Correlation between gene mutation status and molecular subtypes

Bladder Urothelial Carcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

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/C1222SMQ

Overview

Introduction

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

Summary

Testing the association between mutation status of 35 genes and 10 molecular subtypes across 130 patients, 3 significant findings detected with P value < 0.05 and Q value < 0.25.

RB1 mutation correlated to 'CN_CNMF'.
FGFR3 mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
FBXW7 mutation correlated to 'MIRSEQ_MATURE_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 35 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 3 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
RB1	17 (13%)	113	1e-05 (0.0035)	0.39 (1.00)	0.59 (1.00)	0.315 (1.00)	0.573 (1.00)	0.517 (1.00)	0.48 (1.00)	0.681 (1.00)	0.164 (1.00)	0.28 (1.00)
FGFR3	16 (12%)	114	0.118 (1.00)	0.277 (1.00)	0.0911 (1.00)	0.00955 (1.00)	0.21 (1.00)	0.0097 (1.00)	0.12 (1.00)	0.0538 (1.00)	0.00143 (0.493)	1e-05 (0.0035)
FBXW7	13 (10%)	117	0.717 (1.00)	0.0057 (1.00)	0.262 (1.00)	0.533 (1.00)	0.0748 (1.00)	0.0383 (1.00)	0.293 (1.00)	0.0119 (1.00)	0.00039 (0.136)	0.00097 (0.336)
TP53	64 (49%)	66	0.0009 (0.312)	0.35 (1.00)	0.0395 (1.00)	0.00701 (1.00)	0.294 (1.00)	0.18 (1.00)	0.335 (1.00)	0.337 (1.00)	0.642 (1.00)	0.131 (1.00)
KDM6A	31 (24%)	99	0.0891 (1.00)	0.965 (1.00)	0.341 (1.00)	0.134 (1.00)	0.396 (1.00)	0.865 (1.00)	0.266 (1.00)	0.224 (1.00)	0.963 (1.00)	0.866 (1.00)
ARID1A	32 (25%)	98	0.418 (1.00)	0.603 (1.00)	0.588 (1.00)	0.0798 (1.00)	0.405 (1.00)	0.217 (1.00)	0.256 (1.00)	0.0179 (1.00)	0.0712 (1.00)	0.389 (1.00)
CDKN1A	18 (14%)	112	0.315 (1.00)	1 (1.00)	0.829 (1.00)	0.823 (1.00)	0.654 (1.00)	0.652 (1.00)	0.725 (1.00)	0.757 (1.00)	0.774 (1.00)	0.529 (1.00)
MLL2	36 (28%)	94	0.71 (1.00)	0.53 (1.00)	0.368 (1.00)	0.328 (1.00)	0.179 (1.00)	0.259 (1.00)	0.323 (1.00)	0.439 (1.00)	0.387 (1.00)	0.612 (1.00)
ELF3	11 (8%)	119	0.489 (1.00)	0.328 (1.00)	0.755 (1.00)	0.386 (1.00)	0.669 (1.00)	0.237 (1.00)	0.408 (1.00)	0.566 (1.00)	0.644 (1.00)	0.795 (1.00)
CDKN2A	7 (5%)	123	0.272 (1.00)	1 (1.00)	0.391 (1.00)	0.184 (1.00)	1 (1.00)	1 (1.00)	0.411 (1.00)	0.214 (1.00)	0.859 (1.00)	0.411 (1.00)
STAG2	14 (11%)	116	0.68 (1.00)	0.307 (1.00)	0.303 (1.00)	0.555 (1.00)	0.346 (1.00)	0.0988 (1.00)	0.276 (1.00)	0.417 (1.00)	0.412 (1.00)	0.224 (1.00)
NFE2L2	11 (8%)	119	0.0248 (1.00)	0.164 (1.00)	0.305 (1.00)	0.725 (1.00)	0.067 (1.00)	0.102 (1.00)	0.857 (1.00)	0.24 (1.00)	1 (1.00)	0.358 (1.00)
ERCC2	16 (12%)	114	0.799 (1.00)	0.735 (1.00)	0.0865 (1.00)	0.0179 (1.00)	0.162 (1.00)	0.0824 (1.00)	0.272 (1.00)	0.349 (1.00)	0.0415 (1.00)	0.00319 (1.00)
RHOB	7 (5%)	123	0.024 (1.00)	1 (1.00)	0.558 (1.00)	0.32 (1.00)	0.794 (1.00)	0.502 (1.00)	0.884 (1.00)	0.24 (1.00)	0.818 (1.00)	0.723 (1.00)
TSC1	11 (8%)	119	0.391 (1.00)	0.508 (1.00)	0.414 (1.00)	0.568 (1.00)	0.265 (1.00)	0.508 (1.00)	0.856 (1.00)	0.801 (1.00)	0.571 (1.00)	0.845 (1.00)
FOXQ1	7 (5%)	123	0.116 (1.00)	0.474 (1.00)	0.47 (1.00)	0.367 (1.00)	0.884 (1.00)	1 (1.00)	0.202 (1.00)	0.367 (1.00)	0.858 (1.00)	0.869 (1.00)
PIK3CA	26 (20%)	104	0.192 (1.00)	0.417 (1.00)	0.228 (1.00)	0.643 (1.00)	0.645 (1.00)	0.277 (1.00)	0.786 (1.00)	0.46 (1.00)	0.269 (1.00)	0.652 (1.00)
RXRA	12 (9%)	118	0.124 (1.00)	0.102 (1.00)	0.171 (1.00)	0.923 (1.00)	0.596 (1.00)	0.788 (1.00)	0.509 (1.00)	0.233 (1.00)	0.947 (1.00)	0.882 (1.00)
CREBBP	17 (13%)	113	0.0265 (1.00)	0.709 (1.00)	0.921 (1.00)	0.546 (1.00)	0.2 (1.00)	0.467 (1.00)	0.603 (1.00)	0.532 (1.00)	0.3 (1.00)	0.8 (1.00)
ERBB3	14 (11%)	116	0.586 (1.00)	0.617 (1.00)	0.69 (1.00)	0.493 (1.00)	0.769 (1.00)	0.887 (1.00)	0.626 (1.00)	0.654 (1.00)	0.847 (1.00)	0.389 (1.00)
FAT1	15 (12%)	115	0.0106 (1.00)	0.6 (1.00)	0.222 (1.00)	0.436 (1.00)	0.321 (1.00)	0.958 (1.00)	0.606 (1.00)	0.843 (1.00)	0.319 (1.00)	0.108 (1.00)
MLL	18 (14%)	112	0.326 (1.00)	1 (1.00)	0.0298 (1.00)	0.0048 (1.00)	0.289 (1.00)	0.465 (1.00)	0.947 (1.00)	0.417 (1.00)	0.177 (1.00)	0.442 (1.00)
HRAS	6 (5%)	124	0.891 (1.00)	0.308 (1.00)	0.0178 (1.00)	0.338 (1.00)	0.881 (1.00)	0.643 (1.00)	0.657 (1.00)	0.643 (1.00)	0.662 (1.00)	0.771 (1.00)
ACRC	4 (3%)	126	0.744 (1.00)	0.0276 (1.00)	0.855 (1.00)	0.762 (1.00)	0.468 (1.00)	0.824 (1.00)	1 (1.00)	0.556 (1.00)	0.901 (1.00)	0.855 (1.00)
TXNIP	9 (7%)	121	0.919 (1.00)	0.55 (1.00)	0.874 (1.00)	0.706 (1.00)	1 (1.00)	0.238 (1.00)	1 (1.00)	0.985 (1.00)	0.619 (1.00)	0.874 (1.00)
ECM1	5 (4%)	125	0.35 (1.00)	0.723 (1.00)	0.945 (1.00)	0.181 (1.00)	0.729 (1.00)	0.476 (1.00)	0.175 (1.00)	0.0806 (1.00)	0.798 (1.00)	0.713 (1.00)
KLF5	10 (8%)	120	1 (1.00)	0.7 (1.00)	0.301 (1.00)	0.311 (1.00)	0.915 (1.00)	0.435 (1.00)	0.843 (1.00)	0.146 (1.00)	0.313 (1.00)	0.259 (1.00)
RBM26	9 (7%)	121	0.00335 (1.00)	0.741 (1.00)	0.257 (1.00)	0.726 (1.00)	0.344 (1.00)	0.749 (1.00)	0.143 (1.00)	0.143 (1.00)	0.809 (1.00)	0.169 (1.00)
RAD51C	4 (3%)	126	0.385 (1.00)	0.423 (1.00)	0.18 (1.00)	1 (1.00)	0.0362 (1.00)	0.686 (1.00)	0.811 (1.00)	0.605 (1.00)	0.364 (1.00)	0.608 (1.00)
CEP192	5 (4%)	125	0.863 (1.00)	0.725 (1.00)	0.895 (1.00)	0.693 (1.00)	0.731 (1.00)	0.537 (1.00)	0.223 (1.00)	0.0185 (1.00)	0.8 (1.00)	0.321 (1.00)
ASXL2	9 (7%)	121	0.333 (1.00)	0.905 (1.00)	0.348 (1.00)	0.364 (1.00)	0.242 (1.00)	0.136 (1.00)	0.747 (1.00)	0.643 (1.00)	0.134 (1.00)	0.127 (1.00)
PSIP1	7 (5%)	123	0.821 (1.00)	0.148 (1.00)	0.137 (1.00)	0.389 (1.00)	0.884 (1.00)	0.279 (1.00)	0.794 (1.00)	0.561 (1.00)	0.479 (1.00)	0.119 (1.00)
ZNF513	7 (5%)	123	0.408 (1.00)	1 (1.00)	0.208 (1.00)	0.413 (1.00)	0.481 (1.00)	0.311 (1.00)	0.627 (1.00)	0.316 (1.00)	0.817 (1.00)	0.516 (1.00)
FOXA1	7 (5%)	123	0.0437 (1.00)	1 (1.00)	0.535 (1.00)	0.697 (1.00)	0.259 (1.00)	0.95 (1.00)	1 (1.00)	0.936 (1.00)	0.277 (1.00)	0.574 (1.00)
TRIP11	5 (4%)	125	1 (1.00)	0.843 (1.00)	0.802 (1.00)	0.288 (1.00)	0.731 (1.00)	0.929 (1.00)	0.134 (1.00)	0.308 (1.00)	1 (1.00)	0.662 (1.00)

