Correlation between gene mutation status and molecular subtypes

Prostate Adenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1D21WD0

Overview

Introduction

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

Summary

Testing the association between mutation status of 38 genes and 10 molecular subtypes across 261 patients, 7 significant findings detected with P value < 0.05 and Q value < 0.25.

SPOP mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
TP53 mutation correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
FOXA1 mutation correlated to 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 38 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, 7 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
SPOP	26 (10%)	235	2e-05 (0.00712)	1e-05 (0.0036)	0.334 (1.00)	0.283 (1.00)	1e-05 (0.0036)	1e-05 (0.0036)	0.266 (1.00)	0.365 (1.00)	0.461 (1.00)	0.374 (1.00)
TP53	23 (9%)	238	1e-05 (0.0036)	0.273 (1.00)	0.00737 (1.00)	0.00636 (1.00)	0.01 (1.00)	0.00056 (0.198)	0.731 (1.00)	0.0201 (1.00)	0.247 (1.00)	0.296 (1.00)
FOXA1	12 (5%)	249	0.00502 (1.00)	0.00013 (0.0461)	1 (1.00)	0.494 (1.00)	0.00096 (0.339)	0.0172 (1.00)	0.661 (1.00)	0.0368 (1.00)	0.0608 (1.00)	0.473 (1.00)
PTEN	13 (5%)	248	0.505 (1.00)	0.283 (1.00)	0.198 (1.00)	0.303 (1.00)	0.114 (1.00)	0.045 (1.00)	0.161 (1.00)	0.301 (1.00)	0.00985 (1.00)	0.12 (1.00)
CTNNB1	9 (3%)	252	0.345 (1.00)	0.0422 (1.00)	0.0406 (1.00)	0.0395 (1.00)	0.0492 (1.00)	0.251 (1.00)	0.457 (1.00)	0.158 (1.00)	0.0916 (1.00)	0.167 (1.00)
TCEB3	4 (2%)	257	0.341 (1.00)	0.459 (1.00)	0.117 (1.00)	0.636 (1.00)	0.332 (1.00)	0.842 (1.00)	0.229 (1.00)	0.521 (1.00)	0.255 (1.00)	0.244 (1.00)
BRAF	6 (2%)	255	0.504 (1.00)	0.115 (1.00)	0.834 (1.00)	1 (1.00)	0.00924 (1.00)	0.875 (1.00)	0.216 (1.00)	0.861 (1.00)	0.51 (1.00)	0.613 (1.00)
PIK3CA	9 (3%)	252	0.438 (1.00)	0.00335 (1.00)	0.0406 (1.00)	0.039 (1.00)	0.0123 (1.00)	0.0179 (1.00)	0.562 (1.00)	0.182 (1.00)	0.218 (1.00)	0.238 (1.00)
IDH1	4 (2%)	257	0.106 (1.00)	0.00642 (1.00)	0.0618 (1.00)	0.0525 (1.00)	0.00966 (1.00)	0.0362 (1.00)	0.0383 (1.00)	0.0185 (1.00)	0.834 (1.00)	0.0536 (1.00)
FAM47C	8 (3%)	253	0.524 (1.00)	0.174 (1.00)	1 (1.00)	1 (1.00)	0.742 (1.00)	0.545 (1.00)	0.0286 (1.00)	0.806 (1.00)	0.138 (1.00)	0.382 (1.00)
TP53BP1	5 (2%)	256	0.446 (1.00)	0.0236 (1.00)	0.12 (1.00)	0.15 (1.00)	0.0263 (1.00)	0.131 (1.00)	0.874 (1.00)	0.334 (1.00)	0.742 (1.00)	0.308 (1.00)
CNTNAP1	5 (2%)	256	0.107 (1.00)	0.0242 (1.00)			0.0749 (1.00)	0.274 (1.00)	0.535 (1.00)	0.719 (1.00)	0.742 (1.00)	0.642 (1.00)
MLLT10	4 (2%)	257	0.228 (1.00)	0.149 (1.00)	0.56 (1.00)	0.687 (1.00)	1 (1.00)	0.695 (1.00)	0.151 (1.00)	0.394 (1.00)	0.254 (1.00)	0.168 (1.00)
ZMYM3	6 (2%)	255	0.421 (1.00)	0.139 (1.00)	0.446 (1.00)	0.389 (1.00)	0.166 (1.00)	0.0305 (1.00)	0.0776 (1.00)	0.131 (1.00)	0.0106 (1.00)	0.0684 (1.00)
SMG7	4 (2%)	257	0.792 (1.00)	0.685 (1.00)	1 (1.00)	1 (1.00)	0.0096 (1.00)	0.553 (1.00)	0.534 (1.00)	0.314 (1.00)	0.195 (1.00)	0.94 (1.00)
EDC4	3 (1%)	258	0.0597 (1.00)	0.0233 (1.00)			1 (1.00)	0.774 (1.00)	0.287 (1.00)	0.295 (1.00)	0.0612 (1.00)	0.376 (1.00)
