Correlation between gene mutation status and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
28 January 2016 | analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1NG4Q1F
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1NG4Q1F
Overview
Introduction

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

Summary

Testing the association between mutation status of 23 genes and 6 molecular subtypes across 193 patients, 36 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

- IDH1 mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- WT1 mutation correlated to 'METHLYATION_CNMF'.

- U2AF1 mutation correlated to 'MIRSEQ_CNMF'.

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

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

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

- STAG2 mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

- KIT mutation correlated to 'METHLYATION_CNMF' and '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 23 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, 36 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
TP53 | 15 (8%) | 178 | 0.0174 (0.0799) | 1e-05 (0.000197) | 0.00105 (0.00805) | 0.00237 (0.0149) | 1e-05 (0.000197) | 9e-05 (0.00113)
NPM1 | 33 (17%) | 160 | 0.278 (0.547) | 1e-05 (0.000197) | 1e-05 (0.000197) | 1e-05 (0.000197) | 2e-05 (0.000307) | 1e-05 (0.000197)
FLT3 | 52 (27%) | 141 | 0.681 (0.805) | 4e-05 (0.000552) | 1e-05 (0.000197) | 0.00082 (0.00742) | 0.0805 (0.258) | 0.00071 (0.007)
DNMT3A | 48 (25%) | 145 | 0.341 (0.601) | 2e-05 (0.000307) | 0.0507 (0.189) | 0.00218 (0.0147) | 0.00086 (0.00742) | 0.00203 (0.0147)
RUNX1 | 16 (8%) | 177 | 0.459 (0.667) | 0.00871 (0.0462) | 0.00992 (0.0507) | 0.0003 (0.00318) | 0.0565 (0.195) | 0.00224 (0.0147)
CEBPA | 13 (7%) | 180 | 1 (1.00) | 0.0348 (0.145) | 0.226 (0.518) | 0.00021 (0.00241) | 0.0124 (0.0609) | 0.0133 (0.0631)
IDH1 | 18 (9%) | 175 | 0.0234 (0.104) | 0.00096 (0.00779) | 0.0983 (0.302) | 0.262 (0.525) | 0.447 (0.667) | 0.804 (0.881)
STAG2 | 6 (3%) | 187 | 1 (1.00) | 0.337 (0.601) | 0.13 (0.365) | 0.0273 (0.118) | 0.0788 (0.258) | 0.049 (0.188)
KIT | 8 (4%) | 185 | 0.744 (0.839) | 0.00361 (0.0208) | 0.325 (0.601) | 0.00604 (0.0333) | 0.676 (0.805) | 0.222 (0.518)
WT1 | 12 (6%) | 181 | 0.822 (0.894) | 0.00275 (0.0165) | 0.0598 (0.201) | 0.372 (0.603) | 0.0553 (0.195) | 0.252 (0.525)
U2AF1 | 8 (4%) | 185 | 0.242 (0.525) | 0.129 (0.365) | 0.262 (0.525) | 0.263 (0.525) | 0.0487 (0.188) | 0.471 (0.677)
PTPN11 | 9 (5%) | 184 | 0.128 (0.365) | 0.164 (0.436) | 0.0477 (0.188) | 0.513 (0.699) | 0.459 (0.667) | 0.185 (0.46)
IDH2 | 20 (10%) | 173 | 0.391 (0.627) | 0.215 (0.511) | 0.646 (0.783) | 0.344 (0.601) | 0.753 (0.839) | 0.182 (0.46)
TET2 | 17 (9%) | 176 | 0.699 (0.817) | 0.513 (0.699) | 0.35 (0.601) | 0.582 (0.746) | 0.366 (0.601) | 0.753 (0.839)
NRAS | 15 (8%) | 178 | 0.149 (0.404) | 0.353 (0.601) | 0.515 (0.699) | 0.931 (0.953) | 0.928 (0.953) | 0.588 (0.746)
KRAS | 8 (4%) | 185 | 0.864 (0.91) | 0.576 (0.746) | 0.324 (0.601) | 0.637 (0.778) | 0.301 (0.584) | 0.683 (0.805)
PHF6 | 6 (3%) | 187 | 0.517 (0.699) | 0.422 (0.648) | 0.727 (0.836) | 0.476 (0.677) | 0.897 (0.938) | 0.35 (0.601)
RAD21 | 5 (3%) | 188 | 0.932 (0.953) | 0.437 (0.663) | 0.605 (0.746) | 0.182 (0.46) | 0.363 (0.601) | 0.603 (0.746)
EZH2 | 3 (2%) | 190 | 0.0903 (0.283) |  | 0.256 (0.525) | 0.593 (0.746) | 0.19 (0.46) | 0.42 (0.648)
SMC3 | 7 (4%) | 186 | 0.839 (0.899) | 0.418 (0.648) | 0.485 (0.683) | 0.453 (0.667) | 0.744 (0.839) | 0.362 (0.601)
ASXL1 | 5 (3%) | 188 | 0.724 (0.836) | 0.187 (0.46) | 0.255 (0.525) | 0.593 (0.746) | 0.11 (0.331) | 0.416 (0.648)
SMC1A | 6 (3%) | 187 | 0.852 (0.904) | 0.0544 (0.195) | 0.568 (0.746) | 0.229 (0.518) | 0.335 (0.601) | 0.576 (0.746)
SUZ12 | 3 (2%) | 190 | 0.791 (0.873) | 0.84 (0.899) | 0.257 (0.525) | 0.596 (0.746) | 0.326 (0.601) | 0.139 (0.385)

