

'MAMLD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.43

Table S104. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 9 | 8 | 7 | 7 | 7 | 5 | 5
MAMLD1 MUTATED | 0 | 2 | 0 | 0 | 0 | 2 | 0
MAMLD1 WILD-TYPE | 9 | 6 | 7 | 7 | 7 | 3 | 5

Figure S12. Get High-res Image Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.98

Table S105. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
MAMLD1 MUTATED | 0 | 2 | 1 | 1
MAMLD1 WILD-TYPE | 15 | 18 | 11 | 9

'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S106. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
MAMLD1 MUTATED | 0 | 0 | 1 | 1 | 1 | 0 | 1
MAMLD1 WILD-TYPE | 11 | 4 | 7 | 5 | 7 | 6 | 13

'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0645 (Fisher's exact test), Q value = 0.54

Table S107. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
MAMLD1 MUTATED | 0 | 0 | 1 | 3
MAMLD1 WILD-TYPE | 11 | 22 | 3 | 16

'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.678 (Fisher's exact test), Q value = 0.98

Table S108. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
MAMLD1 MUTATED | 2 | 0 | 1 | 1
MAMLD1 WILD-TYPE | 22 | 8 | 17 | 5

'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 0.62

Table S109. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
MAMLD1 MUTATED | 2 | 0 | 2
MAMLD1 WILD-TYPE | 11 | 23 | 18

'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.79

Table S110. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
MAMLD1 MUTATED | 3 | 0 | 0 | 1
MAMLD1 WILD-TYPE | 22 | 7 | 17 | 6

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 0.69

Table S111. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
RB1 MUTATED | 2 | 4 | 0
RB1 WILD-TYPE | 16 | 17 | 17

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0906 (Fisher's exact test), Q value = 0.54

Table S112. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
RB1 MUTATED | 0 | 1 | 3 | 2 | 0
RB1 WILD-TYPE | 12 | 8 | 7 | 11 | 13

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.369 (Fisher's exact test), Q value = 0.79

Table S113. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 27 | 21
RB1 MUTATED | 4 | 1
RB1 WILD-TYPE | 23 | 20

'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 0.79

Table S114. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 9 | 8 | 7 | 7 | 7 | 5 | 5
RB1 MUTATED | 0 | 1 | 0 | 2 | 0 | 1 | 1
RB1 WILD-TYPE | 9 | 7 | 7 | 5 | 7 | 4 | 4

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0787 (Fisher's exact test), Q value = 0.54

Table S115. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
RB1 MUTATED | 0 | 4 | 0 | 2
RB1 WILD-TYPE | 15 | 16 | 12 | 8

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0981 (Fisher's exact test), Q value = 0.54

Table S116. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
RB1 MUTATED | 0 | 0 | 2 | 0 | 3 | 0 | 1
RB1 WILD-TYPE | 11 | 4 | 6 | 6 | 5 | 6 | 13

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S117. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
RB1 MUTATED | 2 | 2 | 0 | 2
RB1 WILD-TYPE | 9 | 20 | 4 | 17

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S118. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
RB1 MUTATED | 3 | 0 | 2 | 1
RB1 WILD-TYPE | 21 | 8 | 16 | 5

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.866 (Fisher's exact test), Q value = 1

Table S119. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
RB1 MUTATED | 2 | 2 | 2
RB1 WILD-TYPE | 11 | 21 | 18

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S120. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
RB1 MUTATED | 3 | 0 | 2 | 1
RB1 WILD-TYPE | 22 | 7 | 15 | 6

'LYPLA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.767 (Fisher's exact test), Q value = 1

Table S121. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
LYPLA2 MUTATED | 1 | 2 | 0
LYPLA2 WILD-TYPE | 17 | 19 | 17

'LYPLA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.617 (Fisher's exact test), Q value = 0.98

Table S122. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
LYPLA2 MUTATED | 0 | 1 | 1 | 0 | 1
LYPLA2 WILD-TYPE | 12 | 8 | 9 | 13 | 12

'LYPLA2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S123. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 27 | 21
LYPLA2 MUTATED | 2 | 1
LYPLA2 WILD-TYPE | 25 | 20

'LYPLA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S124. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 9 | 8 | 7 | 7 | 7 | 5 | 5
LYPLA2 MUTATED | 0 | 1 | 1 | 1 | 0 | 0 | 0
LYPLA2 WILD-TYPE | 9 | 7 | 6 | 6 | 7 | 5 | 5

'LYPLA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.678 (Fisher's exact test), Q value = 0.98

Table S125. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
LYPLA2 MUTATED | 0 | 1 | 1 | 1
LYPLA2 WILD-TYPE | 15 | 19 | 11 | 9

'LYPLA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.348 (Fisher's exact test), Q value = 0.79

Table S126. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
LYPLA2 MUTATED | 0 | 0 | 1 | 0 | 1 | 1 | 0
LYPLA2 WILD-TYPE | 11 | 4 | 7 | 6 | 7 | 5 | 14

'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.79

Table S127. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
LYPLA2 MUTATED | 0 | 1 | 1 | 1
LYPLA2 WILD-TYPE | 11 | 21 | 3 | 18

'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 0.95

Table S128. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
LYPLA2 MUTATED | 1 | 0 | 1 | 1
LYPLA2 WILD-TYPE | 23 | 8 | 17 | 5

'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S129. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
LYPLA2 MUTATED | 1 | 1 | 1
LYPLA2 WILD-TYPE | 12 | 22 | 19

'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 0.98

Table S130. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
LYPLA2 MUTATED | 1 | 0 | 1 | 1
LYPLA2 WILD-TYPE | 24 | 7 | 16 | 6

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/UCS-TP/15165005/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCS-TP/15115115/UCS-TP.transferedmergedcluster.txt

- Number of patients = 57

- Number of significantly mutated genes = 13

- 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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