Correlation between gene mutation status and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1QC02JC
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/C1QC02JC
Overview
Introduction

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

Summary

Testing the association between mutation status of 25 genes and 6 molecular subtypes across 195 patients, 39 significant findings detected with P value < 0.05 and Q value < 0.25.

- FLT3 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- NPM1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- DNMT3A mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- IDH2 mutation correlated to 'METHLYATION_CNMF'.

- IDH1 mutation correlated to 'METHLYATION_CNMF'.

- RUNX1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- WT1 mutation correlated to 'METHLYATION_CNMF'.

- U2AF1 mutation correlated to 'METHLYATION_CNMF'.

- TP53 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- CEBPA mutation correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

- STAG2 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

- PTPN11 mutation correlated to 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 25 genes and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 39 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL
| nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
FLT3 | 53 (27%) | 142 | 0.00026 (0.00244) | 0.00016 (0.00171) | 1e-05 (0.000167) | 0.00011 (0.0015) | 0.00043 (0.00379) | 0.00078 (0.00585)
NPM1 | 52 (27%) | 143 | 1e-05 (0.000167) | 1e-05 (0.000167) | 1e-05 (0.000167) | 1e-05 (0.000167) | 1e-05 (0.000167) | 1e-05 (0.000167)
TP53 | 15 (8%) | 180 | 1e-05 (0.000167) | 1e-05 (0.000167) | 0.0009 (0.00627) | 0.0024 (0.0144) | 0.00018 (0.0018) | 0.00012 (0.0015)
DNMT3A | 49 (25%) | 146 | 0.854 (0.949) | 0.0305 (0.127) | 0.0242 (0.107) | 0.00249 (0.0144) | 0.00235 (0.0144) | 0.00263 (0.0146)
RUNX1 | 18 (9%) | 177 | 0.36 (0.629) | 0.0005 (0.00417) | 0.00205 (0.0134) | 5e-05 (0.00075) | 0.00055 (0.00434) | 0.00092 (0.00627)
CEBPA | 13 (7%) | 182 | 0.59 (0.798) | 0.434 (0.693) | 0.198 (0.488) | 0.00013 (0.0015) | 0.0345 (0.14) | 0.00969 (0.0469)
KIT | 8 (4%) | 187 | 0.103 (0.315) | 0.0136 (0.0638) | 0.327 (0.613) | 0.00593 (0.0296) | 0.357 (0.629) | 0.189 (0.488)
IDH2 | 20 (10%) | 175 | 0.0995 (0.315) | 0.0164 (0.0745) | 0.686 (0.839) | 0.342 (0.629) | 0.748 (0.877) | 0.185 (0.488)
IDH1 | 18 (9%) | 177 | 1 (1.00) | 0.00585 (0.0296) | 0.256 (0.52) | 0.256 (0.52) | 0.235 (0.52) | 0.803 (0.913)
WT1 | 12 (6%) | 183 | 0.421 (0.679) | 0.0046 (0.0246) | 0.0825 (0.275) | 0.365 (0.629) | 0.0678 (0.248) | 0.275 (0.543)
U2AF1 | 8 (4%) | 187 | 1 (1.00) | 0.0481 (0.185) | 0.23 (0.52) | 0.259 (0.52) | 0.0756 (0.263) | 0.469 (0.713)
STAG2 | 6 (3%) | 189 | 0.562 (0.798) | 0.198 (0.488) | 0.132 (0.395) | 0.0278 (0.119) | 0.688 (0.839) | 0.0649 (0.243)
PTPN11 | 9 (5%) | 186 | 0.682 (0.839) | 0.46 (0.711) | 0.0474 (0.185) | 0.504 (0.741) | 0.0996 (0.315) | 0.208 (0.496)
TET2 | 17 (9%) | 178 | 0.354 (0.629) | 0.44 (0.693) | 0.29 (0.558) | 0.572 (0.798) | 0.66 (0.839) | 0.845 (0.946)
NRAS | 15 (8%) | 180 | 0.421 (0.679) | 0.949 (1.00) | 0.601 (0.798) | 0.938 (1.00) | 0.813 (0.917) | 0.668 (0.839)
PHF6 | 6 (3%) | 189 | 1 (1.00) | 0.632 (0.825) | 0.732 (0.871) | 0.473 (0.713) | 0.726 (0.871) | 0.344 (0.629)
KRAS | 8 (4%) | 187 | 0.074 (0.263) | 0.725 (0.871) | 0.324 (0.613) | 0.65 (0.839) | 0.255 (0.52) | 0.682 (0.839)
SMC3 | 7 (4%) | 188 | 1 (1.00) | 0.205 (0.495) | 0.552 (0.796) | 0.444 (0.693) | 0.218 (0.503) | 0.416 (0.679)
RAD21 | 5 (3%) | 190 | 0.48 (0.713) | 0.365 (0.629) | 0.606 (0.798) | 0.187 (0.488) | 0.213 (0.499) | 0.606 (0.798)
EZH2 | 3 (2%) | 192 | 0.103 (0.315) |  | 0.258 (0.52) | 0.589 (0.798) | 0.158 (0.439) | 0.418 (0.679)
ASXL1 | 5 (3%) | 190 | 0.737 (0.871) | 0.0773 (0.263) | 0.259 (0.52) | 0.592 (0.798) | 0.158 (0.439) | 0.416 (0.679)
SUZ12 | 3 (2%) | 192 | 0.288 (0.558) | 0.788 (0.902) | 0.26 (0.52) | 0.592 (0.798) | 0.198 (0.488) | 0.14 (0.403)
PHACTR1 | 3 (2%) | 192 |  | 1 (1.00) |  |  | 0.891 (0.975) | 0.416 (0.679)
SMC1A | 6 (3%) | 189 | 0.763 (0.888) | 0.134 (0.396) | 0.573 (0.798) | 0.246 (0.52) | 0.174 (0.475) | 0.661 (0.839)
KDM6A | 3 (2%) | 192 | 0.547 (0.796) | 0.475 (0.713) |  |  | 0.89 (0.975) | 0.783 (0.902)

