Correlation between gene mutation status and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C17D2T1H
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C17D2T1H
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, 26 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'.

- IDH2 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'.

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

- CEBPA mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

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, 26 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 | 0.00031 (0.0387) | 9e-05 (0.0118) | 1e-05 (0.00144) | 0.00012 (0.0154) | 0.00061 (0.0744) | 0.00036 (0.0446)
NPM1 | 52 (27%) | 143 | 1e-05 (0.00144) | 1e-05 (0.00144) | 1e-05 (0.00144) | 1e-05 (0.00144) | 1e-05 (0.00144) | 1e-05 (0.00144)
RUNX1 | 18 (9%) | 177 | 0.361 (1.00) | 4e-05 (0.00528) | 0.00187 (0.223) | 9e-05 (0.0118) | 0.00043 (0.0529) | 0.00107 (0.128)
TP53 | 15 (8%) | 180 | 1e-05 (0.00144) | 1e-05 (0.00144) | 0.00095 (0.115) | 0.00222 (0.26) | 0.00021 (0.0265) | 0.00011 (0.0142)
DNMT3A | 49 (25%) | 146 | 0.854 (1.00) | 1e-05 (0.00144) | 0.0242 (1.00) | 0.00301 (0.343) | 0.00228 (0.264) | 0.00286 (0.329)
IDH2 | 20 (10%) | 175 | 0.1 (1.00) | 2e-05 (0.00266) | 0.686 (1.00) | 0.343 (1.00) | 0.748 (1.00) | 0.183 (1.00)
WT1 | 12 (6%) | 183 | 0.42 (1.00) | 1e-05 (0.00144) | 0.0817 (1.00) | 0.366 (1.00) | 0.0682 (1.00) | 0.274 (1.00)
CEBPA | 13 (7%) | 182 | 0.593 (1.00) | 0.00804 (0.9) | 0.199 (1.00) | 0.00012 (0.0154) | 0.0355 (1.00) | 0.0101 (1.00)
IDH1 | 18 (9%) | 177 | 1 (1.00) | 0.00218 (0.257) | 0.255 (1.00) | 0.256 (1.00) | 0.236 (1.00) | 0.805 (1.00)
TET2 | 17 (9%) | 178 | 0.355 (1.00) | 0.516 (1.00) | 0.292 (1.00) | 0.572 (1.00) | 0.658 (1.00) | 0.847 (1.00)
NRAS | 15 (8%) | 180 | 0.418 (1.00) | 0.887 (1.00) | 0.605 (1.00) | 0.937 (1.00) | 0.813 (1.00) | 0.665 (1.00)
U2AF1 | 8 (4%) | 187 | 1 (1.00) | 0.149 (1.00) | 0.233 (1.00) | 0.256 (1.00) | 0.0764 (1.00) | 0.471 (1.00)
PHF6 | 6 (3%) | 189 | 1 (1.00) | 0.0843 (1.00) | 0.73 (1.00) | 0.471 (1.00) | 0.729 (1.00) | 0.343 (1.00)
KRAS | 8 (4%) | 187 | 0.0753 (1.00) | 0.363 (1.00) | 0.325 (1.00) | 0.647 (1.00) | 0.254 (1.00) | 0.682 (1.00)
SMC3 | 7 (4%) | 188 | 1 (1.00) | 0.298 (1.00) | 0.551 (1.00) | 0.444 (1.00) | 0.217 (1.00) | 0.417 (1.00)
KIT | 8 (4%) | 187 | 0.102 (1.00) | 0.13 (1.00) | 0.324 (1.00) | 0.00527 (0.596) | 0.357 (1.00) | 0.191 (1.00)
RAD21 | 5 (3%) | 190 | 0.478 (1.00) | 0.663 (1.00) | 0.606 (1.00) | 0.184 (1.00) | 0.214 (1.00) | 0.605 (1.00)
EZH2 | 3 (2%) | 192 | 0.103 (1.00) |  | 0.256 (1.00) | 0.591 (1.00) | 0.159 (1.00) | 0.419 (1.00)
STAG2 | 6 (3%) | 189 | 0.563 (1.00) | 0.331 (1.00) | 0.132 (1.00) | 0.0263 (1.00) | 0.686 (1.00) | 0.0638 (1.00)
PTPN11 | 9 (5%) | 186 | 0.681 (1.00) | 0.39 (1.00) | 0.0466 (1.00) | 0.506 (1.00) | 0.1 (1.00) | 0.205 (1.00)
ASXL1 | 5 (3%) | 190 | 0.737 (1.00) | 0.217 (1.00) | 0.259 (1.00) | 0.591 (1.00) | 0.157 (1.00) | 0.417 (1.00)
SUZ12 | 3 (2%) | 192 | 0.286 (1.00) | 0.332 (1.00) | 0.256 (1.00) | 0.59 (1.00) | 0.198 (1.00) | 0.141 (1.00)
PHACTR1 | 3 (2%) | 192 |  | 0.331 (1.00) |  |  | 0.89 (1.00) | 0.418 (1.00)
SMC1A | 6 (3%) | 189 | 0.761 (1.00) | 0.552 (1.00) | 0.573 (1.00) | 0.244 (1.00) | 0.174 (1.00) | 0.663 (1.00)
KDM6A | 3 (2%) | 192 | 0.55 (1.00) | 1 (1.00) |  |  | 0.89 (1.00) | 0.785 (1.00)

