Correlation between gene mutation status and molecular subtypes

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, no significant finding detected with P value < 0.05 and Q value < 0.25.

No gene mutations related to molecuar subtypes.

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, no significant finding 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
TP53	64 (49%)	66	0.109 (1.00)	0.148 (1.00)	0.04 (1.00)	0.00663 (1.00)	0.244 (1.00)	0.299 (1.00)	0.453 (1.00)	0.315 (1.00)	0.46 (1.00)	0.316 (1.00)
KDM6A	31 (24%)	99	0.154 (1.00)	0.824 (1.00)	0.34 (1.00)	0.136 (1.00)	0.608 (1.00)	0.668 (1.00)	0.121 (1.00)	0.501 (1.00)	0.658 (1.00)	0.326 (1.00)
RB1	17 (13%)	113	0.00472 (1.00)	0.743 (1.00)	0.592 (1.00)	0.316 (1.00)	0.605 (1.00)	0.54 (1.00)	1 (1.00)	0.346 (1.00)	0.217 (1.00)	0.432 (1.00)
ARID1A	32 (25%)	98	0.68 (1.00)	0.828 (1.00)	0.589 (1.00)	0.0803 (1.00)	0.378 (1.00)	0.564 (1.00)	0.125 (1.00)	0.0926 (1.00)	0.376 (1.00)	0.282 (1.00)
CDKN1A	18 (14%)	112	0.9 (1.00)	0.0785 (1.00)	0.831 (1.00)	0.824 (1.00)	0.73 (1.00)	0.498 (1.00)	0.382 (1.00)	0.91 (1.00)	0.842 (1.00)	0.53 (1.00)
MLL2	36 (28%)	94	0.425 (1.00)	0.814 (1.00)	0.366 (1.00)	0.328 (1.00)	0.199 (1.00)	0.308 (1.00)	0.326 (1.00)	0.292 (1.00)	0.71 (1.00)	0.589 (1.00)
ELF3	11 (8%)	119	0.784 (1.00)	0.208 (1.00)	0.759 (1.00)	0.383 (1.00)	0.669 (1.00)	0.222 (1.00)	0.569 (1.00)	0.847 (1.00)	0.916 (1.00)	0.456 (1.00)
FGFR3	16 (12%)	114	0.0186 (1.00)	0.232 (1.00)	0.0924 (1.00)	0.00986 (1.00)	0.186 (1.00)	0.0473 (1.00)	0.197 (1.00)	0.00929 (1.00)	0.011 (1.00)	0.0414 (1.00)
CDKN2A	7 (5%)	123	0.141 (1.00)	0.563 (1.00)	0.389 (1.00)	0.183 (1.00)	0.799 (1.00)	0.866 (1.00)	0.331 (1.00)	0.283 (1.00)	0.301 (1.00)	1 (1.00)
STAG2	14 (11%)	116	0.318 (1.00)	0.183 (1.00)	0.301 (1.00)	0.553 (1.00)	0.322 (1.00)	0.144 (1.00)	0.19 (1.00)	0.26 (1.00)	0.249 (1.00)	0.0177 (1.00)
NFE2L2	11 (8%)	119	0.117 (1.00)	0.655 (1.00)	0.307 (1.00)	0.725 (1.00)	0.0957 (1.00)	0.0416 (1.00)	1 (1.00)	0.0163 (1.00)	0.843 (1.00)	0.75 (1.00)
ERCC2	16 (12%)	114	0.618 (1.00)	0.448 (1.00)	0.0867 (1.00)	0.0178 (1.00)	0.174 (1.00)	0.123 (1.00)	0.395 (1.00)	0.105 (1.00)	0.78 (1.00)	0.933 (1.00)
FBXW7	13 (10%)	117	0.288 (1.00)	0.0415 (1.00)	0.262 (1.00)	0.532 (1.00)	0.104 (1.00)	0.0904 (1.00)	0.214 (1.00)	0.0284 (1.00)	0.0264 (1.00)	0.187 (1.00)
RHOB	7 (5%)	123	1 (1.00)	0.705 (1.00)	0.564 (1.00)	0.317 (1.00)	0.796 (1.00)	0.345 (1.00)	0.704 (1.00)	0.544 (1.00)	0.299 (1.00)	0.498 (1.00)
TSC1	11 (8%)	119	0.167 (1.00)	0.699 (1.00)	0.416 (1.00)	0.569 (1.00)	0.244 (1.00)	0.141 (1.00)	0.621 (1.00)	0.496 (1.00)	0.413 (1.00)	0.0855 (1.00)
FOXQ1	7 (5%)	123	0.423 (1.00)	0.378 (1.00)	0.467 (1.00)	0.366 (1.00)	0.884 (1.00)	1 (1.00)	0.152 (1.00)	0.294 (1.00)	0.299 (1.00)	0.422 (1.00)
PIK3CA	26 (20%)	104	0.407 (1.00)	0.961 (1.00)	0.224 (1.00)	0.642 (1.00)	0.432 (1.00)	0.166 (1.00)	0.789 (1.00)	0.537 (1.00)	0.419 (1.00)	0.6 (1.00)
RXRA	12 (9%)	118	0.119 (1.00)	0.193 (1.00)	0.168 (1.00)	0.923 (1.00)	0.591 (1.00)	0.321 (1.00)	0.549 (1.00)	0.336 (1.00)	0.674 (1.00)	0.315 (1.00)
CREBBP	17 (13%)	113	0.299 (1.00)	0.849 (1.00)	0.921 (1.00)	0.546 (1.00)	0.213 (1.00)	0.288 (1.00)	0.193 (1.00)	0.911 (1.00)	0.651 (1.00)	0.247 (1.00)
ERBB3	14 (11%)	116	0.936 (1.00)	0.593 (1.00)	0.693 (1.00)	0.493 (1.00)	0.675 (1.00)	0.842 (1.00)	0.821 (1.00)	0.731 (1.00)	0.573 (1.00)	1 (1.00)
FAT1	15 (12%)	115	0.205 (1.00)	0.365 (1.00)	0.22 (1.00)	0.436 (1.00)	0.37 (1.00)	1 (1.00)	0.453 (1.00)	0.288 (1.00)	0.0884 (1.00)	0.0737 (1.00)
MLL	18 (14%)	112	0.845 (1.00)	0.984 (1.00)	0.0283 (1.00)	0.00499 (1.00)	0.325 (1.00)	0.532 (1.00)	0.813 (1.00)	0.705 (1.00)	0.891 (1.00)	0.881 (1.00)
HRAS	6 (5%)	124	0.57 (1.00)	0.799 (1.00)	0.0168 (1.00)	0.339 (1.00)	0.88 (1.00)	0.439 (1.00)	0.57 (1.00)	0.648 (1.00)	0.197 (1.00)	0.258 (1.00)
ACRC	4 (3%)	126	0.281 (1.00)	0.11 (1.00)	0.855 (1.00)	0.76 (1.00)	1 (1.00)	0.912 (1.00)	1 (1.00)	0.87 (1.00)	1 (1.00)	0.812 (1.00)
TXNIP	9 (7%)	121	0.588 (1.00)	0.274 (1.00)	0.872 (1.00)	0.703 (1.00)	1 (1.00)	0.0801 (1.00)	0.909 (1.00)	0.983 (1.00)	0.732 (1.00)	0.897 (1.00)
ECM1	5 (4%)	125	0.0794 (1.00)	0.268 (1.00)	0.947 (1.00)	0.181 (1.00)	0.733 (1.00)	0.55 (1.00)	0.52 (1.00)	0.186 (1.00)	0.416 (1.00)	0.698 (1.00)
KLF5	10 (8%)	120	0.0917 (1.00)	0.778 (1.00)	0.303 (1.00)	0.31 (1.00)	0.915 (1.00)	0.679 (1.00)	0.706 (1.00)	0.23 (1.00)	0.192 (1.00)	0.0234 (1.00)
RBM26	9 (7%)	121	0.619 (1.00)	0.964 (1.00)	0.255 (1.00)	0.725 (1.00)	0.382 (1.00)	0.566 (1.00)	0.0938 (1.00)	0.288 (1.00)	0.389 (1.00)	0.246 (1.00)
RAD51C	4 (3%)	126	1 (1.00)	0.165 (1.00)	0.182 (1.00)	1 (1.00)	0.0372 (1.00)	0.21 (1.00)	0.134 (1.00)	0.449 (1.00)	0.134 (1.00)	0.375 (1.00)
CEP192	5 (4%)	125	0.85 (1.00)	0.725 (1.00)	0.895 (1.00)	0.696 (1.00)	0.733 (1.00)	0.587 (1.00)	0.734 (1.00)	0.0615 (1.00)	0.591 (1.00)	0.699 (1.00)
ASXL2	9 (7%)	121	0.0475 (1.00)	0.508 (1.00)	0.348 (1.00)	0.365 (1.00)	0.25 (1.00)	0.817 (1.00)	0.91 (1.00)	0.399 (1.00)	0.484 (1.00)	0.454 (1.00)
PSIP1	7 (5%)	123	0.371 (1.00)	0.625 (1.00)	0.138 (1.00)	0.385 (1.00)	0.884 (1.00)	0.509 (1.00)	0.483 (1.00)	0.847 (1.00)	0.536 (1.00)	0.191 (1.00)
ZNF513	7 (5%)	123	0.16 (1.00)	0.704 (1.00)	0.206 (1.00)	0.414 (1.00)	0.48 (1.00)	0.335 (1.00)	0.89 (1.00)	0.761 (1.00)	1 (1.00)	1 (1.00)
FOXA1	7 (5%)	123	0.611 (1.00)	0.91 (1.00)	0.539 (1.00)	0.694 (1.00)	0.257 (1.00)	0.908 (1.00)	0.888 (1.00)	0.647 (1.00)	0.675 (1.00)	0.661 (1.00)
TRIP11	5 (4%)	125	0.822 (1.00)	0.531 (1.00)	0.804 (1.00)	0.288 (1.00)	0.731 (1.00)	0.869 (1.00)	0.316 (1.00)	0.0933 (1.00)	0.34 (1.00)	0.368 (1.00)