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.31

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
TP53 MUTATED	18	21	12	12
TP53 WILD-TYPE	16	10	33	5

Figure S1. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
TP53 MUTATED	28	26	10
TP53 WILD-TYPE	27	22	17

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
TP53 MUTATED	14	11	23	1	9
TP53 WILD-TYPE	22	17	10	4	8

Figure S2. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00701 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
TP53 MUTATED	16	15	17	10
TP53 WILD-TYPE	27	21	4	9

Figure S3. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.294 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
TP53 MUTATED	20	23	21
TP53 WILD-TYPE	15	32	18

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
TP53 MUTATED	22	12	17	13
TP53 WILD-TYPE	22	21	16	6

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.335 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
TP53 MUTATED	19	14	31
TP53 WILD-TYPE	18	22	26

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.337 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
TP53 MUTATED	17	15	10	8	14
TP53 WILD-TYPE	12	21	17	6	10

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
TP53 MUTATED	15	6	18	23
TP53 WILD-TYPE	12	10	22	21

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
TP53 MUTATED	16	7	16	8	0	15
TP53 WILD-TYPE	15	11	10	9	6	14

'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0891 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
KDM6A MUTATED	14	6	8	3
KDM6A WILD-TYPE	20	25	37	14

'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.965 (Fisher's exact test), Q value = 1

Table S12. Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
KDM6A MUTATED	13	11	7
KDM6A WILD-TYPE	42	37	20

'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
KDM6A MUTATED	9	4	10	2	2
KDM6A WILD-TYPE	27	24	23	3	15

'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
KDM6A MUTATED	9	6	9	3
KDM6A WILD-TYPE	34	30	12	16

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.396 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
KDM6A MUTATED	6	13	12
KDM6A WILD-TYPE	29	42	27

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.865 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
KDM6A MUTATED	11	8	9	3
KDM6A WILD-TYPE	33	25	24	16

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 1

Table S17. Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
KDM6A MUTATED	10	5	16
KDM6A WILD-TYPE	27	31	41

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
KDM6A MUTATED	11	5	5	4	6
KDM6A WILD-TYPE	18	31	22	10	18

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.963 (Fisher's exact test), Q value = 1

Table S19. Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
KDM6A MUTATED	7	3	10	10
KDM6A WILD-TYPE	20	13	30	34

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S20. Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
KDM6A MUTATED	7	3	8	3	2	7
KDM6A WILD-TYPE	24	15	18	14	4	22

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0035

Table S21. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
RB1 MUTATED	1	5	2	9
RB1 WILD-TYPE	33	26	43	8

Figure S4. Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S22. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
RB1 MUTATED	10	5	2
RB1 WILD-TYPE	45	43	25

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S23. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
RB1 MUTATED	3	6	5	0	2
RB1 WILD-TYPE	33	22	28	5	15

'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.315 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
RB1 MUTATED	3	7	4	2
RB1 WILD-TYPE	40	29	17	17

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S25. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
RB1 MUTATED	4	6	7
RB1 WILD-TYPE	31	49	32

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.517 (Fisher's exact test), Q value = 1

Table S26. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
RB1 MUTATED	5	3	7	2
RB1 WILD-TYPE	39	30	26	17

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 1

Table S27. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
RB1 MUTATED	4	3	10
RB1 WILD-TYPE	33	33	47

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S28. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
RB1 MUTATED	5	4	2	3	3
RB1 WILD-TYPE	24	32	25	11	21

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 1

Table S29. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
RB1 MUTATED	7	1	3	6
RB1 WILD-TYPE	20	15	37	38

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 1

Table S30. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
RB1 MUTATED	4	1	3	1	0	8
RB1 WILD-TYPE	27	17	23	16	6	21

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S31. Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
ARID1A MUTATED	7	10	9	6
ARID1A WILD-TYPE	27	21	36	11

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
ARID1A MUTATED	13	14	5
ARID1A WILD-TYPE	42	34	22

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
ARID1A MUTATED	11	8	6	2	3
ARID1A WILD-TYPE	25	20	27	3	14

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0798 (Fisher's exact test), Q value = 1

Table S34. Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
ARID1A MUTATED	11	14	3	2
ARID1A WILD-TYPE	32	22	18	17

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.405 (Fisher's exact test), Q value = 1

Table S35. Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
ARID1A MUTATED	11	14	7
ARID1A WILD-TYPE	24	41	32

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S36. Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
ARID1A MUTATED	12	6	6	8
ARID1A WILD-TYPE	32	27	27	11

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S37. Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
ARID1A MUTATED	11	11	10
ARID1A WILD-TYPE	26	25	47

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 1

Table S38. Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
ARID1A MUTATED	6	11	2	2	11
ARID1A WILD-TYPE	23	25	25	12	13

Figure S5. Get High-res Image Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0712 (Fisher's exact test), Q value = 1

Table S39. Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
ARID1A MUTATED	4	5	6	16
ARID1A WILD-TYPE	23	11	34	28

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 1

Table S40. Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
ARID1A MUTATED	11	6	5	3	0	6
ARID1A WILD-TYPE	20	12	21	14	6	23

'CDKN1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 1

Table S41. Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
CDKN1A MUTATED	2	5	7	4
CDKN1A WILD-TYPE	32	26	38	13

'CDKN1A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S42. Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
CDKN1A MUTATED	8	7	3
CDKN1A WILD-TYPE	47	41	24

'CDKN1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.829 (Fisher's exact test), Q value = 1

Table S43. Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
CDKN1A MUTATED	6	4	5	1	1
CDKN1A WILD-TYPE	30	24	28	4	16

'CDKN1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.823 (Fisher's exact test), Q value = 1