'FLT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.039

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 = 9e-05 (Fisher's exact test), Q value = 0.012

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
FLT3 MUTATED | 24 | 11 | 8 | 2 | 7
FLT3 WILD-TYPE | 22 | 33 | 57 | 12 | 13

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 = 0.0014

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 = 0.00012 (Fisher's exact test), Q value = 0.015

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 = 0.00061 (Fisher's exact test), Q value = 0.074

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 = 0.00036 (Fisher's exact test), Q value = 0.045

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 = 0.0014

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 = 0.0014

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
NPM1 MUTATED | 34 | 0 | 4 | 9 | 4
NPM1 WILD-TYPE | 12 | 44 | 61 | 5 | 16

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 = 0.0014

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 = 0.0014

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 = 0.0014

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 = 0.0014

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 = 1

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 = 1e-05 (Fisher's exact test), Q value = 0.0014

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
DNMT3A MUTATED | 23 | 1 | 19 | 1 | 3
DNMT3A WILD-TYPE | 23 | 43 | 46 | 13 | 17

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 = 1

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 = 0.00301 (Fisher's exact test), Q value = 0.34

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 = 0.00228 (Fisher's exact test), Q value = 0.26

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 = 0.00286 (Fisher's exact test), Q value = 0.33

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 = 0.1 (Fisher's exact test), Q value = 1

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 = 2e-05 (Fisher's exact test), Q value = 0.0027

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
IDH2 MUTATED | 0 | 0 | 11 | 6 | 1
IDH2 WILD-TYPE | 46 | 44 | 54 | 8 | 19

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 = 1

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 = 0.343 (Fisher's exact test), Q value = 1

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 = 1

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

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 = 0.00218 (Fisher's exact test), Q value = 0.26

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
IDH1 MUTATED | 4 | 0 | 10 | 4 | 0
IDH1 WILD-TYPE | 42 | 44 | 55 | 10 | 20

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 = 0.255 (Fisher's exact test), Q value = 1

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 = 1

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 = 0.236 (Fisher's exact test), Q value = 1

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 = 0.805 (Fisher's exact test), Q value = 1

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

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 = 4e-05 (Fisher's exact test), Q value = 0.0053

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
RUNX1 MUTATED | 0 | 0 | 13 | 0 | 3
RUNX1 WILD-TYPE | 46 | 44 | 52 | 14 | 17