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	42	54
TP53 MUTATED	20	21	22
TP53 WILD-TYPE	11	21	32

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.148 (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	CLUS_4
ALL	42	30	33	25
TP53 MUTATED	21	19	16	8
TP53 WILD-TYPE	21	11	17	17

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.04 (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 S1. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00663 (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 S2. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.244 (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	54	35	40
TP53 MUTATED	22	20	22
TP53 WILD-TYPE	32	15	18

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.299 (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	39	21	38	31
TP53 MUTATED	16	14	18	16
TP53 WILD-TYPE	23	7	20	15

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.453 (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	35	52	43
TP53 MUTATED	14	27	23
TP53 WILD-TYPE	21	25	20

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.315 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
TP53 MUTATED	9	6	8	9	15	10	7
TP53 WILD-TYPE	15	7	5	5	12	7	15

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	60	46
TP53 MUTATED	9	31	24
TP53 WILD-TYPE	15	29	22

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.316 (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
ALL	23	74	33
TP53 MUTATED	8	38	18
TP53 WILD-TYPE	15	36	15

'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.154 (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
ALL	31	42	54
KDM6A MUTATED	10	6	15
KDM6A WILD-TYPE	21	36	39

'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.824 (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	CLUS_4
ALL	42	30	33	25
KDM6A MUTATED	9	9	8	5
KDM6A WILD-TYPE	33	21	25	20

'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.34 (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 = 0.136 (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 = 0.608 (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	54	35	40
KDM6A MUTATED	12	7	12
KDM6A WILD-TYPE	42	28	28

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.668 (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	39	21	38	31
KDM6A MUTATED	9	3	10	9
KDM6A WILD-TYPE	30	18	28	22

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.121 (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	35	52	43
KDM6A MUTATED	4	15	12
KDM6A WILD-TYPE	31	37	31

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.501 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
KDM6A MUTATED	3	2	3	3	8	7	5
KDM6A WILD-TYPE	21	11	10	11	19	10	17

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.658 (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
ALL	24	60	46
KDM6A MUTATED	4	16	11
KDM6A WILD-TYPE	20	44	35

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.326 (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
ALL	23	74	33
KDM6A MUTATED	3	18	10
KDM6A WILD-TYPE	20	56	23

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00472 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	42	54
RB1 MUTATED	4	11	2
RB1 WILD-TYPE	27	31	52

Figure S3. Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.743 (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	CLUS_4
ALL	42	30	33	25
RB1 MUTATED	7	3	5	2
RB1 WILD-TYPE	35	27	28	23

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.592 (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 = 0.316 (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 = 0.605 (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	54	35	40
RB1 MUTATED	6	4	7
RB1 WILD-TYPE	48	31	33

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.54 (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	39	21	38	31
RB1 MUTATED	3	3	5	6
RB1 WILD-TYPE	36	18	33	25

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (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	35	52	43
RB1 MUTATED	4	7	6
RB1 WILD-TYPE	31	45	37