'FLT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0024

Table S1. Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
FLT3 MUTATED | 48 | 3 | 0 | 0
FLT3 WILD-TYPE | 95 | 11 | 27 | 2

Figure S1. Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FLT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0017

Table S2. Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
FLT3 MUTATED | 9 | 7 | 13 | 23
FLT3 WILD-TYPE | 24 | 56 | 35 | 22

Figure S2. Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FLT3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S3. Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
FLT3 MUTATED | 6 | 17 | 23
FLT3 WILD-TYPE | 67 | 33 | 22

Figure S3. Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'FLT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0015

Table S4. Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
FLT3 MUTATED | 5 | 2 | 2 | 6 | 14 | 17
FLT3 WILD-TYPE | 11 | 11 | 13 | 51 | 12 | 24

Figure S4. Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0038

Table S5. Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
FLT3 MUTATED | 23 | 4 | 6 | 18
FLT3 WILD-TYPE | 34 | 34 | 36 | 28

Figure S5. Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0058

Table S6. Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
FLT3 MUTATED | 30 | 5 | 16
FLT3 WILD-TYPE | 37 | 30 | 65

Figure S6. Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NPM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S7. Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
NPM1 MUTATED | 50 | 0 | 0 | 0
NPM1 WILD-TYPE | 93 | 14 | 27 | 2

Figure S7. Get High-res Image Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NPM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S8. Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
NPM1 MUTATED | 8 | 4 | 13 | 26
NPM1 WILD-TYPE | 25 | 59 | 35 | 19

Figure S8. Get High-res Image Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NPM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S9. Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
NPM1 MUTATED | 1 | 20 | 25
NPM1 WILD-TYPE | 72 | 30 | 20

Figure S9. Get High-res Image Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'NPM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S10. Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
NPM1 MUTATED | 0 | 0 | 0 | 1 | 23 | 22
NPM1 WILD-TYPE | 16 | 13 | 15 | 56 | 3 | 19

Figure S10. Get High-res Image Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S11. Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
NPM1 MUTATED | 35 | 2 | 1 | 12
NPM1 WILD-TYPE | 22 | 36 | 41 | 34

Figure S11. Get High-res Image Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S12. Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
NPM1 MUTATED | 48 | 1 | 1
NPM1 WILD-TYPE | 19 | 34 | 80

Figure S12. Get High-res Image Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 0.95

Table S13. Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
DNMT3A MUTATED | 36 | 4 | 5 | 0
DNMT3A WILD-TYPE | 107 | 10 | 22 | 2

'DNMT3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.13

Table S14. Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
DNMT3A MUTATED | 5 | 16 | 19 | 7
DNMT3A WILD-TYPE | 28 | 47 | 29 | 38

Figure S13. Get High-res Image Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.11

Table S15. Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
DNMT3A MUTATED | 11 | 18 | 12
DNMT3A WILD-TYPE | 62 | 32 | 33

Figure S14. Get High-res Image Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00249 (Fisher's exact test), Q value = 0.014