'FLT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 0.81

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
FLT3 MUTATED | 12 | 11 | 18 | 9
FLT3 WILD-TYPE | 37 | 31 | 36 | 30

'FLT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00055

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 | 22 | 25 | 62 | 37 | 41
FLT3 MUTATED | 11 | 5 | 7 | 7 | 21
FLT3 WILD-TYPE | 11 | 20 | 55 | 30 | 20

Figure S1. 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 = 2e-04

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
FLT3 MUTATED | 6 | 17 | 22
FLT3 WILD-TYPE | 68 | 31 | 23

Figure S2. Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'FLT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0074

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 | 40
FLT3 MUTATED | 5 | 3 | 2 | 6 | 13 | 16
FLT3 WILD-TYPE | 11 | 10 | 13 | 51 | 13 | 24

Figure S3. Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0805 (Fisher's exact test), Q value = 0.26

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
FLT3 MUTATED | 21 | 4 | 14 | 7 | 4
FLT3 WILD-TYPE | 34 | 27 | 28 | 25 | 17

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.007

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
FLT3 MUTATED | 29 | 5 | 16
FLT3 WILD-TYPE | 36 | 30 | 65

Figure S4. Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 0.6

Table S7. Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
DNMT3A MUTATED | 13 | 6 | 16 | 9
DNMT3A WILD-TYPE | 36 | 36 | 38 | 30

'DNMT3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S8. Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
DNMT3A MUTATED | 16 | 2 | 13 | 6 | 9
DNMT3A WILD-TYPE | 6 | 23 | 49 | 31 | 32

Figure S5. Get High-res Image Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0507 (Fisher's exact test), Q value = 0.19

Table S9. Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
DNMT3A MUTATED | 12 | 17 | 12
DNMT3A WILD-TYPE | 62 | 31 | 33

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00218 (Fisher's exact test), Q value = 0.015

Table S10. Gene #2: '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 | 40
DNMT3A MUTATED | 0 | 3 | 0 | 14 | 11 | 13
DNMT3A WILD-TYPE | 16 | 10 | 15 | 43 | 15 | 27

Figure S6. Get High-res Image Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.0074

Table S11. Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
DNMT3A MUTATED | 23 | 2 | 11 | 3 | 5
DNMT3A WILD-TYPE | 32 | 29 | 31 | 29 | 16

Figure S7. Get High-res Image Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00203 (Fisher's exact test), Q value = 0.015

Table S12. Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
DNMT3A MUTATED | 25 | 3 | 16
DNMT3A WILD-TYPE | 40 | 32 | 65

Figure S8. Get High-res Image Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NPM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.55

Table S13. Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
NPM1 MUTATED | 12 | 8 | 7 | 4
NPM1 WILD-TYPE | 37 | 34 | 47 | 35

'NPM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S14. Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
NPM1 MUTATED | 9 | 3 | 2 | 0 | 18
NPM1 WILD-TYPE | 13 | 22 | 60 | 37 | 23

Figure S9. Get High-res Image Gene #3: '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 = 2e-04

Table S15. Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
NPM1 MUTATED | 1 | 10 | 17
NPM1 WILD-TYPE | 73 | 38 | 28

Figure S10. Get High-res Image Gene #3: '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 = 2e-04