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.346 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
RB1 MUTATED	1	3	3	1	3	4	2
RB1 WILD-TYPE	23	10	10	13	24	13	20

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.217 (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
ALL	24	60	46
RB1 MUTATED	1	11	5
RB1 WILD-TYPE	23	49	41

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.432 (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
ALL	23	74	33
RB1 MUTATED	1	12	4
RB1 WILD-TYPE	22	62	29

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.68 (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
ALL	31	42	54
ARID1A MUTATED	6	12	14
ARID1A WILD-TYPE	25	30	40

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.828 (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	CLUS_4
ALL	42	30	33	25
ARID1A MUTATED	11	9	7	5
ARID1A WILD-TYPE	31	21	26	20

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.589 (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 = 0.0803 (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 = 0.378 (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	54	35	40
ARID1A MUTATED	14	11	7
ARID1A WILD-TYPE	40	24	33

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.564 (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	39	21	38	31
ARID1A MUTATED	8	7	11	6
ARID1A WILD-TYPE	31	14	27	25

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.125 (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	35	52	43
ARID1A MUTATED	10	8	14
ARID1A WILD-TYPE	25	44	29

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0926 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
ARID1A MUTATED	8	3	2	2	12	3	2
ARID1A WILD-TYPE	16	10	11	12	15	14	20

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.376 (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
ALL	24	60	46
ARID1A MUTATED	7	17	8
ARID1A WILD-TYPE	17	43	38

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.282 (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
ALL	23	74	33
ARID1A MUTATED	7	20	5
ARID1A WILD-TYPE	16	54	28

'CDKN1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.9 (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
ALL	31	42	54
CDKN1A MUTATED	5	5	8
CDKN1A WILD-TYPE	26	37	46

'CDKN1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0785 (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	CLUS_4
ALL	42	30	33	25
CDKN1A MUTATED	7	1	8	2
CDKN1A WILD-TYPE	35	29	25	23

'CDKN1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.831 (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 = 0.824 (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 = 0.73 (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	54	35	40
CDKN1A MUTATED	6	6	6
CDKN1A WILD-TYPE	48	29	34

'CDKN1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.498 (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	39	21	38	31
CDKN1A MUTATED	7	4	3	4
CDKN1A WILD-TYPE	32	17	35	27

'CDKN1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.382 (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	35	52	43
CDKN1A MUTATED	7	5	6
CDKN1A WILD-TYPE	28	47	37

'CDKN1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.91 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
CDKN1A MUTATED	5	2	2	2	3	1	3
CDKN1A WILD-TYPE	19	11	11	12	24	16	19

'CDKN1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.842 (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
ALL	24	60	46
CDKN1A MUTATED	4	7	7
CDKN1A WILD-TYPE	20	53	39

'CDKN1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.53 (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
ALL	23	74	33
CDKN1A MUTATED	5	9	4
CDKN1A WILD-TYPE	18	65	29

'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.425 (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
ALL	31	42	54
MLL2 MUTATED	11	11	12
MLL2 WILD-TYPE	20	31	42

'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.814 (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	CLUS_4
ALL	42	30	33	25
MLL2 MUTATED	13	9	7	7
MLL2 WILD-TYPE	29	21	26	18

'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.366 (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 = 0.199 (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	54	35	40
MLL2 MUTATED	12	8	15
MLL2 WILD-TYPE	42	27	25

'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.308 (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	39	21	38	31
MLL2 MUTATED	8	4	11	12
MLL2 WILD-TYPE	31	17	27	19

'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.326 (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	35	52	43
MLL2 MUTATED	9	18	9
MLL2 WILD-TYPE	26	34	34

'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.292 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
MLL2 MUTATED	6	3	7	3	6	7	4
MLL2 WILD-TYPE	18	10	6	11	21	10	18

'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.71 (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
ALL	24	60	46
MLL2 MUTATED	5	17	14
MLL2 WILD-TYPE	19	43	32

'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.589 (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
ALL	23	74	33
MLL2 MUTATED	6	23	7
MLL2 WILD-TYPE	17	51	26

'ELF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.784 (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
ALL	31	42	54
ELF3 MUTATED	2	3	6
ELF3 WILD-TYPE	29	39	48

'ELF3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.208 (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	CLUS_4
ALL	42	30	33	25
ELF3 MUTATED	2	2	2	5
ELF3 WILD-TYPE	40	28	31	20

'ELF3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.759 (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 = 0.383 (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	54	35	40
ELF3 MUTATED	6	3	2
ELF3 WILD-TYPE	48	32	38

'ELF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.222 (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	39	21	38	31
ELF3 MUTATED	3	0	6	2
ELF3 WILD-TYPE	36	21	32	29

'ELF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.569 (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	35	52	43
ELF3 MUTATED	3	3	5
ELF3 WILD-TYPE	32	49	38

'ELF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.847 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
ELF3 MUTATED	2	2	0	1	3	2	1
ELF3 WILD-TYPE	22	11	13	13	24	15	21

'ELF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.916 (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
ALL	24	60	46
ELF3 MUTATED	2	6	3
ELF3 WILD-TYPE	22	54	43

'ELF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.456 (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
ALL	23	74	33
ELF3 MUTATED	2	8	1
ELF3 WILD-TYPE	21	66	32

'FGFR3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0186 (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
ALL	31	42	54
FGFR3 MUTATED	1	3	12
FGFR3 WILD-TYPE	30	39	42

Figure S4. Get High-res Image Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FGFR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.232 (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	CLUS_4
ALL	42	30	33	25
FGFR3 MUTATED	3	2	6	5
FGFR3 WILD-TYPE	39	28	27	20

'FGFR3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0924 (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 = 0.00986 (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 S5. Get High-res Image Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.186 (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	54	35	40
FGFR3 MUTATED	10	2	4
FGFR3 WILD-TYPE	44	33	36

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0473 (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	39	21	38	31
FGFR3 MUTATED	10	1	3	2
FGFR3 WILD-TYPE	29	20	35	29

Figure S6. Get High-res Image Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.197 (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	35	52	43
FGFR3 MUTATED	3	10	3
FGFR3 WILD-TYPE	32	42	40

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00929 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
FGFR3 MUTATED	3	0	0	4	1	1	7
FGFR3 WILD-TYPE	21	13	13	10	26	16	15

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

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	60	46
FGFR3 MUTATED	2	3	11
FGFR3 WILD-TYPE	22	57	35

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 = 0.0414 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	23	74	33
FGFR3 MUTATED	3	5	8
FGFR3 WILD-TYPE	20	69	25

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 = 0.141 (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
ALL	31	42	54
CDKN2A MUTATED	2	0	5
CDKN2A WILD-TYPE	29	42	49