Table S16. Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
DNMT3A MUTATED | 0 | 3 | 0 | 14 | 11 | 13
DNMT3A WILD-TYPE | 16 | 10 | 15 | 43 | 15 | 28

Figure S15. Get High-res Image Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00235 (Fisher's exact test), Q value = 0.014

Table S17. Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
DNMT3A MUTATED | 22 | 4 | 5 | 13
DNMT3A WILD-TYPE | 35 | 34 | 37 | 33

Figure S16. Get High-res Image Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00263 (Fisher's exact test), Q value = 0.015

Table S18. Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
DNMT3A MUTATED | 25 | 3 | 16
DNMT3A WILD-TYPE | 42 | 32 | 65

Figure S17. Get High-res Image Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0995 (Fisher's exact test), Q value = 0.32

Table S19. Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
IDH2 MUTATED | 14 | 4 | 1 | 0
IDH2 WILD-TYPE | 129 | 10 | 26 | 2

'IDH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.074

Table S20. Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
IDH2 MUTATED | 0 | 11 | 2 | 5
IDH2 WILD-TYPE | 33 | 52 | 46 | 40

Figure S18. Get High-res Image Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.84

Table S21. Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
IDH2 MUTATED | 8 | 6 | 3
IDH2 WILD-TYPE | 65 | 44 | 42

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.342 (Fisher's exact test), Q value = 0.63

Table S22. Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
IDH2 MUTATED | 0 | 2 | 0 | 9 | 2 | 4
IDH2 WILD-TYPE | 16 | 11 | 15 | 48 | 24 | 37

'IDH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.748 (Fisher's exact test), Q value = 0.88

Table S23. Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
IDH2 MUTATED | 5 | 2 | 5 | 5
IDH2 WILD-TYPE | 52 | 36 | 37 | 41

'IDH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.49

Table S24. Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
IDH2 MUTATED | 5 | 1 | 11
IDH2 WILD-TYPE | 62 | 34 | 70

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S25. Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
IDH1 MUTATED | 14 | 1 | 2 | 0
IDH1 WILD-TYPE | 129 | 13 | 25 | 2

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00585 (Fisher's exact test), Q value = 0.03

Table S26. Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
IDH1 MUTATED | 6 | 10 | 1 | 1
IDH1 WILD-TYPE | 27 | 53 | 47 | 44

Figure S19. Get High-res Image Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 0.52

Table S27. Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
IDH1 MUTATED | 7 | 2 | 6
IDH1 WILD-TYPE | 66 | 48 | 39

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.256 (Fisher's exact test), Q value = 0.52

Table S28. Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
IDH1 MUTATED | 0 | 0 | 0 | 8 | 4 | 3
IDH1 WILD-TYPE | 16 | 13 | 15 | 49 | 22 | 38

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 0.52

Table S29. Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
IDH1 MUTATED | 4 | 4 | 2 | 8
IDH1 WILD-TYPE | 53 | 34 | 40 | 38

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.803 (Fisher's exact test), Q value = 0.91

Table S30. Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
IDH1 MUTATED | 8 | 3 | 7
IDH1 WILD-TYPE | 59 | 32 | 74

'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.36 (Fisher's exact test), Q value = 0.63

Table S31. Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
RUNX1 MUTATED | 12 | 3 | 3 | 0
RUNX1 WILD-TYPE | 131 | 11 | 24 | 2

'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0042

Table S32. Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
RUNX1 MUTATED | 0 | 13 | 2 | 1
RUNX1 WILD-TYPE | 33 | 50 | 46 | 44

Figure S20. Get High-res Image Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.013

Table S33. Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
RUNX1 MUTATED | 13 | 3 | 0
RUNX1 WILD-TYPE | 60 | 47 | 45

Figure S21. Get High-res Image Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00075

Table S34. Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
RUNX1 MUTATED | 0 | 1 | 0 | 15 | 0 | 0
RUNX1 WILD-TYPE | 16 | 12 | 15 | 42 | 26 | 41

Figure S22. Get High-res Image Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0043

Table S35. Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
RUNX1 MUTATED | 1 | 4 | 10 | 1
RUNX1 WILD-TYPE | 56 | 34 | 32 | 45

Figure S23. Get High-res Image Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0063

Table S36. Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
RUNX1 MUTATED | 0 | 4 | 12
RUNX1 WILD-TYPE | 67 | 31 | 69

Figure S24. Get High-res Image Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'TET2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 0.63

Table S37. Gene #7: 'TET2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
TET2 MUTATED | 11 | 3 | 2 | 0
TET2 WILD-TYPE | 132 | 11 | 25 | 2