ZNF709	4 (2%)	257	0.624 (1.00)	1 (1.00)	0.452 (1.00)	0.389 (1.00)	1 (1.00)	0.124 (1.00)	0.556 (1.00)	0.668 (1.00)	0.143 (1.00)	0.584 (1.00)
CDK12	7 (3%)	254	0.02 (1.00)	0.299 (1.00)	0.0405 (1.00)	0.0392 (1.00)	0.288 (1.00)	0.194 (1.00)	0.47 (1.00)	0.161 (1.00)	0.388 (1.00)	0.346 (1.00)
RPTN	6 (2%)	255	0.339 (1.00)	0.45 (1.00)	0.117 (1.00)	0.114 (1.00)	0.447 (1.00)	0.875 (1.00)	0.605 (1.00)	0.571 (1.00)	0.292 (1.00)	0.45 (1.00)
TNRC18	4 (2%)	257	0.0605 (1.00)	1 (1.00)			0.691 (1.00)	0.123 (1.00)	0.64 (1.00)	1 (1.00)	0.197 (1.00)	0.458 (1.00)
MED15	5 (2%)	256	0.553 (1.00)	0.0354 (1.00)	0.443 (1.00)	0.731 (1.00)	0.453 (1.00)	0.871 (1.00)	0.552 (1.00)	0.85 (1.00)	0.535 (1.00)	0.714 (1.00)
NKX3-1	5 (2%)	256	0.622 (1.00)	0.636 (1.00)	0.0287 (1.00)	0.0498 (1.00)	0.868 (1.00)	1 (1.00)	0.00614 (1.00)	0.261 (1.00)	0.0133 (1.00)	0.00896 (1.00)
KDM6A	6 (2%)	255	0.093 (1.00)	0.188 (1.00)	0.833 (1.00)	0.689 (1.00)	0.291 (1.00)	0.376 (1.00)	0.767 (1.00)	0.0119 (1.00)	0.584 (1.00)	0.673 (1.00)
RNF31	4 (2%)	257	0.744 (1.00)	0.206 (1.00)	0.676 (1.00)	0.561 (1.00)	0.306 (1.00)	0.21 (1.00)	0.641 (1.00)	0.174 (1.00)	0.196 (1.00)	0.457 (1.00)
ESCO1	4 (2%)	257	0.622 (1.00)	0.837 (1.00)	0.474 (1.00)	0.378 (1.00)	0.212 (1.00)	0.0785 (1.00)	0.149 (1.00)	0.394 (1.00)	1 (1.00)	0.112 (1.00)
LMOD2	3 (1%)	258	0.744 (1.00)	0.638 (1.00)			1 (1.00)	1 (1.00)	0.211 (1.00)	0.767 (1.00)	0.781 (1.00)	0.256 (1.00)
FAM120B	3 (1%)	258	0.341 (1.00)	1 (1.00)			0.411 (1.00)	0.539 (1.00)	0.289 (1.00)	0.293 (1.00)	0.0621 (1.00)	0.377 (1.00)
CLEC1A	4 (2%)	257	0.628 (1.00)	0.46 (1.00)			0.213 (1.00)	0.844 (1.00)	0.533 (1.00)	0.523 (1.00)	0.457 (1.00)	0.555 (1.00)
ITGA2B	3 (1%)	258	0.744 (1.00)	1 (1.00)	0.78 (1.00)	0.779 (1.00)	0.416 (1.00)	0.538 (1.00)	0.347 (1.00)	0.408 (1.00)	1 (1.00)	0.447 (1.00)
RNF17	3 (1%)	258	0.338 (1.00)	0.778 (1.00)	0.0157 (1.00)	0.0246 (1.00)	0.11 (1.00)	0.318 (1.00)	0.831 (1.00)	0.587 (1.00)	1 (1.00)	0.058 (1.00)
RP1L1	7 (3%)	254	1 (1.00)	0.895 (1.00)	0.444 (1.00)	0.39 (1.00)	0.893 (1.00)	0.704 (1.00)	0.0775 (1.00)	0.883 (1.00)	0.0386 (1.00)	0.0707 (1.00)
EOMES	4 (2%)	257	0.625 (1.00)	0.686 (1.00)	0.784 (1.00)	0.78 (1.00)	0.392 (1.00)	0.332 (1.00)	0.00566 (1.00)	0.059 (1.00)	1 (1.00)	0.00346 (1.00)
MTF1	3 (1%)	258	0.743 (1.00)	0.392 (1.00)			0.207 (1.00)	0.11 (1.00)	0.0535 (1.00)	0.0396 (1.00)	1 (1.00)	0.00355 (1.00)
NTM	5 (2%)	256	1 (1.00)	0.386 (1.00)	0.122 (1.00)	0.329 (1.00)	0.381 (1.00)	0.167 (1.00)	0.682 (1.00)	0.72 (1.00)	1 (1.00)	0.404 (1.00)
FNBP4	3 (1%)	258	0.338 (1.00)	0.289 (1.00)			0.412 (1.00)	0.775 (1.00)	0.349 (1.00)	0.41 (1.00)	0.373 (1.00)	0.0453 (1.00)
CDKN1B	4 (2%)	257	0.793 (1.00)	0.105 (1.00)	0.242 (1.00)	0.31 (1.00)	0.163 (1.00)	0.551 (1.00)	0.743 (1.00)	0.13 (1.00)	0.682 (1.00)	0.205 (1.00)
EIF2AK3	4 (2%)	257	1 (1.00)	0.267 (1.00)			0.553 (1.00)	0.694 (1.00)	0.388 (1.00)	1 (1.00)	0.382 (1.00)	0.643 (1.00)
LARP1	3 (1%)	258	0.742 (1.00)	0.388 (1.00)			0.777 (1.00)	0.212 (1.00)	0.163 (1.00)	0.124 (1.00)	0.492 (1.00)	0.637 (1.00)