'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.563 (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	CLUS_4
ALL	42	30	33	25
CDKN2A MUTATED	2	2	3	0
CDKN2A WILD-TYPE	40	28	30	25

'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.389 (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 = 0.183 (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 = 0.799 (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	54	35	40
CDKN2A MUTATED	3	1	3
CDKN2A WILD-TYPE	51	34	37

'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.866 (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	39	21	38	31
CDKN2A MUTATED	2	2	2	1
CDKN2A WILD-TYPE	37	19	36	30

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.331 (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	35	52	43
CDKN2A MUTATED	1	5	1
CDKN2A WILD-TYPE	34	47	42

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.283 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
CDKN2A MUTATED	1	0	2	1	0	2	1
CDKN2A WILD-TYPE	23	13	11	13	27	15	21

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.301 (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
ALL	24	60	46
CDKN2A MUTATED	0	3	4
CDKN2A WILD-TYPE	24	57	42

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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
ALL	23	74	33
CDKN2A MUTATED	1	4	2
CDKN2A WILD-TYPE	22	70	31

'STAG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.318 (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
ALL	31	42	54
STAG2 MUTATED	2	3	9
STAG2 WILD-TYPE	29	39	45

'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.183 (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	CLUS_4
ALL	42	30	33	25
STAG2 MUTATED	3	2	3	6
STAG2 WILD-TYPE	39	28	30	19

'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.301 (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 = 0.553 (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 = 0.322 (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	54	35	40
STAG2 MUTATED	8	4	2
STAG2 WILD-TYPE	46	31	38

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.144 (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	39	21	38	31
STAG2 MUTATED	7	0	5	2
STAG2 WILD-TYPE	32	21	33	29

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.19 (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	35	52	43
STAG2 MUTATED	2	9	3
STAG2 WILD-TYPE	33	43	40

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.26 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
STAG2 MUTATED	2	1	0	2	2	1	6
STAG2 WILD-TYPE	22	12	13	12	25	16	16

'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.249 (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
ALL	24	60	46
STAG2 MUTATED	2	4	8
STAG2 WILD-TYPE	22	56	38

'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0177 (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
ALL	23	74	33
STAG2 MUTATED	2	4	8
STAG2 WILD-TYPE	21	70	25

Figure S10. Get High-res Image Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.117 (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
ALL	31	42	54
NFE2L2 MUTATED	0	5	6
NFE2L2 WILD-TYPE	31	37	48

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.655 (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	CLUS_4
ALL	42	30	33	25
NFE2L2 MUTATED	5	1	3	2
NFE2L2 WILD-TYPE	37	29	30	23

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.307 (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 = 0.0957 (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	54	35	40
NFE2L2 MUTATED	1	4	5
NFE2L2 WILD-TYPE	53	31	35

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0416 (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	39	21	38	31
NFE2L2 MUTATED	0	1	4	5
NFE2L2 WILD-TYPE	39	20	34	26

Figure S11. Get High-res Image Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (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	35	52	43
NFE2L2 MUTATED	3	4	4
NFE2L2 WILD-TYPE	32	48	39

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0163 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
NFE2L2 MUTATED	1	3	1	4	0	1	1
NFE2L2 WILD-TYPE	23	10	12	10	27	16	21

Figure S12. Get High-res Image Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.843 (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
ALL	24	60	46
NFE2L2 MUTATED	1	6	4
NFE2L2 WILD-TYPE	23	54	42

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.75 (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
ALL	23	74	33
NFE2L2 MUTATED	1	8	2
NFE2L2 WILD-TYPE	22	66	31

'ERCC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.618 (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
ALL	31	42	54
ERCC2 MUTATED	5	6	5
ERCC2 WILD-TYPE	26	36	49

'ERCC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.448 (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	CLUS_4
ALL	42	30	33	25
ERCC2 MUTATED	5	4	6	1
ERCC2 WILD-TYPE	37	26	27	24

'ERCC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0867 (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 = 0.0178 (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 S13. Get High-res Image Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'ERCC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.174 (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	54	35	40
ERCC2 MUTATED	4	4	8
ERCC2 WILD-TYPE	50	31	32

'ERCC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.123 (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	39	21	38	31
ERCC2 MUTATED	3	2	3	8
ERCC2 WILD-TYPE	36	19	35	23

'ERCC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.395 (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	35	52	43
ERCC2 MUTATED	6	7	3
ERCC2 WILD-TYPE	29	45	40

'ERCC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.105 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
ERCC2 MUTATED	2	5	1	2	1	3	2
ERCC2 WILD-TYPE	22	8	12	12	26	14	20

'ERCC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.78 (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
ALL	24	60	46
ERCC2 MUTATED	4	7	5
ERCC2 WILD-TYPE	20	53	41

'ERCC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.933 (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
ALL	23	74	33
ERCC2 MUTATED	2	10	4
ERCC2 WILD-TYPE	21	64	29

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.288 (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
ALL	31	42	54
FBXW7 MUTATED	1	6	5
FBXW7 WILD-TYPE	30	36	49

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0415 (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	CLUS_4
ALL	42	30	33	25
FBXW7 MUTATED	9	2	1	1
FBXW7 WILD-TYPE	33	28	32	24

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 = 0.532 (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 = 0.104 (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	54	35	40
FBXW7 MUTATED	2	5	6
FBXW7 WILD-TYPE	52	30	34

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0904 (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	39	21	38	31
FBXW7 MUTATED	1	3	3	6
FBXW7 WILD-TYPE	38	18	35	25

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.214 (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	35	52	43
FBXW7 MUTATED	6	3	4
FBXW7 WILD-TYPE	29	49	39

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0284 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
FBXW7 MUTATED	4	2	1	2	0	4	0
FBXW7 WILD-TYPE	20	11	12	12	27	13	22

Figure S15. Get High-res Image Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	60	46
FBXW7 MUTATED	5	7	1
FBXW7 WILD-TYPE	19	53	45

Figure S16. 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 = 0.187 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	23	74	33
FBXW7 MUTATED	4	8	1
FBXW7 WILD-TYPE	19	66	32

'RHOB MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (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
ALL	31	42	54
RHOB MUTATED	2	2	3
RHOB WILD-TYPE	29	40	51

'RHOB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.705 (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	CLUS_4
ALL	42	30	33	25
RHOB MUTATED	2	3	1	1
RHOB WILD-TYPE	40	27	32	24

'RHOB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.564 (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 = 0.317 (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 = 0.796 (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	54	35	40
RHOB MUTATED	3	1	3
RHOB WILD-TYPE	51	34	37