'TET2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.69

Table S38. Gene #7: 'TET2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
TET2 MUTATED | 2 | 8 | 2 | 4
TET2 WILD-TYPE | 31 | 55 | 46 | 41

'TET2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.29 (Fisher's exact test), Q value = 0.56

Table S39. Gene #7: 'TET2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
TET2 MUTATED | 9 | 2 | 4
TET2 WILD-TYPE | 64 | 48 | 41

'TET2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 0.8

Table S40. Gene #7: 'TET2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
TET2 MUTATED | 0 | 0 | 2 | 7 | 3 | 3
TET2 WILD-TYPE | 16 | 13 | 13 | 50 | 23 | 38

'TET2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.66 (Fisher's exact test), Q value = 0.84

Table S41. Gene #7: 'TET2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
TET2 MUTATED | 6 | 2 | 3 | 6
TET2 WILD-TYPE | 51 | 36 | 39 | 40

'TET2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.845 (Fisher's exact test), Q value = 0.95

Table S42. Gene #7: 'TET2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
TET2 MUTATED | 7 | 2 | 8
TET2 WILD-TYPE | 60 | 33 | 73

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.68

Table S43. Gene #8: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
NRAS MUTATED | 10 | 1 | 4 | 0
NRAS WILD-TYPE | 133 | 13 | 23 | 2

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.949 (Fisher's exact test), Q value = 1

Table S44. Gene #8: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
NRAS MUTATED | 3 | 5 | 3 | 4
NRAS WILD-TYPE | 30 | 58 | 45 | 41

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.601 (Fisher's exact test), Q value = 0.8

Table S45. Gene #8: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
NRAS MUTATED | 5 | 5 | 2
NRAS WILD-TYPE | 68 | 45 | 43

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.938 (Fisher's exact test), Q value = 1

Table S46. Gene #8: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
NRAS MUTATED | 0 | 1 | 1 | 4 | 2 | 4
NRAS WILD-TYPE | 16 | 12 | 14 | 53 | 24 | 37

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.813 (Fisher's exact test), Q value = 0.92

Table S47. Gene #8: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
NRAS MUTATED | 5 | 3 | 4 | 2
NRAS WILD-TYPE | 52 | 35 | 38 | 44

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.668 (Fisher's exact test), Q value = 0.84

Table S48. Gene #8: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
NRAS MUTATED | 7 | 2 | 5
NRAS WILD-TYPE | 60 | 33 | 76

'WT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.68

Table S49. Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
WT1 MUTATED | 11 | 1 | 0 | 0
WT1 WILD-TYPE | 132 | 13 | 27 | 2

'WT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0046 (Fisher's exact test), Q value = 0.025

Table S50. Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
WT1 MUTATED | 1 | 0 | 3 | 7
WT1 WILD-TYPE | 32 | 63 | 45 | 38

Figure S25. Get High-res Image Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'WT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0825 (Fisher's exact test), Q value = 0.28

Table S51. Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
WT1 MUTATED | 2 | 2 | 6
WT1 WILD-TYPE | 71 | 48 | 39

'WT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.365 (Fisher's exact test), Q value = 0.63

Table S52. Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
WT1 MUTATED | 0 | 1 | 0 | 3 | 4 | 2
WT1 WILD-TYPE | 16 | 12 | 15 | 54 | 22 | 39

'WT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0678 (Fisher's exact test), Q value = 0.25

Table S53. Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
WT1 MUTATED | 2 | 0 | 3 | 6
WT1 WILD-TYPE | 55 | 38 | 39 | 40

'WT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.54

Table S54. Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
WT1 MUTATED | 5 | 0 | 6
WT1 WILD-TYPE | 62 | 35 | 75

'U2AF1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S55. Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
U2AF1 MUTATED | 5 | 0 | 1 | 0
U2AF1 WILD-TYPE | 138 | 14 | 26 | 2

'U2AF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.18

Table S56. Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
U2AF1 MUTATED | 0 | 6 | 2 | 0
U2AF1 WILD-TYPE | 33 | 57 | 46 | 45

Figure S26. Get High-res Image Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.52

Table S57. Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
U2AF1 MUTATED | 5 | 2 | 0
U2AF1 WILD-TYPE | 68 | 48 | 45

'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.259 (Fisher's exact test), Q value = 0.52

Table S58. Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
U2AF1 MUTATED | 0 | 0 | 0 | 6 | 0 | 1
U2AF1 WILD-TYPE | 16 | 13 | 15 | 51 | 26 | 40

'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0756 (Fisher's exact test), Q value = 0.26

Table S59. Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
U2AF1 MUTATED | 1 | 2 | 4 | 0
U2AF1 WILD-TYPE | 56 | 36 | 38 | 46