Table S44. Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
CDKN1A MUTATED	7	4	4	2
CDKN1A WILD-TYPE	36	32	17	17

'CDKN1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.654 (Fisher's exact test), Q value = 1

Table S45. Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
CDKN1A MUTATED	6	6	6
CDKN1A WILD-TYPE	29	49	33

'CDKN1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.652 (Fisher's exact test), Q value = 1

Table S46. Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
CDKN1A MUTATED	4	6	5	3
CDKN1A WILD-TYPE	40	27	28	16

'CDKN1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.725 (Fisher's exact test), Q value = 1

Table S47. Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
CDKN1A MUTATED	4	6	8
CDKN1A WILD-TYPE	33	30	49

'CDKN1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.757 (Fisher's exact test), Q value = 1

Table S48. Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
CDKN1A MUTATED	3	6	4	3	2
CDKN1A WILD-TYPE	26	30	23	11	22

'CDKN1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S49. Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
CDKN1A MUTATED	3	1	7	6
CDKN1A WILD-TYPE	24	15	33	38

'CDKN1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.529 (Fisher's exact test), Q value = 1

Table S50. Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
CDKN1A MUTATED	2	1	5	3	1	5
CDKN1A WILD-TYPE	29	17	21	14	5	24

'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.71 (Fisher's exact test), Q value = 1

Table S51. Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
MLL2 MUTATED	8	10	13	3
MLL2 WILD-TYPE	26	21	32	14

'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.53 (Fisher's exact test), Q value = 1

Table S52. Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
MLL2 MUTATED	18	11	7
MLL2 WILD-TYPE	37	37	20

'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 1

Table S53. Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
MLL2 MUTATED	9	5	12	1	7
MLL2 WILD-TYPE	27	23	21	4	10

'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.328 (Fisher's exact test), Q value = 1

Table S54. Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
MLL2 MUTATED	12	7	7	8
MLL2 WILD-TYPE	31	29	14	11

'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.179 (Fisher's exact test), Q value = 1

Table S55. Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
MLL2 MUTATED	8	12	15
MLL2 WILD-TYPE	27	43	24

'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S56. Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
MLL2 MUTATED	12	7	13	3
MLL2 WILD-TYPE	32	26	20	16

'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 1

Table S57. Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
MLL2 MUTATED	7	10	19
MLL2 WILD-TYPE	30	26	38

'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.439 (Fisher's exact test), Q value = 1

Table S58. Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
MLL2 MUTATED	8	9	6	7	6
MLL2 WILD-TYPE	21	27	21	7	18

'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 1

Table S59. Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
MLL2 MUTATED	10	2	11	11
MLL2 WILD-TYPE	17	14	29	33

'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.612 (Fisher's exact test), Q value = 1

Table S60. Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
MLL2 MUTATED	10	3	7	5	0	9
MLL2 WILD-TYPE	21	15	19	12	6	20

'ELF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 1

Table S61. Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
ELF3 MUTATED	2	5	3	1
ELF3 WILD-TYPE	32	26	42	16

'ELF3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 1

Table S62. Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
ELF3 MUTATED	3	4	4
ELF3 WILD-TYPE	52	44	23

'ELF3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S63. Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
ELF3 MUTATED	4	3	3	0	0
ELF3 WILD-TYPE	32	25	30	5	17

'ELF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.386 (Fisher's exact test), Q value = 1

Table S64. Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
ELF3 MUTATED	3	4	3	0
ELF3 WILD-TYPE	40	32	18	19

'ELF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.669 (Fisher's exact test), Q value = 1

Table S65. Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
ELF3 MUTATED	3	6	2
ELF3 WILD-TYPE	32	49	37

'ELF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.237 (Fisher's exact test), Q value = 1

Table S66. Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
ELF3 MUTATED	7	2	2	0
ELF3 WILD-TYPE	37	31	31	19

'ELF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 1

Table S67. Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
ELF3 MUTATED	5	3	3
ELF3 WILD-TYPE	32	33	54

'ELF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 1

Table S68. Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
ELF3 MUTATED	4	4	1	0	2
ELF3 WILD-TYPE	25	32	26	14	22

'ELF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S69. Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
ELF3 MUTATED	1	2	3	5
ELF3 WILD-TYPE	26	14	37	39

'ELF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S70. Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
ELF3 MUTATED	4	2	2	2	0	1
ELF3 WILD-TYPE	27	16	24	15	6	28

'FGFR3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.118 (Fisher's exact test), Q value = 1

Table S71. Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
FGFR3 MUTATED	5	2	9	0
FGFR3 WILD-TYPE	29	29	36	17

'FGFR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S72. Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
FGFR3 MUTATED	4	7	5
FGFR3 WILD-TYPE	51	41	22

'FGFR3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0911 (Fisher's exact test), Q value = 1

Table S73. Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
FGFR3 MUTATED	9	2	4	0	0
FGFR3 WILD-TYPE	27	26	29	5	17

'FGFR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00955 (Fisher's exact test), Q value = 1

Table S74. Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
FGFR3 MUTATED	9	0	4	2
FGFR3 WILD-TYPE	34	36	17	17

Figure S6. Get High-res Image Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 1

Table S75. Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
FGFR3 MUTATED	2	10	4
FGFR3 WILD-TYPE	33	45	35

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0097 (Fisher's exact test), Q value = 1

Table S76. Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
FGFR3 MUTATED	3	10	2	1
FGFR3 WILD-TYPE	41	23	31	18

Figure S7. Get High-res Image Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 1

Table S77. Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
FGFR3 MUTATED	2	3	11
FGFR3 WILD-TYPE	35	33	46

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0538 (Fisher's exact test), Q value = 1

Table S78. Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
FGFR3 MUTATED	4	3	7	2	0
FGFR3 WILD-TYPE	25	33	20	12	24

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.49

Table S79. Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
FGFR3 MUTATED	0	0	11	4
FGFR3 WILD-TYPE	27	16	29	40

Figure S8. Get High-res Image Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0035

Table S80. Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
FGFR3 MUTATED	1	0	7	3	4	0
FGFR3 WILD-TYPE	30	18	19	14	2	29

Figure S9. Get High-res Image Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 1

Table S81. Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
CDKN2A MUTATED	4	2	1	0
CDKN2A WILD-TYPE	30	29	44	17

'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S82. Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
CDKN2A MUTATED	3	3	1
CDKN2A WILD-TYPE	52	45	26

'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 1

Table S83. Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
CDKN2A MUTATED	2	0	4	0	1
CDKN2A WILD-TYPE	34	28	29	5	16

'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S84. Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
CDKN2A MUTATED	3	0	2	2
CDKN2A WILD-TYPE	40	36	19	17

'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S85. Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
CDKN2A MUTATED	2	3	2
CDKN2A WILD-TYPE	33	52	37

'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S86. Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
CDKN2A MUTATED	2	2	2	1
CDKN2A WILD-TYPE	42	31	31	18

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.411 (Fisher's exact test), Q value = 1

Table S87. Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
CDKN2A MUTATED	1	1	5
CDKN2A WILD-TYPE	36	35	52

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S88. Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
CDKN2A MUTATED	3	1	1	2	0
CDKN2A WILD-TYPE	26	35	26	12	24

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.859 (Fisher's exact test), Q value = 1

Table S89. Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
CDKN2A MUTATED	2	0	2	3
CDKN2A WILD-TYPE	25	16	38	41

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 1

Table S90. Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
CDKN2A MUTATED	1	0	1	2	1	2
CDKN2A WILD-TYPE	30	18	25	15	5	27

'STAG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S91. Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
STAG2 MUTATED	5	2	6	1
STAG2 WILD-TYPE	29	29	39	16

'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 1

Table S92. Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
STAG2 MUTATED	4	5	5
STAG2 WILD-TYPE	51	43	22

'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 1

Table S93. Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
STAG2 MUTATED	7	3	3	0	0
STAG2 WILD-TYPE	29	25	30	5	17

'STAG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.555 (Fisher's exact test), Q value = 1

Table S94. Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
STAG2 MUTATED	7	3	1	2
STAG2 WILD-TYPE	36	33	20	17

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 1

Table S95. Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
STAG2 MUTATED	4	8	2
STAG2 WILD-TYPE	31	47	37