'RHOB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.345 (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	39	21	38	31
RHOB MUTATED	1	0	4	2
RHOB WILD-TYPE	38	21	34	29

'RHOB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.704 (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	35	52	43
RHOB MUTATED	1	4	2
RHOB WILD-TYPE	34	48	41

'RHOB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.544 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
RHOB MUTATED	1	0	2	1	2	1	0
RHOB WILD-TYPE	23	13	11	13	25	16	22

'RHOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.299 (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
ALL	24	60	46
RHOB MUTATED	0	3	4
RHOB WILD-TYPE	24	57	42

'RHOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.498 (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
ALL	23	74	33
RHOB MUTATED	1	3	3
RHOB WILD-TYPE	22	71	30

'TSC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.167 (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
ALL	31	42	54
TSC1 MUTATED	3	1	7
TSC1 WILD-TYPE	28	41	47

'TSC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.699 (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	CLUS_4
ALL	42	30	33	25
TSC1 MUTATED	2	3	4	2
TSC1 WILD-TYPE	40	27	29	23

'TSC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.416 (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 = 0.569 (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 = 0.244 (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	54	35	40
TSC1 MUTATED	6	4	1
TSC1 WILD-TYPE	48	31	39

'TSC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.141 (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	39	21	38	31
TSC1 MUTATED	4	0	6	1
TSC1 WILD-TYPE	35	21	32	30

'TSC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.621 (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	35	52	43
TSC1 MUTATED	4	3	4
TSC1 WILD-TYPE	31	49	39

'TSC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.496 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
TSC1 MUTATED	3	1	0	2	3	2	0
TSC1 WILD-TYPE	21	12	13	12	24	15	22

'TSC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.413 (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
ALL	24	60	46
TSC1 MUTATED	3	6	2
TSC1 WILD-TYPE	21	54	44

'TSC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0855 (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
ALL	23	74	33
TSC1 MUTATED	3	8	0
TSC1 WILD-TYPE	20	66	33

'FOXQ1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.423 (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
ALL	31	42	54
FOXQ1 MUTATED	3	1	3
FOXQ1 WILD-TYPE	28	41	51

'FOXQ1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.378 (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	CLUS_4
ALL	42	30	33	25
FOXQ1 MUTATED	3	2	0	2
FOXQ1 WILD-TYPE	39	28	33	23

'FOXQ1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.467 (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 = 0.366 (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	54	35	40
FOXQ1 MUTATED	4	1	2
FOXQ1 WILD-TYPE	50	34	38

'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	39	21	38	31
FOXQ1 MUTATED	2	1	2	2
FOXQ1 WILD-TYPE	37	20	36	29

'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.152 (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	35	52	43
FOXQ1 MUTATED	0	5	2
FOXQ1 WILD-TYPE	35	47	41

'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.294 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
FOXQ1 MUTATED	0	0	2	0	2	2	1
FOXQ1 WILD-TYPE	24	13	11	14	25	15	21

'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.299 (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
ALL	24	60	46
FOXQ1 MUTATED	0	3	4
FOXQ1 WILD-TYPE	24	57	42

'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.422 (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
ALL	23	74	33
FOXQ1 MUTATED	0	4	3
FOXQ1 WILD-TYPE	23	70	30

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.407 (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
ALL	31	42	54
PIK3CA MUTATED	4	11	11
PIK3CA WILD-TYPE	27	31	43

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.961 (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	CLUS_4
ALL	42	30	33	25
PIK3CA MUTATED	8	7	6	5
PIK3CA WILD-TYPE	34	23	27	20

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.224 (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 = 0.642 (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 = 0.432 (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	54	35	40
PIK3CA MUTATED	8	9	9
PIK3CA WILD-TYPE	46	26	31

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.166 (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	39	21	38	31
PIK3CA MUTATED	5	2	11	8
PIK3CA WILD-TYPE	34	19	27	23

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.789 (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	35	52	43
PIK3CA MUTATED	6	12	8
PIK3CA WILD-TYPE	29	40	35

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.537 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
PIK3CA MUTATED	3	4	2	2	6	6	3
PIK3CA WILD-TYPE	21	9	11	12	21	11	19

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.419 (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
ALL	24	60	46
PIK3CA MUTATED	3	15	8
PIK3CA WILD-TYPE	21	45	38

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.6 (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
ALL	23	74	33
PIK3CA MUTATED	3	17	6
PIK3CA WILD-TYPE	20	57	27

'RXRA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.119 (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
ALL	31	42	54
RXRA MUTATED	6	2	4
RXRA WILD-TYPE	25	40	50

'RXRA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.193 (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	CLUS_4
ALL	42	30	33	25
RXRA MUTATED	4	5	3	0
RXRA WILD-TYPE	38	25	30	25

'RXRA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.168 (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 = 0.591 (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	54	35	40
RXRA MUTATED	6	4	2
RXRA WILD-TYPE	48	31	38

'RXRA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.321 (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	39	21	38	31
RXRA MUTATED	5	0	5	2
RXRA WILD-TYPE	34	21	33	29

'RXRA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.549 (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	35	52	43
RXRA MUTATED	5	4	3
RXRA WILD-TYPE	30	48	40

'RXRA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.336 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
RXRA MUTATED	4	1	2	0	3	2	0
RXRA WILD-TYPE	20	12	11	14	24	15	22

'RXRA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.674 (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
ALL	24	60	46
RXRA MUTATED	3	6	3
RXRA WILD-TYPE	21	54	43

'RXRA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.315 (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
ALL	23	74	33
RXRA MUTATED	4	6	2
RXRA WILD-TYPE	19	68	31

'CREBBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.299 (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
ALL	31	42	54
CREBBP MUTATED	5	7	4
CREBBP WILD-TYPE	26	35	50

'CREBBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.849 (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	CLUS_4
ALL	42	30	33	25
CREBBP MUTATED	7	4	3	3
CREBBP WILD-TYPE	35	26	30	22

'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 = 0.213 (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	54	35	40
CREBBP MUTATED	4	7	6
CREBBP WILD-TYPE	50	28	34

'CREBBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.288 (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	39	21	38	31
CREBBP MUTATED	2	3	7	5
CREBBP WILD-TYPE	37	18	31	26

'CREBBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.193 (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	35	52	43
CREBBP MUTATED	3	5	9
CREBBP WILD-TYPE	32	47	34

'CREBBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.911 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
CREBBP MUTATED	2	1	2	2	5	3	2
CREBBP WILD-TYPE	22	12	11	12	22	14	20

'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.651 (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
ALL	24	60	46
CREBBP MUTATED	2	10	5
CREBBP WILD-TYPE	22	50	41