'SPOP MUTATION STATUS' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
SPOP MUTATED	5	9	11
SPOP WILD-TYPE	152	50	31

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

'SPOP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
SPOP MUTATED	21	4	1
SPOP WILD-TYPE	54	85	96

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

'SPOP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.334 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
SPOP MUTATED	4	3	8
SPOP WILD-TYPE	38	56	55

'SPOP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.283 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
SPOP MUTATED	5	8	2
SPOP WILD-TYPE	43	58	48

'SPOP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
SPOP MUTATED	19	6	0
SPOP WILD-TYPE	62	78	93

Figure S3. Get High-res Image Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SPOP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
SPOP MUTATED	22	3	0
SPOP WILD-TYPE	68	80	85

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

'SPOP MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
SPOP MUTATED	4	0	8	3	11
SPOP WILD-TYPE	44	18	51	52	68

'SPOP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.365 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
SPOP MUTATED	11	2	13
SPOP WILD-TYPE	81	44	108

'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.461 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
SPOP MUTATED	9	10	7
SPOP WILD-TYPE	61	81	91

'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
SPOP MUTATED	6	1	7	3	9
SPOP WILD-TYPE	36	20	44	59	74

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S11. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
TP53 MUTATED	4	19	0
TP53 WILD-TYPE	153	40	42

Figure S5. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 1

Table S12. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
TP53 MUTATED	6	5	12
TP53 WILD-TYPE	69	84	85

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00737 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
TP53 MUTATED	0	3	10
TP53 WILD-TYPE	42	56	53

Figure S6. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00636 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
TP53 MUTATED	0	10	3
TP53 WILD-TYPE	48	56	47

Figure S7. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
TP53 MUTATED	5	3	15
TP53 WILD-TYPE	76	81	78

Figure S8. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.2

Table S16. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
TP53 MUTATED	5	2	16
TP53 WILD-TYPE	85	81	69

Figure S9. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.731 (Fisher's exact test), Q value = 1

Table S17. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
TP53 MUTATED	2	1	6	5	9
TP53 WILD-TYPE	46	17	53	50	70

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
TP53 MUTATED	5	1	17
TP53 WILD-TYPE	87	45	104

Figure S10. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.247 (Fisher's exact test), Q value = 1

Table S19. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
TP53 MUTATED	8	10	5
TP53 WILD-TYPE	62	81	93

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.296 (Fisher's exact test), Q value = 1

Table S20. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
TP53 MUTATED	3	2	7	2	9
TP53 WILD-TYPE	39	19	44	60	74

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
PTEN MUTATED	6	4	3
PTEN WILD-TYPE	151	55	39

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.283 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
PTEN MUTATED	4	2	7
PTEN WILD-TYPE	71	87	90

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
PTEN MUTATED	4	1	3
PTEN WILD-TYPE	38	58	60

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
PTEN MUTATED	4	3	1
PTEN WILD-TYPE	44	63	49

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
PTEN MUTATED	5	1	7
PTEN WILD-TYPE	76	83	86

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.045 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
PTEN MUTATED	4	1	8
PTEN WILD-TYPE	86	82	77

Figure S11. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.161 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
PTEN MUTATED	0	1	6	3	3
PTEN WILD-TYPE	48	17	53	52	76

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
PTEN MUTATED	3	1	9
PTEN WILD-TYPE	89	45	112

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00985 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
PTEN MUTATED	8	4	1
PTEN WILD-TYPE	62	87	97

Figure S12. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
PTEN MUTATED	0	0	6	3	4
PTEN WILD-TYPE	42	21	45	59	79

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.345 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
CTNNB1 MUTATED	4	2	3
CTNNB1 WILD-TYPE	153	57	39

'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
CTNNB1 MUTATED	3	0	6
CTNNB1 WILD-TYPE	72	89	91

Figure S13. Get High-res Image Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
CTNNB1 MUTATED	0	0	4
CTNNB1 WILD-TYPE	42	59	59

Figure S14. Get High-res Image Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S34. Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
CTNNB1 MUTATED	0	4	0
CTNNB1 WILD-TYPE	48	62	50

Figure S15. Get High-res Image Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 1

Table S35. Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
CTNNB1 MUTATED	3	0	6
CTNNB1 WILD-TYPE	78	84	87

Figure S16. Get High-res Image Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 1

Table S36. Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
CTNNB1 MUTATED	3	1	5
CTNNB1 WILD-TYPE	87	82	80

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 1

Table S37. Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
CTNNB1 MUTATED	0	0	4	2	3
CTNNB1 WILD-TYPE	48	18	55	53	76

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.158 (Fisher's exact test), Q value = 1

Table S38. Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
CTNNB1 MUTATED	2	0	7
CTNNB1 WILD-TYPE	90	46	114

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0916 (Fisher's exact test), Q value = 1

Table S39. Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
CTNNB1 MUTATED	5	3	1
CTNNB1 WILD-TYPE	65	88	97

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 1

Table S40. Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
CTNNB1 MUTATED	2	0	4	0	3
CTNNB1 WILD-TYPE	40	21	47	62	80

'TCEB3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S41. Gene #5: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
TCEB3 MUTATED	2	2	0
TCEB3 WILD-TYPE	155	57	42

'TCEB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.459 (Fisher's exact test), Q value = 1

Table S42. Gene #5: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
TCEB3 MUTATED	0	1	3
TCEB3 WILD-TYPE	75	88	94