Table S16. Gene #3: '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 | 40
NPM1 MUTATED | 0 | 0 | 0 | 1 | 15 | 12
NPM1 WILD-TYPE | 16 | 13 | 15 | 56 | 11 | 28

Figure S11. Get High-res Image Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S17. Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
NPM1 MUTATED | 21 | 0 | 6 | 1 | 4
NPM1 WILD-TYPE | 34 | 31 | 36 | 31 | 17

Figure S12. Get High-res Image Gene #3: '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 = 2e-04

Table S18. Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
NPM1 MUTATED | 30 | 1 | 1
NPM1 WILD-TYPE | 35 | 34 | 80

Figure S13. Get High-res Image Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 0.63

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
IDH2 MUTATED | 6 | 2 | 8 | 3
IDH2 WILD-TYPE | 43 | 40 | 46 | 36

'IDH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.51

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 | 22 | 25 | 62 | 37 | 41
IDH2 MUTATED | 0 | 2 | 10 | 2 | 4
IDH2 WILD-TYPE | 22 | 23 | 52 | 35 | 37

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.646 (Fisher's exact test), Q value = 0.78

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
IDH2 MUTATED | 8 | 6 | 3
IDH2 WILD-TYPE | 66 | 42 | 42

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.6

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 | 40
IDH2 MUTATED | 0 | 2 | 0 | 9 | 2 | 4
IDH2 WILD-TYPE | 16 | 11 | 15 | 48 | 24 | 36

'IDH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.753 (Fisher's exact test), Q value = 0.84

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
IDH2 MUTATED | 6 | 1 | 4 | 4 | 2
IDH2 WILD-TYPE | 49 | 30 | 38 | 28 | 19

'IDH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 0.46

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
IDH2 MUTATED | 5 | 1 | 11
IDH2 WILD-TYPE | 60 | 34 | 70

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
IDH1 MUTATED | 7 | 1 | 2 | 7
IDH1 WILD-TYPE | 42 | 41 | 52 | 32

Figure S14. Get High-res Image Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0078

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 | 22 | 25 | 62 | 37 | 41
IDH1 MUTATED | 3 | 5 | 10 | 0 | 0
IDH1 WILD-TYPE | 19 | 20 | 52 | 37 | 41

Figure S15. Get High-res Image Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0983 (Fisher's exact test), Q value = 0.3

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
IDH1 MUTATED | 8 | 1 | 6
IDH1 WILD-TYPE | 66 | 47 | 39

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 0.53

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 | 40
IDH1 MUTATED | 0 | 0 | 0 | 8 | 4 | 3
IDH1 WILD-TYPE | 16 | 13 | 15 | 49 | 22 | 37

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 0.67

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
IDH1 MUTATED | 5 | 3 | 7 | 1 | 2
IDH1 WILD-TYPE | 50 | 28 | 35 | 31 | 19

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.804 (Fisher's exact test), Q value = 0.88

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
IDH1 MUTATED | 8 | 3 | 7
IDH1 WILD-TYPE | 57 | 32 | 74

'TET2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.699 (Fisher's exact test), Q value = 0.82

Table S31. Gene #6: 'TET2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
TET2 MUTATED | 3 | 4 | 4 | 5
TET2 WILD-TYPE | 46 | 38 | 50 | 34

'TET2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 0.7

Table S32. Gene #6: 'TET2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
TET2 MUTATED | 1 | 2 | 8 | 1 | 4
TET2 WILD-TYPE | 21 | 23 | 54 | 36 | 37

'TET2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.6

Table S33. Gene #6: 'TET2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
TET2 MUTATED | 9 | 2 | 4
TET2 WILD-TYPE | 65 | 46 | 41

'TET2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.582 (Fisher's exact test), Q value = 0.75

Table S34. Gene #6: '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 | 40
TET2 MUTATED | 0 | 0 | 2 | 7 | 3 | 3
TET2 WILD-TYPE | 16 | 13 | 13 | 50 | 23 | 37

'TET2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.6

Table S35. Gene #6: 'TET2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
TET2 MUTATED | 5 | 2 | 5 | 1 | 4
TET2 WILD-TYPE | 50 | 29 | 37 | 31 | 17

'TET2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.753 (Fisher's exact test), Q value = 0.84

Table S36. Gene #6: 'TET2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
TET2 MUTATED | 7 | 2 | 8
TET2 WILD-TYPE | 58 | 33 | 73

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.149 (Fisher's exact test), Q value = 0.4