'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.247 (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
ALL	23	74	33
CREBBP MUTATED	2	13	2
CREBBP WILD-TYPE	21	61	31

'ERBB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.936 (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
ALL	31	42	54
ERBB3 MUTATED	4	4	6
ERBB3 WILD-TYPE	27	38	48

'ERBB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.593 (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	CLUS_4
ALL	42	30	33	25
ERBB3 MUTATED	3	5	4	2
ERBB3 WILD-TYPE	39	25	29	23

'ERBB3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.693 (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 = 0.675 (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	54	35	40
ERBB3 MUTATED	6	5	3
ERBB3 WILD-TYPE	48	30	37

'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.842 (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	39	21	38	31
ERBB3 MUTATED	5	2	5	2
ERBB3 WILD-TYPE	34	19	33	29

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.821 (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	35	52	43
ERBB3 MUTATED	3	7	4
ERBB3 WILD-TYPE	32	45	39

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.731 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
ERBB3 MUTATED	2	1	0	1	3	3	4
ERBB3 WILD-TYPE	22	12	13	13	24	14	18

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.573 (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
ALL	24	60	46
ERBB3 MUTATED	1	8	5
ERBB3 WILD-TYPE	23	52	41

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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
ALL	23	74	33
ERBB3 MUTATED	2	8	4
ERBB3 WILD-TYPE	21	66	29

'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.205 (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
ALL	31	42	54
FAT1 MUTATED	1	7	7
FAT1 WILD-TYPE	30	35	47

'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.365 (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	CLUS_4
ALL	42	30	33	25
FAT1 MUTATED	7	1	4	3
FAT1 WILD-TYPE	35	29	29	22

'FAT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.22 (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 = 0.37 (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	54	35	40
FAT1 MUTATED	4	6	4
FAT1 WILD-TYPE	50	29	36

'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (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	39	21	38	31
FAT1 MUTATED	4	2	4	4
FAT1 WILD-TYPE	35	19	34	27

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.453 (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	35	52	43
FAT1 MUTATED	2	7	6
FAT1 WILD-TYPE	33	45	37

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.288 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
FAT1 MUTATED	0	3	1	2	3	3	3
FAT1 WILD-TYPE	24	10	12	12	24	14	19

'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0884 (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
ALL	24	60	46
FAT1 MUTATED	0	10	5
FAT1 WILD-TYPE	24	50	41

'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0737 (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
ALL	23	74	33
FAT1 MUTATED	0	12	3
FAT1 WILD-TYPE	23	62	30

'MLL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.845 (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
ALL	31	42	54
MLL MUTATED	3	6	8
MLL WILD-TYPE	28	36	46

'MLL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.984 (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	CLUS_4
ALL	42	30	33	25
MLL MUTATED	6	4	4	4
MLL WILD-TYPE	36	26	29	21

'MLL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0283 (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 S17. Get High-res Image Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'MLL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00499 (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 S18. Get High-res Image Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MLL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.325 (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	54	35	40
MLL MUTATED	5	5	8
MLL WILD-TYPE	49	30	32

'MLL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.532 (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	39	21	38	31
MLL MUTATED	3	4	6	5
MLL WILD-TYPE	36	17	32	26

'MLL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.813 (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	35	52	43
MLL MUTATED	5	6	7
MLL WILD-TYPE	30	46	36

'MLL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.705 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
MLL MUTATED	4	2	3	1	5	2	1
MLL WILD-TYPE	20	11	10	13	22	15	21

'MLL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.891 (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
ALL	24	60	46
MLL MUTATED	4	8	6
MLL WILD-TYPE	20	52	40

'MLL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.881 (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
ALL	23	74	33
MLL MUTATED	4	10	4
MLL WILD-TYPE	19	64	29

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.57 (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
ALL	31	42	54
HRAS MUTATED	1	1	4
HRAS WILD-TYPE	30	41	50

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.799 (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	CLUS_4
ALL	42	30	33	25
HRAS MUTATED	1	2	2	1
HRAS WILD-TYPE	41	28	31	24

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0168 (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 S19. Get High-res Image Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.339 (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 = 0.88 (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	54	35	40
HRAS MUTATED	2	2	2
HRAS WILD-TYPE	52	33	38

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.439 (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	39	21	38	31
HRAS MUTATED	2	0	1	3
HRAS WILD-TYPE	37	21	37	28

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.57 (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	35	52	43
HRAS MUTATED	1	4	1
HRAS WILD-TYPE	34	48	42

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.648 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
HRAS MUTATED	1	0	0	0	1	1	3
HRAS WILD-TYPE	23	13	13	14	26	16	19

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.197 (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
ALL	24	60	46
HRAS MUTATED	1	1	4
HRAS WILD-TYPE	23	59	42

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.258 (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
ALL	23	74	33
HRAS MUTATED	1	2	3
HRAS WILD-TYPE	22	72	30

'ACRC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.281 (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
ALL	31	42	54
ACRC MUTATED	2	0	2
ACRC WILD-TYPE	29	42	52

'ACRC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.11 (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	CLUS_4
ALL	42	30	33	25
ACRC MUTATED	0	1	3	0
ACRC WILD-TYPE	42	29	30	25

'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 = 0.76 (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 = 1 (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	54	35	40
ACRC MUTATED	2	1	1
ACRC WILD-TYPE	52	34	39

'ACRC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.912 (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	39	21	38	31
ACRC MUTATED	2	0	1	1
ACRC WILD-TYPE	37	21	37	30

'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	35	52	43
ACRC MUTATED	1	2	1
ACRC WILD-TYPE	34	50	42

'ACRC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.87 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
ACRC MUTATED	1	0	1	0	1	1	0
ACRC WILD-TYPE	23	13	12	14	26	16	22

'ACRC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (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
ALL	24	60	46
ACRC MUTATED	1	2	1
ACRC WILD-TYPE	23	58	45

'ACRC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.812 (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
ALL	23	74	33
ACRC MUTATED	1	2	1
ACRC WILD-TYPE	22	72	32

'TXNIP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.588 (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
ALL	31	42	54
TXNIP MUTATED	1	2	5
TXNIP WILD-TYPE	30	40	49

'TXNIP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.274 (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	CLUS_4
ALL	42	30	33	25
TXNIP MUTATED	3	0	4	2
TXNIP WILD-TYPE	39	30	29	23

'TXNIP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.872 (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 = 0.703 (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	54	35	40
TXNIP MUTATED	4	2	3
TXNIP WILD-TYPE	50	33	37

'TXNIP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0801 (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	39	21	38	31
TXNIP MUTATED	1	0	6	2
TXNIP WILD-TYPE	38	21	32	29