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0988 (Fisher's exact test), Q value = 1

Table S96. Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
STAG2 MUTATED	5	7	2	0
STAG2 WILD-TYPE	39	26	31	19

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 1

Table S97. Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
STAG2 MUTATED	3	2	9
STAG2 WILD-TYPE	34	34	48

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S98. Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
STAG2 MUTATED	2	3	6	1	2
STAG2 WILD-TYPE	27	33	21	13	22

'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.412 (Fisher's exact test), Q value = 1

Table S99. Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
STAG2 MUTATED	2	1	7	3
STAG2 WILD-TYPE	25	15	33	41

'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 1

Table S100. Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
STAG2 MUTATED	2	1	5	1	2	2
STAG2 WILD-TYPE	29	17	21	16	4	27

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 1

Table S101. Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
NFE2L2 MUTATED	3	0	8	0
NFE2L2 WILD-TYPE	31	31	37	17

Figure S10. Get High-res Image Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 1

Table S102. Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
NFE2L2 MUTATED	7	4	0
NFE2L2 WILD-TYPE	48	44	27

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 1

Table S103. Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
NFE2L2 MUTATED	1	4	3	1	2
NFE2L2 WILD-TYPE	35	24	30	4	15

'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.725 (Fisher's exact test), Q value = 1

Table S104. Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
NFE2L2 MUTATED	3	4	3	1
NFE2L2 WILD-TYPE	40	32	18	18

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.067 (Fisher's exact test), Q value = 1

Table S105. Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
NFE2L2 MUTATED	4	1	5
NFE2L2 WILD-TYPE	31	54	34

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S106. Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
NFE2L2 MUTATED	4	0	5	1
NFE2L2 WILD-TYPE	40	33	28	18

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.857 (Fisher's exact test), Q value = 1

Table S107. Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
NFE2L2 MUTATED	3	4	4
NFE2L2 WILD-TYPE	34	32	53

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.24 (Fisher's exact test), Q value = 1

Table S108. Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
NFE2L2 MUTATED	4	4	1	2	0
NFE2L2 WILD-TYPE	25	32	26	12	24

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S109. Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
NFE2L2 MUTATED	2	1	3	4
NFE2L2 WILD-TYPE	25	15	37	40

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 1

Table S110. Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
NFE2L2 MUTATED	2	1	1	4	0	2
NFE2L2 WILD-TYPE	29	17	25	13	6	27

'ERCC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.799 (Fisher's exact test), Q value = 1

Table S111. Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
ERCC2 MUTATED	5	3	5	3
ERCC2 WILD-TYPE	29	28	40	14

'ERCC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.735 (Fisher's exact test), Q value = 1

Table S112. Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
ERCC2 MUTATED	8	6	2
ERCC2 WILD-TYPE	47	42	25

'ERCC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0865 (Fisher's exact test), Q value = 1

Table S113. Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
ERCC2 MUTATED	3	0	6	1	1
ERCC2 WILD-TYPE	33	28	27	4	16

'ERCC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 1

Table S114. Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
ERCC2 MUTATED	3	1	6	1
ERCC2 WILD-TYPE	40	35	15	18

Figure S11. Get High-res Image Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'ERCC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 1

Table S115. Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
ERCC2 MUTATED	4	4	8
ERCC2 WILD-TYPE	31	51	31

'ERCC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0824 (Fisher's exact test), Q value = 1

Table S116. Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
ERCC2 MUTATED	3	2	8	3
ERCC2 WILD-TYPE	41	31	25	16

'ERCC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 1

Table S117. Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
ERCC2 MUTATED	2	6	8
ERCC2 WILD-TYPE	35	30	49

'ERCC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.349 (Fisher's exact test), Q value = 1

Table S118. Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
ERCC2 MUTATED	5	7	2	1	1
ERCC2 WILD-TYPE	24	29	25	13	23

'ERCC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 1

Table S119. Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
ERCC2 MUTATED	7	3	4	2
ERCC2 WILD-TYPE	20	13	36	42

Figure S12. Get High-res Image Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'ERCC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00319 (Fisher's exact test), Q value = 1

Table S120. Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
ERCC2 MUTATED	1	3	2	0	0	10
ERCC2 WILD-TYPE	30	15	24	17	6	19

Figure S13. Get High-res Image Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.717 (Fisher's exact test), Q value = 1

Table S121. Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
FBXW7 MUTATED	2	3	6	1
FBXW7 WILD-TYPE	32	28	39	16

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0057 (Fisher's exact test), Q value = 1

Table S122. Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
FBXW7 MUTATED	11	1	1
FBXW7 WILD-TYPE	44	47	26

Figure S14. Get High-res Image Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 1

Table S123. Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
FBXW7 MUTATED	1	3	5	1	1
FBXW7 WILD-TYPE	35	25	28	4	16

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S124. Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
FBXW7 MUTATED	2	4	3	2
FBXW7 WILD-TYPE	41	32	18	17

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0748 (Fisher's exact test), Q value = 1

Table S125. Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
FBXW7 MUTATED	5	2	6
FBXW7 WILD-TYPE	30	53	33

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 1

Table S126. Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
FBXW7 MUTATED	4	0	6	3
FBXW7 WILD-TYPE	40	33	27	16

Figure S15. Get High-res Image Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 1

Table S127. Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
FBXW7 MUTATED	2	6	5
FBXW7 WILD-TYPE	35	30	52

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 1

Table S128. Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
FBXW7 MUTATED	6	6	0	1	0
FBXW7 WILD-TYPE	23	30	27	13	24

Figure S16. Get High-res Image Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.14

Table S129. Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
FBXW7 MUTATED	7	4	1	1
FBXW7 WILD-TYPE	20	12	39	43

Figure S17. Get High-res Image Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.34

Table S130. Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
FBXW7 MUTATED	0	5	1	0	0	7
FBXW7 WILD-TYPE	31	13	25	17	6	22

Figure S18. Get High-res Image Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RHOB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 1

Table S131. Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
RHOB MUTATED	1	4	0	2
RHOB WILD-TYPE	33	27	45	15

Figure S19. Get High-res Image Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RHOB MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S132. Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
RHOB MUTATED	3	3	1
RHOB WILD-TYPE	52	45	26

'RHOB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 1

Table S133. Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
RHOB MUTATED	2	1	4	0	0
RHOB WILD-TYPE	34	27	29	5	17

'RHOB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.32 (Fisher's exact test), Q value = 1

Table S134. Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
RHOB MUTATED	2	2	3	0
RHOB WILD-TYPE	41	34	18	19

'RHOB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S135. Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
RHOB MUTATED	1	3	3
RHOB WILD-TYPE	34	52	36

'RHOB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.502 (Fisher's exact test), Q value = 1

Table S136. Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
RHOB MUTATED	4	1	2	0
RHOB WILD-TYPE	40	32	31	19

'RHOB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.884 (Fisher's exact test), Q value = 1

Table S137. Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
RHOB MUTATED	2	1	4
RHOB WILD-TYPE	35	35	53

'RHOB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.24 (Fisher's exact test), Q value = 1

Table S138. Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
RHOB MUTATED	2	1	0	2	2
RHOB WILD-TYPE	27	35	27	12	22

'RHOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S139. Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
RHOB MUTATED	1	0	3	3
RHOB WILD-TYPE	26	16	37	41

'RHOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.723 (Fisher's exact test), Q value = 1

Table S140. Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
RHOB MUTATED	2	0	2	2	0	1
RHOB WILD-TYPE	29	18	24	15	6	28

'TSC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 1

Table S141. Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
TSC1 MUTATED	5	2	4	0
TSC1 WILD-TYPE	29	29	41	17

'TSC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 1

Table S142. Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
TSC1 MUTATED	3	6	2
TSC1 WILD-TYPE	52	42	25

'TSC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 1

Table S143. Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
TSC1 MUTATED	6	1	2	0	2
TSC1 WILD-TYPE	30	27	31	5	15

'TSC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 1

Table S144. Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
TSC1 MUTATED	6	2	1	2
TSC1 WILD-TYPE	37	34	20	17

'TSC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 1

Table S145. Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
TSC1 MUTATED	4	6	1
TSC1 WILD-TYPE	31	49	38