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 = 0.00187 (Fisher's exact test), Q value = 0.22

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 = 9e-05 (Fisher's exact test), Q value = 0.012

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 = 0.00043 (Fisher's exact test), Q value = 0.053

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 = 0.00107 (Fisher's exact test), Q value = 0.13

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 = 0.355 (Fisher's exact test), Q value = 1

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 = 0.516 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
TET2 MUTATED | 3 | 2 | 8 | 2 | 1
TET2 WILD-TYPE | 43 | 42 | 57 | 12 | 19

'TET2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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 = 1

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 = 0.658 (Fisher's exact test), Q value = 1

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 = 0.847 (Fisher's exact test), Q value = 1

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 = 0.418 (Fisher's exact test), Q value = 1

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 = 0.887 (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 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
NRAS MUTATED | 4 | 3 | 5 | 2 | 1
NRAS WILD-TYPE | 42 | 41 | 60 | 12 | 19

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 1

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 = 0.937 (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 = 1

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 = 0.665 (Fisher's exact test), Q value = 1

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 = 0.42 (Fisher's exact test), Q value = 1

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 = 1e-05 (Fisher's exact test), Q value = 0.0014

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
WT1 MUTATED | 1 | 1 | 0 | 2 | 7
WT1 WILD-TYPE | 45 | 43 | 65 | 12 | 13

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 = 0.0817 (Fisher's exact test), Q value = 1

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 = 0.366 (Fisher's exact test), Q value = 1

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 = 0.0682 (Fisher's exact test), Q value = 1

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 = 0.274 (Fisher's exact test), Q value = 1

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 = 0.149 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
U2AF1 MUTATED | 1 | 0 | 6 | 0 | 1
U2AF1 WILD-TYPE | 45 | 44 | 59 | 14 | 19

'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 1

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

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 = 0.0764 (Fisher's exact test), Q value = 1

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 = 0.471 (Fisher's exact test), Q value = 1

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 = 0.0014

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 S26. 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 = 0.0014

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
TP53 MUTATED | 0 | 0 | 15 | 0 | 0
TP53 WILD-TYPE | 46 | 44 | 50 | 14 | 20

Figure S27. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.11

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 S28. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00222 (Fisher's exact test), Q value = 0.26

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 S29. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.026

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 S30. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.014

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 S31. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CEBPA MUTATION STATUS' versus 'CN_CNMF'

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

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 = 0.00804 (Fisher's exact test), Q value = 0.9

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
CEBPA MUTATED | 0 | 6 | 2 | 2 | 3
CEBPA WILD-TYPE | 46 | 38 | 63 | 12 | 17

Figure S32. Get High-res Image Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CEBPA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 1

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 = 0.00012 (Fisher's exact test), Q value = 0.015

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 = 0.0355 (Fisher's exact test), Q value = 1

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 = 0.0101 (Fisher's exact test), Q value = 1

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 = 0.0843 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
PHF6 MUTATED | 1 | 1 | 1 | 0 | 3
PHF6 WILD-TYPE | 45 | 43 | 64 | 14 | 17

'PHF6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.73 (Fisher's exact test), Q value = 1

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 = 0.471 (Fisher's exact test), Q value = 1

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 = 0.729 (Fisher's exact test), Q value = 1

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 = 0.343 (Fisher's exact test), Q value = 1

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 = 0.0753 (Fisher's exact test), Q value = 1

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 = 0.363 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
KRAS MUTATED | 1 | 0 | 3 | 1 | 1
KRAS WILD-TYPE | 45 | 44 | 62 | 13 | 19

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 1

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 = 0.647 (Fisher's exact test), Q value = 1

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 = 0.254 (Fisher's exact test), Q value = 1

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 = 1

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

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
SMC3 MUTATED | 3 | 1 | 1 | 0 | 2
SMC3 WILD-TYPE | 43 | 43 | 64 | 14 | 18

'SMC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.551 (Fisher's exact test), Q value = 1