'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 0.71

Table S60. Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
U2AF1 MUTATED | 1 | 2 | 4
U2AF1 WILD-TYPE | 66 | 33 | 77

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S61. Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
TP53 MUTATED | 0 | 2 | 13 | 0
TP53 WILD-TYPE | 143 | 12 | 14 | 2

Figure S27. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S62. Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
TP53 MUTATED | 0 | 15 | 0 | 0
TP53 WILD-TYPE | 33 | 48 | 48 | 45

Figure S28. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0063

Table S63. Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
TP53 MUTATED | 12 | 1 | 0
TP53 WILD-TYPE | 61 | 49 | 45

Figure S29. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0024 (Fisher's exact test), Q value = 0.014

Table S64. Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
TP53 MUTATED | 0 | 0 | 0 | 12 | 0 | 1
TP53 WILD-TYPE | 16 | 13 | 15 | 45 | 26 | 40

Figure S30. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0018

Table S65. Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
TP53 MUTATED | 0 | 9 | 3 | 2
TP53 WILD-TYPE | 57 | 29 | 39 | 44

Figure S31. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0015

Table S66. Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
TP53 MUTATED | 0 | 8 | 6
TP53 WILD-TYPE | 67 | 27 | 75

Figure S32. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CEBPA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 0.8

Table S67. Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
CEBPA MUTATED | 9 | 0 | 3 | 0
CEBPA WILD-TYPE | 134 | 14 | 24 | 2

'CEBPA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.69

Table S68. Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
CEBPA MUTATED | 2 | 2 | 5 | 4
CEBPA WILD-TYPE | 31 | 61 | 43 | 41

'CEBPA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.49

Table S69. Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
CEBPA MUTATED | 9 | 2 | 2
CEBPA WILD-TYPE | 64 | 48 | 43

'CEBPA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0015

Table S70. Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
CEBPA MUTATED | 0 | 0 | 7 | 4 | 1 | 1
CEBPA WILD-TYPE | 16 | 13 | 8 | 53 | 25 | 40

Figure S33. Get High-res Image Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.14

Table S71. Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
CEBPA MUTATED | 1 | 1 | 4 | 7
CEBPA WILD-TYPE | 56 | 37 | 38 | 39

Figure S34. Get High-res Image Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00969 (Fisher's exact test), Q value = 0.047

Table S72. Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
CEBPA MUTATED | 2 | 0 | 11
CEBPA WILD-TYPE | 65 | 35 | 70

Figure S35. Get High-res Image Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'PHF6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S73. Gene #13: 'PHF6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
PHF6 MUTATED | 5 | 0 | 1 | 0
PHF6 WILD-TYPE | 138 | 14 | 26 | 2

'PHF6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 0.82

Table S74. Gene #13: 'PHF6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
PHF6 MUTATED | 1 | 1 | 3 | 1
PHF6 WILD-TYPE | 32 | 62 | 45 | 44

'PHF6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.732 (Fisher's exact test), Q value = 0.87

Table S75. Gene #13: 'PHF6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
PHF6 MUTATED | 2 | 1 | 2
PHF6 WILD-TYPE | 71 | 49 | 43

'PHF6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 0.71

Table S76. Gene #13: 'PHF6 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
PHF6 MUTATED | 0 | 0 | 0 | 4 | 1 | 0
PHF6 WILD-TYPE | 16 | 13 | 15 | 53 | 25 | 41

'PHF6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 0.87

Table S77. Gene #13: 'PHF6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
PHF6 MUTATED | 2 | 0 | 2 | 1
PHF6 WILD-TYPE | 55 | 38 | 40 | 45

'PHF6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.63

Table S78. Gene #13: 'PHF6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
PHF6 MUTATED | 1 | 0 | 4
PHF6 WILD-TYPE | 66 | 35 | 77

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.074 (Fisher's exact test), Q value = 0.26

Table S79. Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
KRAS MUTATED | 5 | 0 | 2 | 1
KRAS WILD-TYPE | 138 | 14 | 25 | 1

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.725 (Fisher's exact test), Q value = 0.87

Table S80. Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
KRAS MUTATED | 0 | 3 | 2 | 1
KRAS WILD-TYPE | 33 | 60 | 46 | 44

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 0.61

Table S81. Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
KRAS MUTATED | 4 | 3 | 0
KRAS WILD-TYPE | 69 | 47 | 45

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.65 (Fisher's exact test), Q value = 0.84

Table S82. Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
KRAS MUTATED | 0 | 0 | 0 | 4 | 0 | 3
KRAS WILD-TYPE | 16 | 13 | 15 | 53 | 26 | 38