'TSC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.508 (Fisher's exact test), Q value = 1

Table S146. Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
TSC1 MUTATED	5	4	1	1
TSC1 WILD-TYPE	39	29	32	18

'TSC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S147. Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
TSC1 MUTATED	3	4	4
TSC1 WILD-TYPE	34	32	53

'TSC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.801 (Fisher's exact test), Q value = 1

Table S148. Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
TSC1 MUTATED	2	4	1	1	3
TSC1 WILD-TYPE	27	32	26	13	21

'TSC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.571 (Fisher's exact test), Q value = 1

Table S149. Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
TSC1 MUTATED	1	1	3	6
TSC1 WILD-TYPE	26	15	37	38

'TSC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.845 (Fisher's exact test), Q value = 1

Table S150. Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
TSC1 MUTATED	3	1	2	3	0	2
TSC1 WILD-TYPE	28	17	24	14	6	27

'FOXQ1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 1

Table S151. Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
FOXQ1 MUTATED	0	4	2	1
FOXQ1 WILD-TYPE	34	27	43	16

'FOXQ1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.474 (Fisher's exact test), Q value = 1

Table S152. Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
FOXQ1 MUTATED	4	1	2
FOXQ1 WILD-TYPE	51	47	25

'FOXQ1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 1

Table S153. Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
FOXQ1 MUTATED	2	0	2	0	2
FOXQ1 WILD-TYPE	34	28	31	5	15

'FOXQ1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 1

Table S154. Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
FOXQ1 MUTATED	3	1	0	2
FOXQ1 WILD-TYPE	40	35	21	17

'FOXQ1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.884 (Fisher's exact test), Q value = 1

Table S155. Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
FOXQ1 MUTATED	1	4	2
FOXQ1 WILD-TYPE	34	51	37

'FOXQ1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S156. Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
FOXQ1 MUTATED	2	2	2	1
FOXQ1 WILD-TYPE	42	31	31	18

'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 1

Table S157. Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
FOXQ1 MUTATED	2	0	5
FOXQ1 WILD-TYPE	35	36	52

'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 1

Table S158. Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
FOXQ1 MUTATED	2	0	2	1	2
FOXQ1 WILD-TYPE	27	36	25	13	22

'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.858 (Fisher's exact test), Q value = 1

Table S159. Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
FOXQ1 MUTATED	2	0	2	3
FOXQ1 WILD-TYPE	25	16	38	41

'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S160. Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
FOXQ1 MUTATED	3	0	1	1	0	2
FOXQ1 WILD-TYPE	28	18	25	16	6	27

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 1

Table S161. Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
PIK3CA MUTATED	9	4	7	6
PIK3CA WILD-TYPE	25	27	38	11

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S162. Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
PIK3CA MUTATED	14	7	5
PIK3CA WILD-TYPE	41	41	22

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.228 (Fisher's exact test), Q value = 1

Table S163. Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
PIK3CA MUTATED	5	6	11	0	2
PIK3CA WILD-TYPE	31	22	22	5	15

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.643 (Fisher's exact test), Q value = 1

Table S164. Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
PIK3CA MUTATED	8	9	5	2
PIK3CA WILD-TYPE	35	27	16	17

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S165. Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
PIK3CA MUTATED	8	9	9
PIK3CA WILD-TYPE	27	46	30

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S166. Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
PIK3CA MUTATED	11	4	9	2
PIK3CA WILD-TYPE	33	29	24	17

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.786 (Fisher's exact test), Q value = 1

Table S167. Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
PIK3CA MUTATED	7	6	13
PIK3CA WILD-TYPE	30	30	44

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.46 (Fisher's exact test), Q value = 1

Table S168. Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
PIK3CA MUTATED	9	7	3	2	5
PIK3CA WILD-TYPE	20	29	24	12	19

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 1

Table S169. Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
PIK3CA MUTATED	8	2	5	11
PIK3CA WILD-TYPE	19	14	35	33

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.652 (Fisher's exact test), Q value = 1

Table S170. Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
PIK3CA MUTATED	6	2	4	4	1	9
PIK3CA WILD-TYPE	25	16	22	13	5	20

'RXRA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 1

Table S171. Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
RXRA MUTATED	5	5	2	0
RXRA WILD-TYPE	29	26	43	17

'RXRA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S172. Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
RXRA MUTATED	5	7	0
RXRA WILD-TYPE	50	41	27

'RXRA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 1

Table S173. Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
RXRA MUTATED	7	1	2	1	1
RXRA WILD-TYPE	29	27	31	4	16

'RXRA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.923 (Fisher's exact test), Q value = 1

Table S174. Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
RXRA MUTATED	5	4	1	2
RXRA WILD-TYPE	38	32	20	17

'RXRA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.596 (Fisher's exact test), Q value = 1

Table S175. Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
RXRA MUTATED	4	6	2
RXRA WILD-TYPE	31	49	37

'RXRA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S176. Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
RXRA MUTATED	5	4	2	1
RXRA WILD-TYPE	39	29	31	18

'RXRA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 1

Table S177. Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
RXRA MUTATED	3	5	4
RXRA WILD-TYPE	34	31	53

'RXRA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S178. Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
RXRA MUTATED	2	5	0	2	3
RXRA WILD-TYPE	27	31	27	12	21

'RXRA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.947 (Fisher's exact test), Q value = 1

Table S179. Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
RXRA MUTATED	2	2	4	4
RXRA WILD-TYPE	25	14	36	40

'RXRA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S180. Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
RXRA MUTATED	2	2	4	1	0	3
RXRA WILD-TYPE	29	16	22	16	6	26

'CREBBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 1

Table S181. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
CREBBP MUTATED	2	1	8	5
CREBBP WILD-TYPE	32	30	37	12

Figure S20. Get High-res Image Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CREBBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.709 (Fisher's exact test), Q value = 1

Table S182. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
CREBBP MUTATED	9	5	3
CREBBP WILD-TYPE	46	43	24

'CREBBP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.921 (Fisher's exact test), Q value = 1

Table S183. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
CREBBP MUTATED	4	4	5	0	1
CREBBP WILD-TYPE	32	24	28	5	16

'CREBBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.546 (Fisher's exact test), Q value = 1

Table S184. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
CREBBP MUTATED	6	3	4	1
CREBBP WILD-TYPE	37	33	17	18

'CREBBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 1

Table S185. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
CREBBP MUTATED	7	4	6
CREBBP WILD-TYPE	28	51	33

'CREBBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.467 (Fisher's exact test), Q value = 1

Table S186. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
CREBBP MUTATED	8	2	5	2
CREBBP WILD-TYPE	36	31	28	17

'CREBBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 1

Table S187. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
CREBBP MUTATED	6	3	8
CREBBP WILD-TYPE	31	33	49

'CREBBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 1

Table S188. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
CREBBP MUTATED	5	3	2	3	4
CREBBP WILD-TYPE	24	33	25	11	20

'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 1

Table S189. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
CREBBP MUTATED	6	1	3	7
CREBBP WILD-TYPE	21	15	37	37

'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.8 (Fisher's exact test), Q value = 1

Table S190. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
CREBBP MUTATED	6	2	2	2	0	5
CREBBP WILD-TYPE	25	16	24	15	6	24

'ERBB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.586 (Fisher's exact test), Q value = 1

Table S191. Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
ERBB3 MUTATED	4	5	3	2
ERBB3 WILD-TYPE	30	26	42	15

'ERBB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.617 (Fisher's exact test), Q value = 1

Table S192. Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
ERBB3 MUTATED	5	7	2
ERBB3 WILD-TYPE	50	41	25

'ERBB3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 1

Table S193. Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
ERBB3 MUTATED	6	3	3	1	1
ERBB3 WILD-TYPE	30	25	30	4	16

'ERBB3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.493 (Fisher's exact test), Q value = 1

Table S194. Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
ERBB3 MUTATED	6	6	1	1
ERBB3 WILD-TYPE	37	30	20	18

'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 1

Table S195. Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
ERBB3 MUTATED	4	7	3
ERBB3 WILD-TYPE	31	48	36

'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.887 (Fisher's exact test), Q value = 1