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
NRAS MUTATED | 3 | 2 | 3 | 7
NRAS WILD-TYPE | 46 | 40 | 51 | 32

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 0.6

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
NRAS MUTATED | 0 | 1 | 5 | 3 | 6
NRAS WILD-TYPE | 22 | 24 | 57 | 34 | 35

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 0.7

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
NRAS MUTATED | 5 | 5 | 2
NRAS WILD-TYPE | 69 | 43 | 43

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.931 (Fisher's exact test), Q value = 0.95

Table S40. Gene #7: '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 | 40
NRAS MUTATED | 0 | 1 | 1 | 4 | 2 | 4
NRAS WILD-TYPE | 16 | 12 | 14 | 53 | 24 | 36

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.928 (Fisher's exact test), Q value = 0.95

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
NRAS MUTATED | 5 | 2 | 2 | 3 | 2
NRAS WILD-TYPE | 50 | 29 | 40 | 29 | 19

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.588 (Fisher's exact test), Q value = 0.75

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
NRAS MUTATED | 7 | 2 | 5
NRAS WILD-TYPE | 58 | 33 | 76

'WT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.822 (Fisher's exact test), Q value = 0.89

Table S43. Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
WT1 MUTATED | 3 | 2 | 3 | 4
WT1 WILD-TYPE | 46 | 40 | 51 | 35

'WT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.016

Table S44. Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
WT1 MUTATED | 0 | 2 | 0 | 2 | 7
WT1 WILD-TYPE | 22 | 23 | 62 | 35 | 34

Figure S16. Get High-res Image Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'WT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0598 (Fisher's exact test), Q value = 0.2

Table S45. Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
WT1 MUTATED | 2 | 2 | 6
WT1 WILD-TYPE | 72 | 46 | 39

'WT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 0.6

Table S46. Gene #8: '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 | 40
WT1 MUTATED | 0 | 1 | 0 | 3 | 4 | 2
WT1 WILD-TYPE | 16 | 12 | 15 | 54 | 22 | 38

'WT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0553 (Fisher's exact test), Q value = 0.19

Table S47. Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
WT1 MUTATED | 2 | 0 | 6 | 3 | 0
WT1 WILD-TYPE | 53 | 31 | 36 | 29 | 21

'WT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 0.53

Table S48. Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
WT1 MUTATED | 5 | 0 | 6
WT1 WILD-TYPE | 60 | 35 | 75

'U2AF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.53

Table S49. Gene #9: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
U2AF1 MUTATED | 2 | 0 | 1 | 3
U2AF1 WILD-TYPE | 47 | 42 | 53 | 36

'U2AF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.37

Table S50. Gene #9: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
U2AF1 MUTATED | 1 | 0 | 6 | 1 | 0
U2AF1 WILD-TYPE | 21 | 25 | 56 | 36 | 41

'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.53

Table S51. Gene #9: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
U2AF1 MUTATED | 5 | 2 | 0
U2AF1 WILD-TYPE | 69 | 46 | 45

'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.53

Table S52. Gene #9: '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 | 40
U2AF1 MUTATED | 0 | 0 | 0 | 6 | 0 | 1
U2AF1 WILD-TYPE | 16 | 13 | 15 | 51 | 26 | 39

'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.19

Table S53. Gene #9: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
U2AF1 MUTATED | 1 | 1 | 0 | 2 | 3
U2AF1 WILD-TYPE | 54 | 30 | 42 | 30 | 18

Figure S17. Get High-res Image Gene #9: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.471 (Fisher's exact test), Q value = 0.68

Table S54. Gene #9: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
U2AF1 MUTATED | 1 | 2 | 4
U2AF1 WILD-TYPE | 64 | 33 | 77

'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.459 (Fisher's exact test), Q value = 0.67

Table S55. Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
RUNX1 MUTATED | 2 | 4 | 7 | 3
RUNX1 WILD-TYPE | 47 | 38 | 47 | 36

'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00871 (Fisher's exact test), Q value = 0.046

Table S56. Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
RUNX1 MUTATED | 0 | 0 | 11 | 2 | 1
RUNX1 WILD-TYPE | 22 | 25 | 51 | 35 | 40

Figure S18. Get High-res Image Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00992 (Fisher's exact test), Q value = 0.051

Table S57. Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
RUNX1 MUTATED | 11 | 3 | 0
RUNX1 WILD-TYPE | 63 | 45 | 45