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 0.52

Table S83. Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
KRAS MUTATED | 3 | 3 | 0 | 1
KRAS WILD-TYPE | 54 | 35 | 42 | 45

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.682 (Fisher's exact test), Q value = 0.84

Table S84. Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
KRAS MUTATED | 3 | 2 | 2
KRAS WILD-TYPE | 64 | 33 | 79

'SMC3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S85. Gene #15: 'SMC3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
SMC3 MUTATED | 6 | 0 | 1 | 0
SMC3 WILD-TYPE | 137 | 14 | 26 | 2

'SMC3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.5

Table S86. Gene #15: 'SMC3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
SMC3 MUTATED | 0 | 1 | 4 | 2
SMC3 WILD-TYPE | 33 | 62 | 44 | 43

'SMC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.552 (Fisher's exact test), Q value = 0.8

Table S87. Gene #15: 'SMC3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
SMC3 MUTATED | 2 | 2 | 3
SMC3 WILD-TYPE | 71 | 48 | 42

'SMC3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 0.69

Table S88. Gene #15: 'SMC3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
SMC3 MUTATED | 0 | 0 | 1 | 2 | 3 | 1
SMC3 WILD-TYPE | 16 | 13 | 14 | 55 | 23 | 40

'SMC3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 0.5

Table S89. Gene #15: 'SMC3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
SMC3 MUTATED | 1 | 0 | 3 | 3
SMC3 WILD-TYPE | 56 | 38 | 39 | 43

'SMC3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 0.68

Table S90. Gene #15: 'SMC3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
SMC3 MUTATED | 4 | 0 | 3
SMC3 WILD-TYPE | 63 | 35 | 78

'KIT MUTATION STATUS' versus 'CN_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.32

Table S91. Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
KIT MUTATED | 6 | 0 | 0 | 1
KIT WILD-TYPE | 137 | 14 | 27 | 1

'KIT MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.064

Table S92. Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
KIT MUTATED | 1 | 1 | 6 | 0
KIT WILD-TYPE | 32 | 62 | 42 | 45

Figure S36. Get High-res Image Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KIT MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 0.61

Table S93. Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
KIT MUTATED | 4 | 3 | 0
KIT WILD-TYPE | 69 | 47 | 45

'KIT MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00593 (Fisher's exact test), Q value = 0.03

Table S94. Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
KIT MUTATED | 0 | 3 | 2 | 2 | 0 | 0
KIT WILD-TYPE | 16 | 10 | 13 | 55 | 26 | 41

Figure S37. Get High-res Image Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 0.63

Table S95. Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
KIT MUTATED | 1 | 3 | 3 | 1
KIT WILD-TYPE | 56 | 35 | 39 | 45

'KIT MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 0.49

Table S96. Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
KIT MUTATED | 1 | 3 | 4
KIT WILD-TYPE | 66 | 32 | 77

'RAD21 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.71

Table S97. Gene #17: 'RAD21 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
RAD21 MUTATED | 4 | 1 | 0 | 0
RAD21 WILD-TYPE | 139 | 13 | 27 | 2

'RAD21 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.63

Table S98. Gene #17: 'RAD21 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
RAD21 MUTATED | 0 | 1 | 1 | 3
RAD21 WILD-TYPE | 33 | 62 | 47 | 42

'RAD21 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 0.8

Table S99. Gene #17: 'RAD21 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
RAD21 MUTATED | 1 | 2 | 2
RAD21 WILD-TYPE | 72 | 48 | 43

'RAD21 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 0.49

Table S100. Gene #17: 'RAD21 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
RAD21 MUTATED | 0 | 0 | 1 | 0 | 2 | 2
RAD21 WILD-TYPE | 16 | 13 | 14 | 57 | 24 | 39

'RAD21 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 0.5

Table S101. Gene #17: 'RAD21 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
RAD21 MUTATED | 2 | 0 | 0 | 3
RAD21 WILD-TYPE | 55 | 38 | 42 | 43

'RAD21 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 0.8

Table S102. Gene #17: 'RAD21 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
RAD21 MUTATED | 3 | 0 | 2
RAD21 WILD-TYPE | 64 | 35 | 79

'EZH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.32

Table S103. Gene #18: 'EZH2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
EZH2 MUTATED | 1 | 0 | 2 | 0
EZH2 WILD-TYPE | 142 | 14 | 25 | 2

'EZH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 0.52

Table S104. Gene #18: 'EZH2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
EZH2 MUTATED | 3 | 0 | 0
EZH2 WILD-TYPE | 70 | 50 | 45