Table S196. Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
ERBB3 MUTATED	4	5	3	2
ERBB3 WILD-TYPE	40	28	30	17

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S197. Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
ERBB3 MUTATED	3	3	8
ERBB3 WILD-TYPE	34	33	49

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.654 (Fisher's exact test), Q value = 1

Table S198. Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
ERBB3 MUTATED	4	3	4	0	3
ERBB3 WILD-TYPE	25	33	23	14	21

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S199. Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
ERBB3 MUTATED	2	1	5	6
ERBB3 WILD-TYPE	25	15	35	38

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 1

Table S200. Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
ERBB3 MUTATED	3	1	2	1	2	5
ERBB3 WILD-TYPE	28	17	24	16	4	24

'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 1

Table S201. Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
FAT1 MUTATED	3	1	11	0
FAT1 WILD-TYPE	31	30	34	17

Figure S21. Get High-res Image Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.6 (Fisher's exact test), Q value = 1

Table S202. Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
FAT1 MUTATED	8	4	3
FAT1 WILD-TYPE	47	44	24

'FAT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.222 (Fisher's exact test), Q value = 1

Table S203. Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
FAT1 MUTATED	3	2	6	2	2
FAT1 WILD-TYPE	33	26	27	3	15

'FAT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 1

Table S204. Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
FAT1 MUTATED	4	4	5	2
FAT1 WILD-TYPE	39	32	16	17

'FAT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 1

Table S205. Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
FAT1 MUTATED	6	4	4
FAT1 WILD-TYPE	29	51	35

'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.958 (Fisher's exact test), Q value = 1

Table S206. Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
FAT1 MUTATED	4	4	4	2
FAT1 WILD-TYPE	40	29	29	17

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S207. Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
FAT1 MUTATED	6	3	6
FAT1 WILD-TYPE	31	33	51

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.843 (Fisher's exact test), Q value = 1

Table S208. Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
FAT1 MUTATED	5	3	3	1	3
FAT1 WILD-TYPE	24	33	24	13	21

'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 1

Table S209. Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
FAT1 MUTATED	5	0	4	6
FAT1 WILD-TYPE	22	16	36	38

'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 1

Table S210. Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
FAT1 MUTATED	4	0	1	3	2	5
FAT1 WILD-TYPE	27	18	25	14	4	24

'MLL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 1

Table S211. Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
MLL MUTATED	2	4	7	4
MLL WILD-TYPE	32	27	38	13

'MLL MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S212. Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
MLL MUTATED	8	6	4
MLL WILD-TYPE	47	42	23

'MLL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 1

Table S213. Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
MLL MUTATED	5	1	7	2	0
MLL WILD-TYPE	31	27	26	3	17

Figure S22. Get High-res Image Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'MLL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0048 (Fisher's exact test), Q value = 1

Table S214. Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
MLL MUTATED	8	1	6	0
MLL WILD-TYPE	35	35	15	19

Figure S23. Get High-res Image Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MLL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 1

Table S215. Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
MLL MUTATED	5	5	8
MLL WILD-TYPE	30	50	31

'MLL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S216. Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
MLL MUTATED	7	2	6	3
MLL WILD-TYPE	37	31	27	16

'MLL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.947 (Fisher's exact test), Q value = 1

Table S217. Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
MLL MUTATED	6	5	7
MLL WILD-TYPE	31	31	50

'MLL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S218. Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
MLL MUTATED	4	6	1	3	4
MLL WILD-TYPE	25	30	26	11	20

'MLL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.177 (Fisher's exact test), Q value = 1

Table S219. Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
MLL MUTATED	6	2	2	7
MLL WILD-TYPE	21	14	38	37

'MLL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S220. Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
MLL MUTATED	5	3	1	4	0	4
MLL WILD-TYPE	26	15	25	13	6	25

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S221. Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
HRAS MUTATED	2	2	2	0
HRAS WILD-TYPE	32	29	43	17

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.308 (Fisher's exact test), Q value = 1

Table S222. Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
HRAS MUTATED	2	4	0
HRAS WILD-TYPE	53	44	27

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 1

Table S223. Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
HRAS MUTATED	2	0	1	2	0
HRAS WILD-TYPE	34	28	32	3	17

Figure S24. Get High-res Image Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.338 (Fisher's exact test), Q value = 1

Table S224. Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
HRAS MUTATED	3	0	1	1
HRAS WILD-TYPE	40	36	20	18

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.881 (Fisher's exact test), Q value = 1

Table S225. Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
HRAS MUTATED	2	2	2
HRAS WILD-TYPE	33	53	37

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.643 (Fisher's exact test), Q value = 1

Table S226. Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
HRAS MUTATED	2	1	3	0
HRAS WILD-TYPE	42	32	30	19

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.657 (Fisher's exact test), Q value = 1

Table S227. Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
HRAS MUTATED	1	1	4
HRAS WILD-TYPE	36	35	53

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.643 (Fisher's exact test), Q value = 1

Table S228. Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
HRAS MUTATED	1	1	3	0	1
HRAS WILD-TYPE	28	35	24	14	23

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S229. Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
HRAS MUTATED	1	1	3	1
HRAS WILD-TYPE	26	15	37	43

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.771 (Fisher's exact test), Q value = 1

Table S230. Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
HRAS MUTATED	1	1	1	0	0	3
HRAS WILD-TYPE	30	17	25	17	6	26

'ACRC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S231. Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
ACRC MUTATED	1	2	1	0
ACRC WILD-TYPE	33	29	44	17

'ACRC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 1

Table S232. Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
ACRC MUTATED	1	0	3
ACRC WILD-TYPE	54	48	24

Figure S25. Get High-res Image Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ACRC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.855 (Fisher's exact test), Q value = 1

Table S233. Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
ACRC MUTATED	1	1	2	0	0
ACRC WILD-TYPE	35	27	31	5	17

'ACRC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S234. Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
ACRC MUTATED	1	2	1	0
ACRC WILD-TYPE	42	34	20	19

'ACRC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 1

Table S235. Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
ACRC MUTATED	0	3	1
ACRC WILD-TYPE	35	52	38

'ACRC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S236. Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
ACRC MUTATED	1	2	1	0
ACRC WILD-TYPE	43	31	32	19

'ACRC MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S237. Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
ACRC MUTATED	1	1	2
ACRC WILD-TYPE	36	35	55

'ACRC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.556 (Fisher's exact test), Q value = 1

Table S238. Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
ACRC MUTATED	1	0	1	1	1
ACRC WILD-TYPE	28	36	26	13	23

'ACRC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S239. Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
ACRC MUTATED	1	0	2	1
ACRC WILD-TYPE	26	16	38	43

'ACRC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.855 (Fisher's exact test), Q value = 1

Table S240. Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
ACRC MUTATED	1	0	2	0	0	1
ACRC WILD-TYPE	30	18	24	17	6	28

'TXNIP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.919 (Fisher's exact test), Q value = 1

Table S241. Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
TXNIP MUTATED	3	1	3	1
TXNIP WILD-TYPE	31	30	42	16

'TXNIP MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S242. Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
TXNIP MUTATED	3	5	1
TXNIP WILD-TYPE	52	43	26

'TXNIP MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S243. Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
TXNIP MUTATED	2	2	4	0	1
TXNIP WILD-TYPE	34	26	29	5	16

'TXNIP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.706 (Fisher's exact test), Q value = 1

Table S244. Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
TXNIP MUTATED	3	2	3	1
TXNIP WILD-TYPE	40	34	18	18

'TXNIP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S245. Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
TXNIP MUTATED	2	4	3
TXNIP WILD-TYPE	33	51	36

'TXNIP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.238 (Fisher's exact test), Q value = 1

Table S246. Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
TXNIP MUTATED	6	1	2	0
TXNIP WILD-TYPE	38	32	31	19

'TXNIP MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S247. Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
TXNIP MUTATED	3	2	4
TXNIP WILD-TYPE	34	34	53

'TXNIP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.985 (Fisher's exact test), Q value = 1

Table S248. Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
TXNIP MUTATED	2	3	2	1	1
TXNIP WILD-TYPE	27	33	25	13	23

'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S249. Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
TXNIP MUTATED	1	2	2	4
TXNIP WILD-TYPE	26	14	38	40