Figure S19. Get High-res Image Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0032

Table S58. Gene #10: '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 | 40
RUNX1 MUTATED | 0 | 1 | 0 | 13 | 0 | 0
RUNX1 WILD-TYPE | 16 | 12 | 15 | 44 | 26 | 40

Figure S20. Get High-res Image Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0565 (Fisher's exact test), Q value = 0.19

Table S59. Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
RUNX1 MUTATED | 1 | 3 | 2 | 4 | 4
RUNX1 WILD-TYPE | 54 | 28 | 40 | 28 | 17

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00224 (Fisher's exact test), Q value = 0.015

Table S60. Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
RUNX1 MUTATED | 0 | 3 | 11
RUNX1 WILD-TYPE | 65 | 32 | 70

Figure S21. Get High-res Image Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CEBPA MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
CEBPA MUTATED | 3 | 3 | 4 | 2
CEBPA WILD-TYPE | 46 | 39 | 50 | 37

'CEBPA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.15

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
CEBPA MUTATED | 0 | 2 | 2 | 7 | 2
CEBPA WILD-TYPE | 22 | 23 | 60 | 30 | 39

Figure S22. Get High-res Image Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CEBPA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.52

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
CEBPA MUTATED | 9 | 2 | 2
CEBPA WILD-TYPE | 65 | 46 | 43

'CEBPA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0024

Table S64. Gene #11: '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 | 40
CEBPA MUTATED | 0 | 0 | 7 | 4 | 1 | 1
CEBPA WILD-TYPE | 16 | 13 | 8 | 53 | 25 | 39

Figure S23. Get High-res Image Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.061

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
CEBPA MUTATED | 1 | 0 | 7 | 4 | 1
CEBPA WILD-TYPE | 54 | 31 | 35 | 28 | 20

Figure S24. Get High-res Image Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.063

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
CEBPA MUTATED | 2 | 0 | 11
CEBPA WILD-TYPE | 63 | 35 | 70

Figure S25. Get High-res Image Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.08

Table S67. Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
TP53 MUTATED | 0 | 7 | 5 | 3
TP53 WILD-TYPE | 49 | 35 | 49 | 36

Figure S26. Get High-res Image Gene #12: '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 = 2e-04

Table S68. Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
TP53 MUTATED | 0 | 0 | 15 | 0 | 0
TP53 WILD-TYPE | 22 | 25 | 47 | 37 | 41

Figure S27. Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.008

Table S69. Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
TP53 MUTATED | 12 | 1 | 0
TP53 WILD-TYPE | 62 | 47 | 45

Figure S28. Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00237 (Fisher's exact test), Q value = 0.015

Table S70. Gene #12: '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 | 40
TP53 MUTATED | 0 | 0 | 0 | 12 | 0 | 1
TP53 WILD-TYPE | 16 | 13 | 15 | 45 | 26 | 39

Figure S29. Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S71. Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
TP53 MUTATED | 0 | 6 | 0 | 2 | 6
TP53 WILD-TYPE | 55 | 25 | 42 | 30 | 15

Figure S30. Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011

Table S72. Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
TP53 MUTATED | 0 | 8 | 6
TP53 WILD-TYPE | 65 | 27 | 75

Figure S31. Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.864 (Fisher's exact test), Q value = 0.91

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
KRAS MUTATED | 3 | 1 | 2 | 2
KRAS WILD-TYPE | 46 | 41 | 52 | 37

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.576 (Fisher's exact test), Q value = 0.75

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
KRAS MUTATED | 2 | 0 | 2 | 1 | 1
KRAS WILD-TYPE | 20 | 25 | 60 | 36 | 40

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 0.6

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
KRAS MUTATED | 4 | 3 | 0
KRAS WILD-TYPE | 70 | 45 | 45

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 0.78

Table S76. Gene #13: '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 | 40
KRAS MUTATED | 0 | 0 | 0 | 4 | 0 | 3
KRAS WILD-TYPE | 16 | 13 | 15 | 53 | 26 | 37

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.301 (Fisher's exact test), Q value = 0.58

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
KRAS MUTATED | 3 | 3 | 1 | 0 | 0
KRAS WILD-TYPE | 52 | 28 | 41 | 32 | 21

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.683 (Fisher's exact test), Q value = 0.81

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
KRAS MUTATED | 3 | 2 | 2
KRAS WILD-TYPE | 62 | 33 | 79