'EZH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.589 (Fisher's exact test), Q value = 0.8

Table S105. Gene #18: 'EZH2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
EZH2 MUTATED | 0 | 0 | 0 | 3 | 0 | 0
EZH2 WILD-TYPE | 16 | 13 | 15 | 54 | 26 | 41

'EZH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 0.44

Table S106. Gene #18: 'EZH2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
EZH2 MUTATED | 0 | 1 | 2 | 0
EZH2 WILD-TYPE | 57 | 37 | 40 | 46

'EZH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.418 (Fisher's exact test), Q value = 0.68

Table S107. Gene #18: 'EZH2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
EZH2 MUTATED | 0 | 1 | 2
EZH2 WILD-TYPE | 67 | 34 | 79

'STAG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 0.8

Table S108. Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
STAG2 MUTATED | 5 | 1 | 0 | 0
STAG2 WILD-TYPE | 138 | 13 | 27 | 2

'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.49

Table S109. Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
STAG2 MUTATED | 0 | 2 | 0 | 3
STAG2 WILD-TYPE | 33 | 61 | 48 | 42

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.39

Table S110. Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
STAG2 MUTATED | 2 | 0 | 3
STAG2 WILD-TYPE | 71 | 50 | 42

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.12

Table S111. Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
STAG2 MUTATED | 0 | 0 | 0 | 1 | 4 | 0
STAG2 WILD-TYPE | 16 | 13 | 15 | 56 | 22 | 41

Figure S38. Get High-res Image Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.84

Table S112. Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
STAG2 MUTATED | 2 | 1 | 0 | 2
STAG2 WILD-TYPE | 55 | 37 | 42 | 44

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0649 (Fisher's exact test), Q value = 0.24

Table S113. Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
STAG2 MUTATED | 4 | 1 | 0
STAG2 WILD-TYPE | 63 | 34 | 81

'PTPN11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 0.84

Table S114. Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
PTPN11 MUTATED | 6 | 0 | 2 | 0
PTPN11 WILD-TYPE | 137 | 14 | 25 | 2

'PTPN11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 0.71

Table S115. Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
PTPN11 MUTATED | 2 | 1 | 3 | 3
PTPN11 WILD-TYPE | 31 | 62 | 45 | 42

'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0474 (Fisher's exact test), Q value = 0.18

Table S116. Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
PTPN11 MUTATED | 1 | 2 | 5
PTPN11 WILD-TYPE | 72 | 48 | 40

Figure S39. Get High-res Image Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.504 (Fisher's exact test), Q value = 0.74

Table S117. Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
PTPN11 MUTATED | 0 | 1 | 0 | 2 | 3 | 2
PTPN11 WILD-TYPE | 16 | 12 | 15 | 55 | 23 | 39

'PTPN11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0996 (Fisher's exact test), Q value = 0.32

Table S118. Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
PTPN11 MUTATED | 6 | 1 | 0 | 2
PTPN11 WILD-TYPE | 51 | 37 | 42 | 44

'PTPN11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.208 (Fisher's exact test), Q value = 0.5

Table S119. Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
PTPN11 MUTATED | 6 | 1 | 2
PTPN11 WILD-TYPE | 61 | 34 | 79

'ASXL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.737 (Fisher's exact test), Q value = 0.87

Table S120. Gene #21: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
ASXL1 MUTATED | 4 | 0 | 1 | 0
ASXL1 WILD-TYPE | 139 | 14 | 26 | 2

'ASXL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0773 (Fisher's exact test), Q value = 0.26

Table S121. Gene #21: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
ASXL1 MUTATED | 0 | 4 | 0 | 0
ASXL1 WILD-TYPE | 33 | 59 | 48 | 45

'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.52

Table S122. Gene #21: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
ASXL1 MUTATED | 3 | 0 | 0
ASXL1 WILD-TYPE | 70 | 50 | 45

'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.592 (Fisher's exact test), Q value = 0.8

Table S123. Gene #21: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
ASXL1 MUTATED | 0 | 0 | 0 | 3 | 0 | 0
ASXL1 WILD-TYPE | 16 | 13 | 15 | 54 | 26 | 41

'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 0.44

Table S124. Gene #21: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
ASXL1 MUTATED | 0 | 1 | 2 | 0
ASXL1 WILD-TYPE | 57 | 37 | 40 | 46

'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 0.68

Table S125. Gene #21: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
ASXL1 MUTATED | 0 | 1 | 2
ASXL1 WILD-TYPE | 67 | 34 | 79