'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S250. Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
TXNIP MUTATED	2	2	2	2	0	1
TXNIP WILD-TYPE	29	16	24	15	6	28

'ECM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 1

Table S251. Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
ECM1 MUTATED	1	1	1	2
ECM1 WILD-TYPE	33	30	44	15

'ECM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.723 (Fisher's exact test), Q value = 1

Table S252. Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
ECM1 MUTATED	3	2	0
ECM1 WILD-TYPE	52	46	27

'ECM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.945 (Fisher's exact test), Q value = 1

Table S253. Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
ECM1 MUTATED	2	1	2	0	0
ECM1 WILD-TYPE	34	27	31	5	17

'ECM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.181 (Fisher's exact test), Q value = 1

Table S254. Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
ECM1 MUTATED	1	4	0	0
ECM1 WILD-TYPE	42	32	21	19

'ECM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S255. Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
ECM1 MUTATED	2	2	1
ECM1 WILD-TYPE	33	53	38

'ECM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.476 (Fisher's exact test), Q value = 1

Table S256. Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
ECM1 MUTATED	1	1	1	2
ECM1 WILD-TYPE	43	32	32	17

'ECM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 1

Table S257. Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
ECM1 MUTATED	3	0	2
ECM1 WILD-TYPE	34	36	55

'ECM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0806 (Fisher's exact test), Q value = 1

Table S258. Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
ECM1 MUTATED	0	1	0	1	3
ECM1 WILD-TYPE	29	35	27	13	21

'ECM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 1

Table S259. Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
ECM1 MUTATED	1	0	1	3
ECM1 WILD-TYPE	26	16	39	41

'ECM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.713 (Fisher's exact test), Q value = 1

Table S260. Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
ECM1 MUTATED	3	0	1	0	0	1
ECM1 WILD-TYPE	28	18	25	17	6	28

'KLF5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S261. Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
KLF5 MUTATED	3	2	4	1
KLF5 WILD-TYPE	31	29	41	16

'KLF5 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S262. Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
KLF5 MUTATED	4	5	1
KLF5 WILD-TYPE	51	43	26

'KLF5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.301 (Fisher's exact test), Q value = 1

Table S263. Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
KLF5 MUTATED	4	1	4	1	0
KLF5 WILD-TYPE	32	27	29	4	17

'KLF5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 1

Table S264. Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
KLF5 MUTATED	6	2	2	0
KLF5 WILD-TYPE	37	34	19	19

'KLF5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S265. Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
KLF5 MUTATED	2	5	3
KLF5 WILD-TYPE	33	50	36

'KLF5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.435 (Fisher's exact test), Q value = 1

Table S266. Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
KLF5 MUTATED	2	3	2	3
KLF5 WILD-TYPE	42	30	31	16

'KLF5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.843 (Fisher's exact test), Q value = 1

Table S267. Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
KLF5 MUTATED	2	3	5
KLF5 WILD-TYPE	35	33	52

'KLF5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S268. Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
KLF5 MUTATED	0	3	2	3	2
KLF5 WILD-TYPE	29	33	25	11	22

'KLF5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.313 (Fisher's exact test), Q value = 1

Table S269. Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
KLF5 MUTATED	0	2	3	4
KLF5 WILD-TYPE	27	14	37	40

'KLF5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S270. Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
KLF5 MUTATED	2	2	2	3	0	0
KLF5 WILD-TYPE	29	16	24	14	6	29

'RBM26 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 1

Table S271. Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
RBM26 MUTATED	2	0	2	5
RBM26 WILD-TYPE	32	31	43	12

Figure S26. Get High-res Image Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RBM26 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S272. Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
RBM26 MUTATED	5	3	1
RBM26 WILD-TYPE	50	45	26

'RBM26 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 1

Table S273. Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
RBM26 MUTATED	1	2	5	0	0
RBM26 WILD-TYPE	35	26	28	5	17

'RBM26 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.726 (Fisher's exact test), Q value = 1

Table S274. Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
RBM26 MUTATED	3	3	2	0
RBM26 WILD-TYPE	40	33	19	19

'RBM26 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 1

Table S275. Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
RBM26 MUTATED	4	2	3
RBM26 WILD-TYPE	31	53	36

'RBM26 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.749 (Fisher's exact test), Q value = 1

Table S276. Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
RBM26 MUTATED	3	1	3	2
RBM26 WILD-TYPE	41	32	30	17

'RBM26 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 1

Table S277. Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
RBM26 MUTATED	3	0	6
RBM26 WILD-TYPE	34	36	51

'RBM26 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 1

Table S278. Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
RBM26 MUTATED	2	0	2	2	3
RBM26 WILD-TYPE	27	36	25	12	21

'RBM26 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.809 (Fisher's exact test), Q value = 1

Table S279. Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
RBM26 MUTATED	2	0	3	4
RBM26 WILD-TYPE	25	16	37	40

'RBM26 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 1

Table S280. Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
RBM26 MUTATED	2	0	1	2	2	2
RBM26 WILD-TYPE	29	18	25	15	4	27

'RAD51C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S281. Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
RAD51C MUTATED	2	0	1	1
RAD51C WILD-TYPE	32	31	44	16

'RAD51C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 1

Table S282. Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
RAD51C MUTATED	1	3	0
RAD51C WILD-TYPE	54	45	27

'RAD51C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.18 (Fisher's exact test), Q value = 1

Table S283. Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
RAD51C MUTATED	1	0	2	1	0
RAD51C WILD-TYPE	35	28	31	4	17

'RAD51C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S284. Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
RAD51C MUTATED	2	1	1	0
RAD51C WILD-TYPE	41	35	20	19

'RAD51C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 1

Table S285. Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
RAD51C MUTATED	3	0	1
RAD51C WILD-TYPE	32	55	38

Figure S27. Get High-res Image Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RAD51C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S286. Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
RAD51C MUTATED	2	0	1	1
RAD51C WILD-TYPE	42	33	32	18

'RAD51C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.811 (Fisher's exact test), Q value = 1

Table S287. Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
RAD51C MUTATED	2	1	1
RAD51C WILD-TYPE	35	35	56

'RAD51C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S288. Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
RAD51C MUTATED	1	1	0	0	2
RAD51C WILD-TYPE	28	35	27	14	22

'RAD51C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.364 (Fisher's exact test), Q value = 1

Table S289. Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
RAD51C MUTATED	1	0	0	3
RAD51C WILD-TYPE	26	16	40	41

'RAD51C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S290. Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
RAD51C MUTATED	2	0	0	0	0	2
RAD51C WILD-TYPE	29	18	26	17	6	27

'CEP192 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S291. Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
CEP192 MUTATED	1	2	2	0
CEP192 WILD-TYPE	33	29	43	17

'CEP192 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.725 (Fisher's exact test), Q value = 1

Table S292. Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
CEP192 MUTATED	3	2	0
CEP192 WILD-TYPE	52	46	27

'CEP192 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.895 (Fisher's exact test), Q value = 1

Table S293. Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
CEP192 MUTATED	1	1	2	0	1
CEP192 WILD-TYPE	35	27	31	5	16

'CEP192 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 1

Table S294. Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
CEP192 MUTATED	3	1	0	1
CEP192 WILD-TYPE	40	35	21	18

'CEP192 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.731 (Fisher's exact test), Q value = 1

Table S295. Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
CEP192 MUTATED	2	2	1
CEP192 WILD-TYPE	33	53	38

'CEP192 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.537 (Fisher's exact test), Q value = 1

Table S296. Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
CEP192 MUTATED	3	0	1	1
CEP192 WILD-TYPE	41	33	32	18

'CEP192 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 1

Table S297. Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
CEP192 MUTATED	0	1	4
CEP192 WILD-TYPE	37	35	53

'CEP192 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 1

Table S298. Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
CEP192 MUTATED	1	1	0	3	0
CEP192 WILD-TYPE	28	35	27	11	24

Figure S28. Get High-res Image Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CEP192 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.8 (Fisher's exact test), Q value = 1

Table S299. Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
CEP192 MUTATED	1	0	1	3
CEP192 WILD-TYPE	26	16	39	41