'PHF6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 0.7

Table S79. Gene #14: 'PHF6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
PHF6 MUTATED | 1 | 2 | 3 | 0
PHF6 WILD-TYPE | 48 | 40 | 51 | 39

'PHF6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.422 (Fisher's exact test), Q value = 0.65

Table S80. Gene #14: 'PHF6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
PHF6 MUTATED | 0 | 1 | 1 | 3 | 1
PHF6 WILD-TYPE | 22 | 24 | 61 | 34 | 40

'PHF6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 0.84

Table S81. Gene #14: 'PHF6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
PHF6 MUTATED | 2 | 1 | 2
PHF6 WILD-TYPE | 72 | 47 | 43

'PHF6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.476 (Fisher's exact test), Q value = 0.68

Table S82. Gene #14: '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 | 40
PHF6 MUTATED | 0 | 0 | 0 | 4 | 1 | 0
PHF6 WILD-TYPE | 16 | 13 | 15 | 53 | 25 | 40

'PHF6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.897 (Fisher's exact test), Q value = 0.94

Table S83. Gene #14: 'PHF6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
PHF6 MUTATED | 2 | 0 | 1 | 1 | 1
PHF6 WILD-TYPE | 53 | 31 | 41 | 31 | 20

'PHF6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.35 (Fisher's exact test), Q value = 0.6

Table S84. Gene #14: 'PHF6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
PHF6 MUTATED | 1 | 0 | 4
PHF6 WILD-TYPE | 64 | 35 | 77

'STAG2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S85. Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
STAG2 MUTATED | 2 | 1 | 2 | 1
STAG2 WILD-TYPE | 47 | 41 | 52 | 38

'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 0.6

Table S86. Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
STAG2 MUTATED | 0 | 0 | 2 | 0 | 3
STAG2 WILD-TYPE | 22 | 25 | 60 | 37 | 38

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.37

Table S87. Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
STAG2 MUTATED | 2 | 0 | 3
STAG2 WILD-TYPE | 72 | 48 | 42

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.12

Table S88. Gene #15: '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 | 40
STAG2 MUTATED | 0 | 0 | 0 | 1 | 4 | 0
STAG2 WILD-TYPE | 16 | 13 | 15 | 56 | 22 | 40

Figure S32. Get High-res Image Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0788 (Fisher's exact test), Q value = 0.26

Table S89. Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
STAG2 MUTATED | 0 | 1 | 2 | 0 | 2
STAG2 WILD-TYPE | 55 | 30 | 40 | 32 | 19

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.049 (Fisher's exact test), Q value = 0.19

Table S90. Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
STAG2 MUTATED | 4 | 1 | 0
STAG2 WILD-TYPE | 61 | 34 | 81

Figure S33. Get High-res Image Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'CN_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 0.84

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
KIT MUTATED | 1 | 1 | 3 | 2
KIT WILD-TYPE | 48 | 41 | 51 | 37

'KIT MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00361 (Fisher's exact test), Q value = 0.021

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 | 22 | 25 | 62 | 37 | 41
KIT MUTATED | 1 | 0 | 1 | 6 | 0
KIT WILD-TYPE | 21 | 25 | 61 | 31 | 41

Figure S34. Get High-res Image Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KIT MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 0.6

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
KIT MUTATED | 4 | 3 | 0
KIT WILD-TYPE | 70 | 45 | 45

'KIT MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00604 (Fisher's exact test), Q value = 0.033

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 | 40
KIT MUTATED | 0 | 3 | 2 | 2 | 0 | 0
KIT WILD-TYPE | 16 | 10 | 13 | 55 | 26 | 40

Figure S35. Get High-res Image Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 0.81

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
KIT MUTATED | 1 | 2 | 3 | 1 | 1
KIT WILD-TYPE | 54 | 29 | 39 | 31 | 20

'KIT MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.52

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
KIT MUTATED | 1 | 3 | 4
KIT WILD-TYPE | 64 | 32 | 77

'RAD21 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.932 (Fisher's exact test), Q value = 0.95

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
RAD21 MUTATED | 2 | 1 | 1 | 1
RAD21 WILD-TYPE | 47 | 41 | 53 | 38

'RAD21 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.437 (Fisher's exact test), Q value = 0.66

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 | 22 | 25 | 62 | 37 | 41
RAD21 MUTATED | 0 | 0 | 1 | 1 | 3
RAD21 WILD-TYPE | 22 | 25 | 61 | 36 | 38