'TCEB3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 1

Table S43. Gene #5: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
TCEB3 MUTATED	0	0	3
TCEB3 WILD-TYPE	42	59	60

'TCEB3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.636 (Fisher's exact test), Q value = 1

Table S44. Gene #5: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
TCEB3 MUTATED	1	2	0
TCEB3 WILD-TYPE	47	64	50

'TCEB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S45. Gene #5: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
TCEB3 MUTATED	0	1	3
TCEB3 WILD-TYPE	81	83	90

'TCEB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.842 (Fisher's exact test), Q value = 1

Table S46. Gene #5: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
TCEB3 MUTATED	1	1	2
TCEB3 WILD-TYPE	89	82	83

'TCEB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 1

Table S47. Gene #5: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
TCEB3 MUTATED	0	0	2	2	0
TCEB3 WILD-TYPE	48	18	57	53	79

'TCEB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.521 (Fisher's exact test), Q value = 1

Table S48. Gene #5: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
TCEB3 MUTATED	2	1	1
TCEB3 WILD-TYPE	90	45	120

'TCEB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S49. Gene #5: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
TCEB3 MUTATED	1	0	3
TCEB3 WILD-TYPE	69	91	95

'TCEB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S50. Gene #5: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
TCEB3 MUTATED	1	1	1	1	0
TCEB3 WILD-TYPE	41	20	50	61	83

'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00502 (Fisher's exact test), Q value = 1

Table S51. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
FOXA1 MUTATED	3	3	6
FOXA1 WILD-TYPE	154	56	36

Figure S17. Get High-res Image Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.046

Table S52. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
FOXA1 MUTATED	10	1	1
FOXA1 WILD-TYPE	65	88	96

Figure S18. Get High-res Image Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S53. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
FOXA1 MUTATED	2	2	3
FOXA1 WILD-TYPE	40	57	60

'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 1

Table S54. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
FOXA1 MUTATED	3	3	1
FOXA1 WILD-TYPE	45	63	49

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.34

Table S55. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
FOXA1 MUTATED	9	3	0
FOXA1 WILD-TYPE	72	81	93

Figure S19. Get High-res Image Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 1

Table S56. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
FOXA1 MUTATED	9	2	1
FOXA1 WILD-TYPE	81	81	84

Figure S20. Get High-res Image Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.661 (Fisher's exact test), Q value = 1

Table S57. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
FOXA1 MUTATED	2	0	4	1	5
FOXA1 WILD-TYPE	46	18	55	54	74

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0368 (Fisher's exact test), Q value = 1

Table S58. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
FOXA1 MUTATED	1	1	10
FOXA1 WILD-TYPE	91	45	111

Figure S21. Get High-res Image Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0608 (Fisher's exact test), Q value = 1

Table S59. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
FOXA1 MUTATED	4	7	1
FOXA1 WILD-TYPE	66	84	97

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 1

Table S60. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
FOXA1 MUTATED	2	0	4	1	5
FOXA1 WILD-TYPE	40	21	47	61	78

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.504 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
BRAF MUTATED	3	1	2
BRAF WILD-TYPE	154	58	40

'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
BRAF MUTATED	3	3	0
BRAF WILD-TYPE	72	86	97

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
BRAF MUTATED	1	2	1
BRAF WILD-TYPE	41	57	62

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
BRAF MUTATED	1	2	1
BRAF WILD-TYPE	47	64	49

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00924 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
BRAF MUTATED	5	1	0
BRAF WILD-TYPE	76	83	93

Figure S22. Get High-res Image Gene #7: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
BRAF MUTATED	3	1	2
BRAF WILD-TYPE	87	82	83

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
BRAF MUTATED	0	0	4	1	1
BRAF WILD-TYPE	48	18	55	54	78

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.861 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
BRAF MUTATED	3	1	2
BRAF WILD-TYPE	89	45	119

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.51 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
BRAF MUTATED	3	1	2
BRAF WILD-TYPE	67	90	96

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.613 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
BRAF MUTATED	2	0	2	1	1
BRAF WILD-TYPE	40	21	49	61	82

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 1

Table S71. Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
PIK3CA MUTATED	6	3	0
PIK3CA WILD-TYPE	151	56	42

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 1

Table S72. Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
PIK3CA MUTATED	1	0	8
PIK3CA WILD-TYPE	74	89	89

Figure S23. Get High-res Image Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 1

Table S73. Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
PIK3CA MUTATED	0	0	4
PIK3CA WILD-TYPE	42	59	59

Figure S24. Get High-res Image Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.039 (Fisher's exact test), Q value = 1

Table S74. Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
PIK3CA MUTATED	0	4	0
PIK3CA WILD-TYPE	48	62	50

Figure S25. Get High-res Image Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 1

Table S75. Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
PIK3CA MUTATED	2	0	7
PIK3CA WILD-TYPE	79	84	86

Figure S26. Get High-res Image Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S76. Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
PIK3CA MUTATED	1	1	7
PIK3CA WILD-TYPE	89	82	78

Figure S27. Get High-res Image Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 1

Table S77. Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
PIK3CA MUTATED	0	0	3	2	4
PIK3CA WILD-TYPE	48	18	56	53	75

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 1

Table S78. Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
PIK3CA MUTATED	1	1	7
PIK3CA WILD-TYPE	91	45	114

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 1

Table S79. Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
PIK3CA MUTATED	4	4	1
PIK3CA WILD-TYPE	66	87	97

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S80. Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
PIK3CA MUTATED	0	0	4	1	4
PIK3CA WILD-TYPE	42	21	47	61	79