'CEP192 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 1

Table S300. Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
CEP192 MUTATED	0	0	1	2	0	2
CEP192 WILD-TYPE	31	18	25	15	6	27

'ASXL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 1

Table S301. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
ASXL2 MUTATED	1	4	4	0
ASXL2 WILD-TYPE	33	27	41	17

'ASXL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S302. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
ASXL2 MUTATED	3	4	2
ASXL2 WILD-TYPE	52	44	25

'ASXL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 1

Table S303. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
ASXL2 MUTATED	4	1	3	1	0
ASXL2 WILD-TYPE	32	27	30	4	17

'ASXL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.364 (Fisher's exact test), Q value = 1

Table S304. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
ASXL2 MUTATED	4	2	3	0
ASXL2 WILD-TYPE	39	34	18	19

'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 1

Table S305. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
ASXL2 MUTATED	1	3	5
ASXL2 WILD-TYPE	34	52	34

'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test), Q value = 1

Table S306. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
ASXL2 MUTATED	6	0	2	1
ASXL2 WILD-TYPE	38	33	31	18

'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.747 (Fisher's exact test), Q value = 1

Table S307. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
ASXL2 MUTATED	3	3	3
ASXL2 WILD-TYPE	34	33	54

'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.643 (Fisher's exact test), Q value = 1

Table S308. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
ASXL2 MUTATED	1	3	1	2	2
ASXL2 WILD-TYPE	28	33	26	12	22

'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S309. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
ASXL2 MUTATED	0	3	3	3
ASXL2 WILD-TYPE	27	13	37	41

'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 1

Table S310. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
ASXL2 MUTATED	2	3	1	2	1	0
ASXL2 WILD-TYPE	29	15	25	15	5	29

'PSIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 1

Table S311. Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
PSIP1 MUTATED	3	1	2	1
PSIP1 WILD-TYPE	31	30	43	16

'PSIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 1

Table S312. Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
PSIP1 MUTATED	1	5	1
PSIP1 WILD-TYPE	54	43	26

'PSIP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S313. Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
PSIP1 MUTATED	3	2	0	1	0
PSIP1 WILD-TYPE	33	26	33	4	17

'PSIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 1

Table S314. Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
PSIP1 MUTATED	4	2	0	0
PSIP1 WILD-TYPE	39	34	21	19

'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.884 (Fisher's exact test), Q value = 1

Table S315. Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
PSIP1 MUTATED	1	4	2
PSIP1 WILD-TYPE	34	51	37

'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.279 (Fisher's exact test), Q value = 1

Table S316. Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
PSIP1 MUTATED	1	4	1	1
PSIP1 WILD-TYPE	43	29	32	18

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S317. Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
PSIP1 MUTATED	1	2	4
PSIP1 WILD-TYPE	36	34	53

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.561 (Fisher's exact test), Q value = 1

Table S318. Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
PSIP1 MUTATED	0	3	2	1	1
PSIP1 WILD-TYPE	29	33	25	13	23

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 1

Table S319. Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
PSIP1 MUTATED	1	1	4	1
PSIP1 WILD-TYPE	26	15	36	43

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 1

Table S320. Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
PSIP1 MUTATED	1	1	2	0	2	1
PSIP1 WILD-TYPE	30	17	24	17	4	28

'ZNF513 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 1

Table S321. Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
ZNF513 MUTATED	4	1	2	0
ZNF513 WILD-TYPE	30	30	43	17

'ZNF513 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S322. Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
ZNF513 MUTATED	3	3	1
ZNF513 WILD-TYPE	52	45	26

'ZNF513 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 1

Table S323. Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
ZNF513 MUTATED	3	0	1	1	1
ZNF513 WILD-TYPE	33	28	32	4	16

'ZNF513 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.413 (Fisher's exact test), Q value = 1

Table S324. Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
ZNF513 MUTATED	4	1	0	1
ZNF513 WILD-TYPE	39	35	21	18

'ZNF513 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S325. Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
ZNF513 MUTATED	3	3	1
ZNF513 WILD-TYPE	32	52	38

'ZNF513 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 1

Table S326. Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
ZNF513 MUTATED	3	2	0	2
ZNF513 WILD-TYPE	41	31	33	17

'ZNF513 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S327. Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
ZNF513 MUTATED	3	2	2
ZNF513 WILD-TYPE	34	34	55

'ZNF513 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 1

Table S328. Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
ZNF513 MUTATED	0	2	1	1	3
ZNF513 WILD-TYPE	29	34	26	13	21

'ZNF513 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S329. Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
ZNF513 MUTATED	1	0	3	3
ZNF513 WILD-TYPE	26	16	37	41

'ZNF513 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S330. Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
ZNF513 MUTATED	3	0	3	0	0	1
ZNF513 WILD-TYPE	28	18	23	17	6	28

'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 1

Table S331. Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
FOXA1 MUTATED	5	0	1	1
FOXA1 WILD-TYPE	29	31	44	16

Figure S29. Get High-res Image Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S332. Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
FOXA1 MUTATED	3	3	1
FOXA1 WILD-TYPE	52	45	26

'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 1

Table S333. Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
FOXA1 MUTATED	2	2	1	1	1
FOXA1 WILD-TYPE	34	26	32	4	16

'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.697 (Fisher's exact test), Q value = 1

Table S334. Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
FOXA1 MUTATED	4	2	1	0
FOXA1 WILD-TYPE	39	34	20	19

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S335. Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
FOXA1 MUTATED	4	2	1
FOXA1 WILD-TYPE	31	53	38

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.95 (Fisher's exact test), Q value = 1

Table S336. Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
FOXA1 MUTATED	3	2	1	1
FOXA1 WILD-TYPE	41	31	32	18

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S337. Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
FOXA1 MUTATED	2	2	3
FOXA1 WILD-TYPE	35	34	54

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.936 (Fisher's exact test), Q value = 1

Table S338. Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
FOXA1 MUTATED	1	2	1	1	2
FOXA1 WILD-TYPE	28	34	26	13	22

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S339. Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
FOXA1 MUTATED	0	2	2	3
FOXA1 WILD-TYPE	27	14	38	41

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S340. Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
FOXA1 MUTATED	2	2	2	1	0	0
FOXA1 WILD-TYPE	29	16	24	16	6	29

'TRIP11 MUTATION STATUS' versus 'CN_CNMF'

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

Table S341. Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	31	45	17
TRIP11 MUTATED	1	1	2	0
TRIP11 WILD-TYPE	33	30	43	17

'TRIP11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.843 (Fisher's exact test), Q value = 1

Table S342. Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	48	27
TRIP11 MUTATED	3	1	1
TRIP11 WILD-TYPE	52	47	26

'TRIP11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S343. Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	28	33	5	17
TRIP11 MUTATED	1	2	1	0	1
TRIP11 WILD-TYPE	35	26	32	5	16

'TRIP11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 1

Table S344. Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	36	21	19
TRIP11 MUTATED	4	1	0	0
TRIP11 WILD-TYPE	39	35	21	19

'TRIP11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.731 (Fisher's exact test), Q value = 1

Table S345. Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	55	39
TRIP11 MUTATED	2	2	1
TRIP11 WILD-TYPE	33	53	38

'TRIP11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.929 (Fisher's exact test), Q value = 1

Table S346. Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	33	33	19
TRIP11 MUTATED	2	2	1	0
TRIP11 WILD-TYPE	42	31	32	19

'TRIP11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S347. Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	36	57
TRIP11 MUTATED	0	3	2
TRIP11 WILD-TYPE	37	33	55

'TRIP11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 1

Table S348. Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	29	36	27	14	24
TRIP11 MUTATED	0	3	1	1	0
TRIP11 WILD-TYPE	29	33	26	13	24

'TRIP11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S349. Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	16	40	44
TRIP11 MUTATED	1	0	2	2
TRIP11 WILD-TYPE	26	16	38	42

'TRIP11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S350. Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	31	18	26	17	6	29
TRIP11 MUTATED	1	1	2	1	0	0
TRIP11 WILD-TYPE	30	17	24	16	6	29

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = BLCA-TP.transferedmergedcluster.txt
Number of patients = 130
Number of significantly mutated genes = 35
Number of Molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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