'RAD21 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 0.75

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
RAD21 MUTATED | 1 | 2 | 2
RAD21 WILD-TYPE | 73 | 46 | 43

'RAD21 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 0.46

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 | 40
RAD21 MUTATED | 0 | 0 | 1 | 0 | 2 | 2
RAD21 WILD-TYPE | 16 | 13 | 14 | 57 | 24 | 38

'RAD21 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 0.6

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
RAD21 MUTATED | 2 | 0 | 3 | 0 | 0
RAD21 WILD-TYPE | 53 | 31 | 39 | 32 | 21

'RAD21 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.603 (Fisher's exact test), Q value = 0.75

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
RAD21 MUTATED | 3 | 0 | 2
RAD21 WILD-TYPE | 62 | 35 | 79

'EZH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0903 (Fisher's exact test), Q value = 0.28

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
EZH2 MUTATED | 0 | 1 | 0 | 2
EZH2 WILD-TYPE | 49 | 41 | 54 | 37

'EZH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 0.53

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
EZH2 MUTATED | 3 | 0 | 0
EZH2 WILD-TYPE | 71 | 48 | 45

'EZH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 0.75

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 | 40
EZH2 MUTATED | 0 | 0 | 0 | 3 | 0 | 0
EZH2 WILD-TYPE | 16 | 13 | 15 | 54 | 26 | 40

'EZH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 0.46

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
EZH2 MUTATED | 0 | 1 | 0 | 1 | 1
EZH2 WILD-TYPE | 55 | 30 | 42 | 31 | 20

'EZH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.42 (Fisher's exact test), Q value = 0.65

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
EZH2 MUTATED | 0 | 1 | 2
EZH2 WILD-TYPE | 65 | 34 | 79

'SMC3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.839 (Fisher's exact test), Q value = 0.9

Table S108. Gene #19: 'SMC3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
SMC3 MUTATED | 3 | 1 | 2 | 1
SMC3 WILD-TYPE | 46 | 41 | 52 | 38

'SMC3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.418 (Fisher's exact test), Q value = 0.65

Table S109. Gene #19: 'SMC3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
SMC3 MUTATED | 1 | 0 | 1 | 2 | 3
SMC3 WILD-TYPE | 21 | 25 | 61 | 35 | 38

'SMC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 0.68

Table S110. Gene #19: 'SMC3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
SMC3 MUTATED | 2 | 2 | 3
SMC3 WILD-TYPE | 72 | 46 | 42

'SMC3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.453 (Fisher's exact test), Q value = 0.67

Table S111. Gene #19: '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 | 40
SMC3 MUTATED | 0 | 0 | 1 | 2 | 3 | 1
SMC3 WILD-TYPE | 16 | 13 | 14 | 55 | 23 | 39

'SMC3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 0.84

Table S112. Gene #19: 'SMC3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
SMC3 MUTATED | 2 | 0 | 2 | 2 | 1
SMC3 WILD-TYPE | 53 | 31 | 40 | 30 | 20

'SMC3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.362 (Fisher's exact test), Q value = 0.6

Table S113. Gene #19: 'SMC3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
SMC3 MUTATED | 4 | 0 | 3
SMC3 WILD-TYPE | 61 | 35 | 78

'ASXL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 0.84

Table S114. Gene #20: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
ASXL1 MUTATED | 2 | 0 | 2 | 1
ASXL1 WILD-TYPE | 47 | 42 | 52 | 38

'ASXL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.46

Table S115. Gene #20: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
ASXL1 MUTATED | 0 | 0 | 4 | 0 | 0
ASXL1 WILD-TYPE | 22 | 25 | 58 | 37 | 41

'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 0.53

Table S116. Gene #20: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
ASXL1 MUTATED | 3 | 0 | 0
ASXL1 WILD-TYPE | 71 | 48 | 45

'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 0.75

Table S117. Gene #20: '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 | 40
ASXL1 MUTATED | 0 | 0 | 0 | 3 | 0 | 0
ASXL1 WILD-TYPE | 16 | 13 | 15 | 54 | 26 | 40

'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.33

Table S118. Gene #20: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
ASXL1 MUTATED | 0 | 1 | 0 | 2 | 0
ASXL1 WILD-TYPE | 55 | 30 | 42 | 30 | 21

'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 0.65

Table S119. Gene #20: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
ASXL1 MUTATED | 0 | 1 | 2
ASXL1 WILD-TYPE | 65 | 34 | 79