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.106 (Fisher's exact test), Q value = 1

Table S81. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
IDH1 MUTATED	1	1	2
IDH1 WILD-TYPE	156	58	40

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00642 (Fisher's exact test), Q value = 1

Table S82. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
IDH1 MUTATED	4	0	0
IDH1 WILD-TYPE	71	89	97

Figure S28. Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0618 (Fisher's exact test), Q value = 1

Table S83. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
IDH1 MUTATED	0	3	0
IDH1 WILD-TYPE	42	56	63

'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0525 (Fisher's exact test), Q value = 1

Table S84. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
IDH1 MUTATED	0	0	3
IDH1 WILD-TYPE	48	66	47

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00966 (Fisher's exact test), Q value = 1

Table S85. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
IDH1 MUTATED	4	0	0
IDH1 WILD-TYPE	77	84	93

Figure S29. Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 1

Table S86. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
IDH1 MUTATED	4	0	0
IDH1 WILD-TYPE	86	83	85

Figure S30. Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S87. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
IDH1 MUTATED	0	2	1	0	1
IDH1 WILD-TYPE	48	16	58	55	78

Figure S31. Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 1

Table S88. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
IDH1 MUTATED	0	3	1
IDH1 WILD-TYPE	92	43	120

Figure S32. Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S89. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
IDH1 MUTATED	1	2	1
IDH1 WILD-TYPE	69	89	97

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0536 (Fisher's exact test), Q value = 1

Table S90. Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
IDH1 MUTATED	0	2	1	0	1
IDH1 WILD-TYPE	42	19	50	62	82

'FAM47C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.524 (Fisher's exact test), Q value = 1

Table S91. Gene #10: 'FAM47C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
FAM47C MUTATED	6	2	0
FAM47C WILD-TYPE	151	57	42

'FAM47C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 1

Table S92. Gene #10: 'FAM47C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
FAM47C MUTATED	0	4	4
FAM47C WILD-TYPE	75	85	93

'FAM47C MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S93. Gene #10: 'FAM47C MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
FAM47C MUTATED	1	1	1
FAM47C WILD-TYPE	41	58	62

'FAM47C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S94. Gene #10: 'FAM47C MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
FAM47C MUTATED	1	1	1
FAM47C WILD-TYPE	47	65	49

'FAM47C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.742 (Fisher's exact test), Q value = 1

Table S95. Gene #10: 'FAM47C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
FAM47C MUTATED	2	2	4
FAM47C WILD-TYPE	79	82	89

'FAM47C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.545 (Fisher's exact test), Q value = 1

Table S96. Gene #10: 'FAM47C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
FAM47C MUTATED	4	1	3
FAM47C WILD-TYPE	86	82	82

'FAM47C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 1

Table S97. Gene #10: 'FAM47C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
FAM47C MUTATED	3	2	0	0	3
FAM47C WILD-TYPE	45	16	59	55	76

Figure S33. Get High-res Image Gene #10: 'FAM47C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'FAM47C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.806 (Fisher's exact test), Q value = 1

Table S98. Gene #10: 'FAM47C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
FAM47C MUTATED	3	2	3
FAM47C WILD-TYPE	89	44	118

'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 1

Table S99. Gene #10: 'FAM47C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
FAM47C MUTATED	0	5	3
FAM47C WILD-TYPE	70	86	95

'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S100. Gene #10: 'FAM47C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
FAM47C MUTATED	2	1	0	1	4
FAM47C WILD-TYPE	40	20	51	61	79

'TP53BP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 1

Table S101. Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
TP53BP1 MUTATED	2	2	1
TP53BP1 WILD-TYPE	155	57	41

'TP53BP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 1

Table S102. Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
TP53BP1 MUTATED	4	1	0
TP53BP1 WILD-TYPE	71	88	97

Figure S34. Get High-res Image Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53BP1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S103. Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
TP53BP1 MUTATED	1	0	4
TP53BP1 WILD-TYPE	41	59	59

'TP53BP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.15 (Fisher's exact test), Q value = 1

Table S104. Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
TP53BP1 MUTATED	1	4	0
TP53BP1 WILD-TYPE	47	62	50

'TP53BP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S105. Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
TP53BP1 MUTATED	4	1	0
TP53BP1 WILD-TYPE	77	83	93

Figure S35. Get High-res Image Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53BP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S106. Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
TP53BP1 MUTATED	4	0	1
TP53BP1 WILD-TYPE	86	83	84

'TP53BP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S107. Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
TP53BP1 MUTATED	0	0	2	1	2
TP53BP1 WILD-TYPE	48	18	57	54	77

'TP53BP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 1

Table S108. Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
TP53BP1 MUTATED	1	2	2
TP53BP1 WILD-TYPE	91	44	119

'TP53BP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.742 (Fisher's exact test), Q value = 1

Table S109. Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
TP53BP1 MUTATED	2	2	1
TP53BP1 WILD-TYPE	68	89	97

'TP53BP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S110. Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
TP53BP1 MUTATED	1	1	2	0	1
TP53BP1 WILD-TYPE	41	20	49	62	82

'CNTNAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 1

Table S111. Gene #12: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
CNTNAP1 MUTATED	1	1	2
CNTNAP1 WILD-TYPE	156	58	40

'CNTNAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 1

Table S112. Gene #12: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
CNTNAP1 MUTATED	4	1	0
CNTNAP1 WILD-TYPE	71	88	97

Figure S36. Get High-res Image Gene #12: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CNTNAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0749 (Fisher's exact test), Q value = 1