'TXNIP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.909 (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	35	52	43
TXNIP MUTATED	3	3	3
TXNIP WILD-TYPE	32	49	40

'TXNIP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.983 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
TXNIP MUTATED	2	1	1	0	2	1	2
TXNIP WILD-TYPE	22	12	12	14	25	16	20

'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.732 (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
ALL	24	60	46
TXNIP MUTATED	2	5	2
TXNIP WILD-TYPE	22	55	44

'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.897 (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
ALL	23	74	33
TXNIP MUTATED	2	5	2
TXNIP WILD-TYPE	21	69	31

'ECM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0794 (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
ALL	31	42	54
ECM1 MUTATED	2	3	0
ECM1 WILD-TYPE	29	39	54

'ECM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.268 (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	CLUS_4
ALL	42	30	33	25
ECM1 MUTATED	3	2	0	0
ECM1 WILD-TYPE	39	28	33	25

'ECM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.947 (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 = 0.733 (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	54	35	40
ECM1 MUTATED	2	2	1
ECM1 WILD-TYPE	52	33	39

'ECM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.55 (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	39	21	38	31
ECM1 MUTATED	1	2	1	1
ECM1 WILD-TYPE	38	19	37	30

'ECM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.52 (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	35	52	43
ECM1 MUTATED	1	1	3
ECM1 WILD-TYPE	34	51	40

'ECM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.186 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
ECM1 MUTATED	0	1	1	0	3	0	0
ECM1 WILD-TYPE	24	12	12	14	24	17	22

'ECM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.416 (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
ALL	24	60	46
ECM1 MUTATED	0	4	1
ECM1 WILD-TYPE	24	56	45

'ECM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.698 (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
ALL	23	74	33
ECM1 MUTATED	0	3	2
ECM1 WILD-TYPE	23	71	31

'KLF5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0917 (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
ALL	31	42	54
KLF5 MUTATED	0	3	7
KLF5 WILD-TYPE	31	39	47

'KLF5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.778 (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	CLUS_4
ALL	42	30	33	25
KLF5 MUTATED	3	2	4	1
KLF5 WILD-TYPE	39	28	29	24

'KLF5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.303 (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 = 0.31 (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	54	35	40
KLF5 MUTATED	5	2	3
KLF5 WILD-TYPE	49	33	37

'KLF5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.679 (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	39	21	38	31
KLF5 MUTATED	3	3	2	2
KLF5 WILD-TYPE	36	18	36	29

'KLF5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.706 (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	35	52	43
KLF5 MUTATED	3	5	2
KLF5 WILD-TYPE	32	47	41

'KLF5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.23 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
KLF5 MUTATED	3	0	3	0	2	0	2
KLF5 WILD-TYPE	21	13	10	14	25	17	20

'KLF5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.192 (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
ALL	24	60	46
KLF5 MUTATED	3	2	5
KLF5 WILD-TYPE	21	58	41

'KLF5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0234 (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
ALL	23	74	33
KLF5 MUTATED	3	2	5
KLF5 WILD-TYPE	20	72	28

Figure S20. Get High-res Image Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RBM26 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.619 (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
ALL	31	42	54
RBM26 MUTATED	1	3	5
RBM26 WILD-TYPE	30	39	49

'RBM26 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.964 (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	CLUS_4
ALL	42	30	33	25
RBM26 MUTATED	3	2	3	1
RBM26 WILD-TYPE	39	28	30	24

'RBM26 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.255 (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 = 0.725 (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 = 0.382 (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	54	35	40
RBM26 MUTATED	2	4	3
RBM26 WILD-TYPE	52	31	37

'RBM26 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.566 (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	39	21	38	31
RBM26 MUTATED	1	2	3	3
RBM26 WILD-TYPE	38	19	35	28

'RBM26 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0938 (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	35	52	43
RBM26 MUTATED	0	6	3
RBM26 WILD-TYPE	35	46	40

'RBM26 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.288 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
RBM26 MUTATED	0	0	2	0	3	2	2
RBM26 WILD-TYPE	24	13	11	14	24	15	20

'RBM26 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.389 (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
ALL	24	60	46
RBM26 MUTATED	0	5	4
RBM26 WILD-TYPE	24	55	42

'RBM26 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.246 (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
ALL	23	74	33
RBM26 MUTATED	0	5	4
RBM26 WILD-TYPE	23	69	29

'RAD51C MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (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
ALL	31	42	54
RAD51C MUTATED	1	1	2
RAD51C WILD-TYPE	30	41	52

'RAD51C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.165 (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	CLUS_4
ALL	42	30	33	25
RAD51C MUTATED	0	2	2	0
RAD51C WILD-TYPE	42	28	31	25

'RAD51C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.182 (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 = 0.0372 (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	54	35	40
RAD51C MUTATED	0	3	1
RAD51C WILD-TYPE	54	32	39

Figure S21. Get High-res Image Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RAD51C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.21 (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	39	21	38	31
RAD51C MUTATED	0	0	3	1
RAD51C WILD-TYPE	39	21	35	30

'RAD51C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.134 (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	35	52	43
RAD51C MUTATED	1	0	3
RAD51C WILD-TYPE	34	52	40

'RAD51C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.449 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
RAD51C MUTATED	0	1	0	0	2	1	0
RAD51C WILD-TYPE	24	12	13	14	25	16	22

'RAD51C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.134 (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
ALL	24	60	46
RAD51C MUTATED	0	4	0
RAD51C WILD-TYPE	24	56	46

'RAD51C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.375 (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
ALL	23	74	33
RAD51C MUTATED	0	4	0
RAD51C WILD-TYPE	23	70	33

'CEP192 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.85 (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
ALL	31	42	54
CEP192 MUTATED	1	1	3
CEP192 WILD-TYPE	30	41	51

'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	CLUS_4
ALL	42	30	33	25
CEP192 MUTATED	2	2	1	0
CEP192 WILD-TYPE	40	28	32	25

'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 = 0.696 (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 = 0.733 (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	54	35	40
CEP192 MUTATED	2	2	1
CEP192 WILD-TYPE	52	33	39

'CEP192 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.587 (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	39	21	38	31
CEP192 MUTATED	1	0	3	1
CEP192 WILD-TYPE	38	21	35	30

'CEP192 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.734 (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	35	52	43
CEP192 MUTATED	1	3	1
CEP192 WILD-TYPE	34	49	42

'CEP192 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0615 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
CEP192 MUTATED	0	1	2	1	0	1	0
CEP192 WILD-TYPE	24	12	11	13	27	16	22