'SMC1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.852 (Fisher's exact test), Q value = 0.9

Table S120. Gene #21: 'SMC1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
SMC1A MUTATED | 2 | 2 | 1 | 1
SMC1A WILD-TYPE | 47 | 40 | 53 | 38

'SMC1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0544 (Fisher's exact test), Q value = 0.19

Table S121. Gene #21: 'SMC1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
SMC1A MUTATED | 0 | 1 | 0 | 1 | 4
SMC1A WILD-TYPE | 22 | 24 | 62 | 36 | 37

'SMC1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 0.75

Table S122. Gene #21: 'SMC1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
SMC1A MUTATED | 2 | 3 | 1
SMC1A WILD-TYPE | 72 | 45 | 44

'SMC1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 0.52

Table S123. Gene #21: '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 | 40
SMC1A MUTATED | 0 | 0 | 1 | 1 | 0 | 4
SMC1A WILD-TYPE | 16 | 13 | 14 | 56 | 26 | 36

'SMC1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.335 (Fisher's exact test), Q value = 0.6

Table S124. Gene #21: 'SMC1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
SMC1A MUTATED | 3 | 0 | 3 | 0 | 0
SMC1A WILD-TYPE | 52 | 31 | 39 | 32 | 21

'SMC1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.576 (Fisher's exact test), Q value = 0.75

Table S125. Gene #21: 'SMC1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
SMC1A MUTATED | 3 | 0 | 3
SMC1A WILD-TYPE | 62 | 35 | 78

'PTPN11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.37

Table S126. Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
PTPN11 MUTATED | 3 | 4 | 1 | 0
PTPN11 WILD-TYPE | 46 | 38 | 53 | 39

'PTPN11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.44

Table S127. Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
PTPN11 MUTATED | 2 | 0 | 1 | 2 | 4
PTPN11 WILD-TYPE | 20 | 25 | 61 | 35 | 37

'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.19

Table S128. Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
PTPN11 MUTATED | 1 | 2 | 5
PTPN11 WILD-TYPE | 73 | 46 | 40

Figure S36. Get High-res Image Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.513 (Fisher's exact test), Q value = 0.7

Table S129. Gene #22: '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 | 40
PTPN11 MUTATED | 0 | 1 | 0 | 2 | 3 | 2
PTPN11 WILD-TYPE | 16 | 12 | 15 | 55 | 23 | 38

'PTPN11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.459 (Fisher's exact test), Q value = 0.67

Table S130. Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
PTPN11 MUTATED | 4 | 1 | 2 | 0 | 2
PTPN11 WILD-TYPE | 51 | 30 | 40 | 32 | 19

'PTPN11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.46

Table S131. Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
PTPN11 MUTATED | 6 | 1 | 2
PTPN11 WILD-TYPE | 59 | 34 | 79

'SUZ12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 0.87

Table S132. Gene #23: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 42 | 54 | 39
SUZ12 MUTATED | 0 | 1 | 1 | 1
SUZ12 WILD-TYPE | 49 | 41 | 53 | 38

'SUZ12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 0.9

Table S133. Gene #23: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 22 | 25 | 62 | 37 | 41
SUZ12 MUTATED | 0 | 0 | 2 | 1 | 0
SUZ12 WILD-TYPE | 22 | 25 | 60 | 36 | 41

'SUZ12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 0.53

Table S134. Gene #23: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 48 | 45
SUZ12 MUTATED | 3 | 0 | 0
SUZ12 WILD-TYPE | 71 | 48 | 45

'SUZ12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 0.75

Table S135. Gene #23: '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 | 40
SUZ12 MUTATED | 0 | 0 | 0 | 3 | 0 | 0
SUZ12 WILD-TYPE | 16 | 13 | 15 | 54 | 26 | 40

'SUZ12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 0.6

Table S136. Gene #23: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 55 | 31 | 42 | 32 | 21
SUZ12 MUTATED | 0 | 1 | 1 | 0 | 1
SUZ12 WILD-TYPE | 55 | 30 | 41 | 32 | 20

'SUZ12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 0.38

Table S137. Gene #23: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 65 | 35 | 81
SUZ12 MUTATED | 0 | 2 | 1
SUZ12 WILD-TYPE | 65 | 33 | 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/22570965/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/22541002/LAML-TB.transferedmergedcluster.txt

- Number of patients = 193

- Number of significantly mutated genes = 23

- 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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