Table S113. Gene #12: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
CNTNAP1 MUTATED	3	1	0
CNTNAP1 WILD-TYPE	78	83	93

'CNTNAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S114. Gene #12: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
CNTNAP1 MUTATED	3	1	0
CNTNAP1 WILD-TYPE	87	82	85

'CNTNAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 1

Table S115. Gene #12: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
CNTNAP1 MUTATED	2	0	2	0	1
CNTNAP1 WILD-TYPE	46	18	57	55	78

'CNTNAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S116. Gene #12: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
CNTNAP1 MUTATED	2	0	3
CNTNAP1 WILD-TYPE	90	46	118

'CNTNAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.742 (Fisher's exact test), Q value = 1

Table S117. Gene #12: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
CNTNAP1 MUTATED	2	2	1
CNTNAP1 WILD-TYPE	68	89	97

'CNTNAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S118. Gene #12: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
CNTNAP1 MUTATED	1	0	1	0	3
CNTNAP1 WILD-TYPE	41	21	50	62	80

'MLLT10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S119. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
MLLT10 MUTATED	1	2	1
MLLT10 WILD-TYPE	156	57	41

'MLLT10 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S120. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
MLLT10 MUTATED	1	3	0
MLLT10 WILD-TYPE	74	86	97

'MLLT10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S121. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
MLLT10 MUTATED	2	1	1
MLLT10 WILD-TYPE	40	58	62

'MLLT10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S122. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
MLLT10 MUTATED	2	1	1
MLLT10 WILD-TYPE	46	65	49

'MLLT10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S123. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
MLLT10 MUTATED	1	1	2
MLLT10 WILD-TYPE	80	83	91

'MLLT10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.695 (Fisher's exact test), Q value = 1

Table S124. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
MLLT10 MUTATED	1	2	1
MLLT10 WILD-TYPE	89	81	84

'MLLT10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 1

Table S125. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
MLLT10 MUTATED	2	0	0	2	0
MLLT10 WILD-TYPE	46	18	59	53	79

'MLLT10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.394 (Fisher's exact test), Q value = 1

Table S126. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
MLLT10 MUTATED	3	0	1
MLLT10 WILD-TYPE	89	46	120

'MLLT10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S127. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
MLLT10 MUTATED	1	0	3
MLLT10 WILD-TYPE	69	91	95

'MLLT10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 1

Table S128. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
MLLT10 MUTATED	0	0	1	3	0
MLLT10 WILD-TYPE	42	21	50	59	83

'ZMYM3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 1

Table S129. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
ZMYM3 MUTATED	5	0	1
ZMYM3 WILD-TYPE	152	59	41

'ZMYM3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 1

Table S130. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
ZMYM3 MUTATED	2	0	4
ZMYM3 WILD-TYPE	73	89	93

'ZMYM3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 1

Table S131. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
ZMYM3 MUTATED	0	2	3
ZMYM3 WILD-TYPE	42	57	60

'ZMYM3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S132. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
ZMYM3 MUTATED	0	3	2
ZMYM3 WILD-TYPE	48	63	48

'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.166 (Fisher's exact test), Q value = 1

Table S133. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
ZMYM3 MUTATED	2	0	4
ZMYM3 WILD-TYPE	79	84	89

'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 1

Table S134. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
ZMYM3 MUTATED	1	0	5
ZMYM3 WILD-TYPE	89	83	80

Figure S37. Get High-res Image Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0776 (Fisher's exact test), Q value = 1

Table S135. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
ZMYM3 MUTATED	0	1	3	2	0
ZMYM3 WILD-TYPE	48	17	56	53	79

'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S136. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
ZMYM3 MUTATED	0	1	5
ZMYM3 WILD-TYPE	92	45	116

'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S137. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
ZMYM3 MUTATED	5	0	1
ZMYM3 WILD-TYPE	65	91	97

Figure S38. Get High-res Image Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0684 (Fisher's exact test), Q value = 1

Table S138. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
ZMYM3 MUTATED	0	1	3	2	0
ZMYM3 WILD-TYPE	42	20	48	60	83

'SMG7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S139. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
SMG7 MUTATED	2	1	1
SMG7 WILD-TYPE	155	58	41

'SMG7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.685 (Fisher's exact test), Q value = 1

Table S140. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
SMG7 MUTATED	2	1	1
SMG7 WILD-TYPE	73	88	96

'SMG7 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S141. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
SMG7 MUTATED	1	1	1
SMG7 WILD-TYPE	41	58	62

'SMG7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S142. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
SMG7 MUTATED	1	1	1
SMG7 WILD-TYPE	47	65	49

'SMG7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0096 (Fisher's exact test), Q value = 1

Table S143. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
SMG7 MUTATED	4	0	0
SMG7 WILD-TYPE	77	84	93

Figure S39. Get High-res Image Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SMG7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.553 (Fisher's exact test), Q value = 1

Table S144. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
SMG7 MUTATED	2	0	2
SMG7 WILD-TYPE	88	83	83

'SMG7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.534 (Fisher's exact test), Q value = 1

Table S145. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
SMG7 MUTATED	0	1	1	1	1
SMG7 WILD-TYPE	48	17	58	54	78

'SMG7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.314 (Fisher's exact test), Q value = 1

Table S146. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
SMG7 MUTATED	0	1	3
SMG7 WILD-TYPE	92	45	118

'SMG7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 1

Table S147. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
SMG7 MUTATED	2	2	0
SMG7 WILD-TYPE	68	89	98