'SUZ12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.56

Table S126. Gene #22: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
SUZ12 MUTATED | 2 | 1 | 0 | 0
SUZ12 WILD-TYPE | 141 | 13 | 27 | 2

'SUZ12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.788 (Fisher's exact test), Q value = 0.9

Table S127. Gene #22: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
SUZ12 MUTATED | 0 | 2 | 1 | 0
SUZ12 WILD-TYPE | 33 | 61 | 47 | 45

'SUZ12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 0.52

Table S128. Gene #22: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
SUZ12 MUTATED | 3 | 0 | 0
SUZ12 WILD-TYPE | 70 | 50 | 45

'SUZ12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.592 (Fisher's exact test), Q value = 0.8

Table S129. Gene #22: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
SUZ12 MUTATED | 0 | 0 | 0 | 3 | 0 | 0
SUZ12 WILD-TYPE | 16 | 13 | 15 | 54 | 26 | 41

'SUZ12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.49

Table S130. Gene #22: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
SUZ12 MUTATED | 0 | 1 | 0 | 2
SUZ12 WILD-TYPE | 57 | 37 | 42 | 44

'SUZ12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.14 (Fisher's exact test), Q value = 0.4

Table S131. Gene #22: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
SUZ12 MUTATED | 0 | 2 | 1
SUZ12 WILD-TYPE | 67 | 33 | 80

'PHACTR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S132. Gene #23: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
PHACTR1 MUTATED | 0 | 1 | 1 | 1
PHACTR1 WILD-TYPE | 33 | 62 | 47 | 44

'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 0.98

Table S133. Gene #23: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
PHACTR1 MUTATED | 1 | 1 | 0 | 1
PHACTR1 WILD-TYPE | 56 | 37 | 42 | 45

'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 0.68

Table S134. Gene #23: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
PHACTR1 MUTATED | 0 | 1 | 2
PHACTR1 WILD-TYPE | 67 | 34 | 79

'SMC1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.763 (Fisher's exact test), Q value = 0.89

Table S135. Gene #24: 'SMC1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
SMC1A MUTATED | 6 | 0 | 0 | 0
SMC1A WILD-TYPE | 137 | 14 | 27 | 2

'SMC1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.4

Table S136. Gene #24: 'SMC1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
SMC1A MUTATED | 0 | 1 | 1 | 4
SMC1A WILD-TYPE | 33 | 62 | 47 | 41

'SMC1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 0.8

Table S137. Gene #24: 'SMC1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 73 | 50 | 45
SMC1A MUTATED | 2 | 3 | 1
SMC1A WILD-TYPE | 71 | 47 | 44

'SMC1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.246 (Fisher's exact test), Q value = 0.52

Table S138. Gene #24: 'SMC1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 15 | 57 | 26 | 41
SMC1A MUTATED | 0 | 0 | 1 | 1 | 0 | 4
SMC1A WILD-TYPE | 16 | 13 | 14 | 56 | 26 | 37

'SMC1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.47

Table S139. Gene #24: 'SMC1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
SMC1A MUTATED | 3 | 0 | 0 | 3
SMC1A WILD-TYPE | 54 | 38 | 42 | 43

'SMC1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.661 (Fisher's exact test), Q value = 0.84

Table S140. Gene #24: 'SMC1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
SMC1A MUTATED | 3 | 0 | 3
SMC1A WILD-TYPE | 64 | 35 | 78

'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.547 (Fisher's exact test), Q value = 0.8

Table S141. Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 143 | 14 | 27 | 2
KDM6A MUTATED | 2 | 0 | 1 | 0
KDM6A WILD-TYPE | 141 | 14 | 26 | 2

'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.475 (Fisher's exact test), Q value = 0.71

Table S142. Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 63 | 48 | 45
KDM6A MUTATED | 0 | 1 | 2 | 0
KDM6A WILD-TYPE | 33 | 62 | 46 | 45

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.89 (Fisher's exact test), Q value = 0.98

Table S143. Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 57 | 38 | 42 | 46
KDM6A MUTATED | 1 | 1 | 0 | 1
KDM6A WILD-TYPE | 56 | 37 | 42 | 45

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.783 (Fisher's exact test), Q value = 0.9

Table S144. Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 35 | 81
KDM6A MUTATED | 1 | 1 | 1
KDM6A WILD-TYPE | 66 | 34 | 80

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/LAML-TB/15166008/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/15098833/LAML-TB.transferedmergedcluster.txt

- Number of patients = 195

- Number of significantly mutated genes = 25

- Number of Molecular subtypes = 6

- 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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