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 = 1

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 = 0.217 (Fisher's exact test), Q value = 1

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 = 0.417 (Fisher's exact test), Q value = 1

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 = 0.102 (Fisher's exact test), Q value = 1

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 = 0.13 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
KIT MUTATED | 1 | 5 | 1 | 0 | 1
KIT WILD-TYPE | 45 | 39 | 64 | 14 | 19

'KIT MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

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 = 0.00527 (Fisher's exact test), Q value = 0.6

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 S36. 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 = 1

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 = 0.191 (Fisher's exact test), Q value = 1

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 = 0.478 (Fisher's exact test), Q value = 1

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 = 0.663 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
RAD21 MUTATED | 3 | 1 | 1 | 0 | 0
RAD21 WILD-TYPE | 43 | 43 | 64 | 14 | 20

'RAD21 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 1

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 = 0.184 (Fisher's exact test), Q value = 1

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 = 0.214 (Fisher's exact test), Q value = 1

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 = 0.605 (Fisher's exact test), Q value = 1

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 = 1

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

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 = 0.591 (Fisher's exact test), Q value = 1

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 = 0.159 (Fisher's exact test), Q value = 1

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 = 0.419 (Fisher's exact test), Q value = 1

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 = 0.563 (Fisher's exact test), Q value = 1

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 = 0.331 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
STAG2 MUTATED | 1 | 0 | 2 | 1 | 1
STAG2 WILD-TYPE | 45 | 44 | 63 | 13 | 19

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 1

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 = 0.0263 (Fisher's exact test), Q value = 1

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 S37. Get High-res Image Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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 = 0.0638 (Fisher's exact test), Q value = 1

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

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

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
PTPN11 MUTATED | 4 | 1 | 2 | 0 | 2
PTPN11 WILD-TYPE | 42 | 43 | 63 | 14 | 18

'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 1

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 S38. Get High-res Image Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.506 (Fisher's exact test), Q value = 1

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 = 0.1 (Fisher's exact test), Q value = 1

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

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 = 1

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 = 0.217 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
ASXL1 MUTATED | 0 | 0 | 4 | 0 | 0
ASXL1 WILD-TYPE | 46 | 44 | 61 | 14 | 20

'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 1

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 = 0.591 (Fisher's exact test), Q value = 1

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 = 0.157 (Fisher's exact test), Q value = 1

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 = 0.417 (Fisher's exact test), Q value = 1

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 = 0.286 (Fisher's exact test), Q value = 1

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 = 0.332 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
SUZ12 MUTATED | 0 | 0 | 2 | 0 | 1
SUZ12 WILD-TYPE | 46 | 44 | 63 | 14 | 19

'SUZ12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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 = 1

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 = 0.141 (Fisher's exact test), Q value = 1

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 = 0.331 (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 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
PHACTR1 MUTATED | 0 | 0 | 2 | 0 | 1
PHACTR1 WILD-TYPE | 46 | 44 | 63 | 14 | 19

'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.89 (Fisher's exact test), Q value = 1

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 = 0.418 (Fisher's exact test), Q value = 1

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 = 0.761 (Fisher's exact test), Q value = 1

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 = 0.552 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
SMC1A MUTATED | 2 | 1 | 1 | 1 | 1
SMC1A WILD-TYPE | 44 | 43 | 64 | 13 | 19

'SMC1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 1

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

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 = 1

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 = 0.663 (Fisher's exact test), Q value = 1

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 = 0.55 (Fisher's exact test), Q value = 1

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

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 65 | 14 | 20
KDM6A MUTATED | 1 | 1 | 1 | 0 | 0
KDM6A WILD-TYPE | 45 | 43 | 64 | 14 | 20

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.89 (Fisher's exact test), Q value = 1

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 = 0.785 (Fisher's exact test), Q value = 1

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 = transformed.cor.cli.txt

- Molecular subtypes file = 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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