'SMG7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.94 (Fisher's exact test), Q value = 1

Table S148. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
SMG7 MUTATED	0	0	1	1	2
SMG7 WILD-TYPE	42	21	50	61	81

'EDC4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0597 (Fisher's exact test), Q value = 1

Table S149. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
EDC4 MUTATED	0	2	1
EDC4 WILD-TYPE	157	57	41

'EDC4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 1

Table S150. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
EDC4 MUTATED	3	0	0
EDC4 WILD-TYPE	72	89	97

Figure S40. Get High-res Image Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EDC4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S151. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
EDC4 MUTATED	1	1	1
EDC4 WILD-TYPE	80	83	92

'EDC4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S152. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
EDC4 MUTATED	2	0	1
EDC4 WILD-TYPE	88	83	84

'EDC4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.287 (Fisher's exact test), Q value = 1

Table S153. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
EDC4 MUTATED	0	0	0	0	3
EDC4 WILD-TYPE	48	18	59	55	76

'EDC4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 1

Table S154. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
EDC4 MUTATED	0	0	3
EDC4 WILD-TYPE	92	46	118

'EDC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0612 (Fisher's exact test), Q value = 1

Table S155. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
EDC4 MUTATED	0	3	0
EDC4 WILD-TYPE	70	88	98

'EDC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.376 (Fisher's exact test), Q value = 1

Table S156. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
EDC4 MUTATED	0	0	0	0	3
EDC4 WILD-TYPE	42	21	51	62	80

'ZNF709 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 1

Table S157. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
ZNF709 MUTATED	3	0	1
ZNF709 WILD-TYPE	154	59	41

'ZNF709 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S158. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
ZNF709 MUTATED	1	1	2
ZNF709 WILD-TYPE	74	88	95

'ZNF709 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S159. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
ZNF709 MUTATED	0	1	3
ZNF709 WILD-TYPE	42	58	60

'ZNF709 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S160. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
ZNF709 MUTATED	0	3	1
ZNF709 WILD-TYPE	48	63	49

'ZNF709 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S161. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
ZNF709 MUTATED	1	1	2
ZNF709 WILD-TYPE	80	83	91

'ZNF709 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S162. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
ZNF709 MUTATED	0	1	3
ZNF709 WILD-TYPE	90	82	82

'ZNF709 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S163. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
ZNF709 MUTATED	0	0	1	0	3
ZNF709 WILD-TYPE	48	18	58	55	76

'ZNF709 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S164. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
ZNF709 MUTATED	1	0	3
ZNF709 WILD-TYPE	91	46	118

'ZNF709 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 1

Table S165. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
ZNF709 MUTATED	1	3	0
ZNF709 WILD-TYPE	69	88	98

'ZNF709 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S166. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
ZNF709 MUTATED	0	0	1	0	3
ZNF709 WILD-TYPE	42	21	50	62	80

'CDK12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 1

Table S167. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
CDK12 MUTATED	1	4	1
CDK12 WILD-TYPE	156	55	41

Figure S41. Get High-res Image Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CDK12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 1

Table S168. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
CDK12 MUTATED	4	1	2
CDK12 WILD-TYPE	71	88	95

'CDK12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 1

Table S169. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
CDK12 MUTATED	0	0	4
CDK12 WILD-TYPE	42	59	59

Figure S42. Get High-res Image Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CDK12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0392 (Fisher's exact test), Q value = 1

Table S170. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
CDK12 MUTATED	0	4	0
CDK12 WILD-TYPE	48	62	50

Figure S43. Get High-res Image Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CDK12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 1

Table S171. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
CDK12 MUTATED	4	1	1
CDK12 WILD-TYPE	77	83	92

'CDK12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 1

Table S172. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
CDK12 MUTATED	4	0	2
CDK12 WILD-TYPE	86	83	83

'CDK12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S173. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
CDK12 MUTATED	2	0	3	0	2
CDK12 WILD-TYPE	46	18	56	55	77

'CDK12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 1

Table S174. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
CDK12 MUTATED	1	0	6
CDK12 WILD-TYPE	91	46	115

'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 1

Table S175. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
CDK12 MUTATED	3	3	1
CDK12 WILD-TYPE	67	88	97

'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S176. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
CDK12 MUTATED	1	0	3	0	3
CDK12 WILD-TYPE	41	21	48	62	80

'RPTN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 1

Table S177. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
RPTN MUTATED	4	0	2
RPTN WILD-TYPE	153	59	40

'RPTN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 1

Table S178. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
RPTN MUTATED	3	2	1
RPTN WILD-TYPE	72	87	96

'RPTN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 1

Table S179. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
RPTN MUTATED	0	0	3
RPTN WILD-TYPE	42	59	60

'RPTN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 1

Table S180. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
RPTN MUTATED	0	3	0
RPTN WILD-TYPE	48	63	50

'RPTN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 1

Table S181. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
RPTN MUTATED	3	2	1
RPTN WILD-TYPE	78	82	92

'RPTN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S182. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
RPTN MUTATED	3	1	2
RPTN WILD-TYPE	87	82	83

'RPTN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S183. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
RPTN MUTATED	2	0	1	0	3
RPTN WILD-TYPE	46	18	58	55	76

'RPTN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S184. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
RPTN MUTATED	2	0	4
RPTN WILD-TYPE	90	46	117

'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S185. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
RPTN MUTATED	1	4	1
RPTN WILD-TYPE	69	87	97