'CEP192 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.591 (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
ALL	24	60	46
CEP192 MUTATED	0	2	3
CEP192 WILD-TYPE	24	58	43

'CEP192 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.699 (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
ALL	23	74	33
CEP192 MUTATED	0	3	2
CEP192 WILD-TYPE	23	71	31

'ASXL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0475 (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
ALL	31	42	54
ASXL2 MUTATED	3	0	6
ASXL2 WILD-TYPE	28	42	48

Figure S22. Get High-res Image Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ASXL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.508 (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	CLUS_4
ALL	42	30	33	25
ASXL2 MUTATED	1	3	3	2
ASXL2 WILD-TYPE	41	27	30	23

'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 = 0.365 (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 = 0.25 (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	54	35	40
ASXL2 MUTATED	3	1	5
ASXL2 WILD-TYPE	51	34	35

'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.817 (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	39	21	38	31
ASXL2 MUTATED	2	1	4	2
ASXL2 WILD-TYPE	37	20	34	29

'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.91 (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	35	52	43
ASXL2 MUTATED	3	3	3
ASXL2 WILD-TYPE	32	49	40

'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.399 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
ASXL2 MUTATED	3	0	2	0	3	0	1
ASXL2 WILD-TYPE	21	13	11	14	24	17	21

'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.484 (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
ALL	24	60	46
ASXL2 MUTATED	3	3	3
ASXL2 WILD-TYPE	21	57	43

'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.454 (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
ALL	23	74	33
ASXL2 MUTATED	3	4	2
ASXL2 WILD-TYPE	20	70	31

'PSIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.371 (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
ALL	31	42	54
PSIP1 MUTATED	1	1	5
PSIP1 WILD-TYPE	30	41	49

'PSIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.625 (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	CLUS_4
ALL	42	30	33	25
PSIP1 MUTATED	1	2	3	1
PSIP1 WILD-TYPE	41	28	30	24

'PSIP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.138 (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 = 0.385 (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	54	35	40
PSIP1 MUTATED	4	1	2
PSIP1 WILD-TYPE	50	34	38

'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.509 (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	39	21	38	31
PSIP1 MUTATED	4	1	1	1
PSIP1 WILD-TYPE	35	20	37	30

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.483 (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	35	52	43
PSIP1 MUTATED	3	3	1
PSIP1 WILD-TYPE	32	49	42

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.847 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
PSIP1 MUTATED	2	1	0	1	1	0	2
PSIP1 WILD-TYPE	22	12	13	13	26	17	20

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.536 (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
ALL	24	60	46
PSIP1 MUTATED	1	2	4
PSIP1 WILD-TYPE	23	58	42

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.191 (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
ALL	23	74	33
PSIP1 MUTATED	2	2	3
PSIP1 WILD-TYPE	21	72	30

'ZNF513 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.16 (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
ALL	31	42	54
ZNF513 MUTATED	4	1	2
ZNF513 WILD-TYPE	27	41	52

'ZNF513 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.704 (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	CLUS_4
ALL	42	30	33	25
ZNF513 MUTATED	2	3	1	1
ZNF513 WILD-TYPE	40	27	32	24

'ZNF513 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.206 (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 = 0.414 (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 = 0.48 (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	54	35	40
ZNF513 MUTATED	3	3	1
ZNF513 WILD-TYPE	51	32	39

'ZNF513 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.335 (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	39	21	38	31
ZNF513 MUTATED	2	2	3	0
ZNF513 WILD-TYPE	37	19	35	31

'ZNF513 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.89 (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	35	52	43
ZNF513 MUTATED	2	2	3
ZNF513 WILD-TYPE	33	50	40

'ZNF513 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.761 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
ZNF513 MUTATED	1	1	1	0	3	0	1
ZNF513 WILD-TYPE	23	12	12	14	24	17	21

'ZNF513 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (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
ALL	24	60	46
ZNF513 MUTATED	1	3	3
ZNF513 WILD-TYPE	23	57	43

'ZNF513 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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
ALL	23	74	33
ZNF513 MUTATED	1	4	2
ZNF513 WILD-TYPE	22	70	31

'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.611 (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
ALL	31	42	54
FOXA1 MUTATED	2	1	4
FOXA1 WILD-TYPE	29	41	50

'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.91 (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	CLUS_4
ALL	42	30	33	25
FOXA1 MUTATED	3	2	1	1
FOXA1 WILD-TYPE	39	28	32	24

'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.539 (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 = 0.694 (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 = 0.257 (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	54	35	40
FOXA1 MUTATED	2	4	1
FOXA1 WILD-TYPE	52	31	39

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.908 (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	39	21	38	31
FOXA1 MUTATED	2	1	3	1
FOXA1 WILD-TYPE	37	20	35	30

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.888 (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	35	52	43
FOXA1 MUTATED	2	2	3
FOXA1 WILD-TYPE	33	50	40

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.647 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
FOXA1 MUTATED	2	0	0	2	2	0	1
FOXA1 WILD-TYPE	22	13	13	12	25	17	21

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.675 (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
ALL	24	60	46
FOXA1 MUTATED	2	2	3
FOXA1 WILD-TYPE	22	58	43

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.661 (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
ALL	23	74	33
FOXA1 MUTATED	2	3	2
FOXA1 WILD-TYPE	21	71	31

'TRIP11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.822 (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
ALL	31	42	54
TRIP11 MUTATED	1	2	1
TRIP11 WILD-TYPE	30	40	53

'TRIP11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.531 (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	CLUS_4
ALL	42	30	33	25
TRIP11 MUTATED	2	2	0	1
TRIP11 WILD-TYPE	40	28	33	24

'TRIP11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.804 (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	54	35	40
TRIP11 MUTATED	2	2	1
TRIP11 WILD-TYPE	52	33	39

'TRIP11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.869 (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	39	21	38	31
TRIP11 MUTATED	2	0	2	1
TRIP11 WILD-TYPE	37	21	36	30

'TRIP11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.316 (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	35	52	43
TRIP11 MUTATED	3	1	1
TRIP11 WILD-TYPE	32	51	42

'TRIP11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0933 (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	CLUS_6	CLUS_7
ALL	24	13	13	14	27	17	22
TRIP11 MUTATED	2	1	0	2	0	0	0
TRIP11 WILD-TYPE	22	12	13	12	27	17	22

'TRIP11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.34 (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
ALL	24	60	46
TRIP11 MUTATED	1	1	3
TRIP11 WILD-TYPE	23	59	43

'TRIP11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.368 (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
ALL	23	74	33
TRIP11 MUTATED	2	2	1
TRIP11 WILD-TYPE	21	72	32

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.

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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