'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.45 (Fisher's exact test), Q value = 1

Table S186. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
RPTN MUTATED	2	0	1	0	3
RPTN WILD-TYPE	40	21	50	62	80

'TNRC18 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0605 (Fisher's exact test), Q value = 1

Table S187. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
TNRC18 MUTATED	1	3	0
TNRC18 WILD-TYPE	156	56	42

'TNRC18 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S188. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
TNRC18 MUTATED	1	1	2
TNRC18 WILD-TYPE	74	88	95

'TNRC18 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.691 (Fisher's exact test), Q value = 1

Table S189. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
TNRC18 MUTATED	2	1	1
TNRC18 WILD-TYPE	79	83	92

'TNRC18 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.123 (Fisher's exact test), Q value = 1

Table S190. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
TNRC18 MUTATED	0	1	3
TNRC18 WILD-TYPE	90	82	82

'TNRC18 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.64 (Fisher's exact test), Q value = 1

Table S191. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
TNRC18 MUTATED	0	0	2	0	2
TNRC18 WILD-TYPE	48	18	57	55	77

'TNRC18 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S192. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
TNRC18 MUTATED	1	1	2
TNRC18 WILD-TYPE	91	45	119

'TNRC18 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 1

Table S193. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
TNRC18 MUTATED	2	2	0
TNRC18 WILD-TYPE	68	89	98

'TNRC18 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 1

Table S194. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
TNRC18 MUTATED	0	0	2	0	2
TNRC18 WILD-TYPE	42	21	49	62	81

'MED15 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 1

Table S195. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
MED15 MUTATED	4	0	1
MED15 WILD-TYPE	153	59	41

'MED15 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 1

Table S196. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
MED15 MUTATED	4	0	1
MED15 WILD-TYPE	71	89	96

Figure S44. Get High-res Image Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MED15 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.443 (Fisher's exact test), Q value = 1

Table S197. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
MED15 MUTATED	0	2	3
MED15 WILD-TYPE	42	57	60

'MED15 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.731 (Fisher's exact test), Q value = 1

Table S198. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
MED15 MUTATED	1	3	1
MED15 WILD-TYPE	47	63	49

'MED15 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 1

Table S199. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
MED15 MUTATED	3	1	1
MED15 WILD-TYPE	78	83	92

'MED15 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.871 (Fisher's exact test), Q value = 1

Table S200. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
MED15 MUTATED	2	2	1
MED15 WILD-TYPE	88	81	84

'MED15 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S201. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
MED15 MUTATED	1	1	1	0	2
MED15 WILD-TYPE	47	17	58	55	77

'MED15 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S202. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
MED15 MUTATED	1	1	3
MED15 WILD-TYPE	91	45	118

'MED15 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 1

Table S203. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
MED15 MUTATED	1	3	1
MED15 WILD-TYPE	69	88	97

'MED15 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S204. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
MED15 MUTATED	0	1	1	1	2
MED15 WILD-TYPE	42	20	50	61	81

'NKX3-1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S205. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
NKX3-1 MUTATED	3	0	1
NKX3-1 WILD-TYPE	154	59	41

'NKX3-1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.636 (Fisher's exact test), Q value = 1

Table S206. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
NKX3-1 MUTATED	1	1	3
NKX3-1 WILD-TYPE	74	88	94

'NKX3-1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 1

Table S207. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
NKX3-1 MUTATED	4	0	1
NKX3-1 WILD-TYPE	38	59	62

Figure S45. Get High-res Image Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'NKX3-1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0498 (Fisher's exact test), Q value = 1

Table S208. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
NKX3-1 MUTATED	4	1	0
NKX3-1 WILD-TYPE	44	65	50

Figure S46. Get High-res Image Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NKX3-1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S209. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
NKX3-1 MUTATED	2	1	2
NKX3-1 WILD-TYPE	79	83	91

'NKX3-1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S210. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
NKX3-1 MUTATED	2	1	2
NKX3-1 WILD-TYPE	88	82	83

'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00614 (Fisher's exact test), Q value = 1

Table S211. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
NKX3-1 MUTATED	0	1	0	4	0
NKX3-1 WILD-TYPE	48	17	59	51	79

Figure S47. Get High-res Image Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 1

Table S212. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
NKX3-1 MUTATED	2	2	1
NKX3-1 WILD-TYPE	90	44	120

'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 1

Table S213. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
NKX3-1 MUTATED	0	0	5
NKX3-1 WILD-TYPE	70	91	93

Figure S48. Get High-res Image Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00896 (Fisher's exact test), Q value = 1

Table S214. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
NKX3-1 MUTATED	0	2	0	3	0
NKX3-1 WILD-TYPE	42	19	51	59	83

Figure S49. Get High-res Image Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.093 (Fisher's exact test), Q value = 1

Table S215. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
KDM6A MUTATED	2	1	3
KDM6A WILD-TYPE	155	58	39

'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.188 (Fisher's exact test), Q value = 1

Table S216. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
KDM6A MUTATED	4	1	1
KDM6A WILD-TYPE	71	88	96

'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S217. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
KDM6A MUTATED	1	2	1
KDM6A WILD-TYPE	41	57	62

'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.689 (Fisher's exact test), Q value = 1

Table S218. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
KDM6A MUTATED	2	1	1
KDM6A WILD-TYPE	46	65	49

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 1

Table S219. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
KDM6A MUTATED	4	1	1
KDM6A WILD-TYPE	77	83	92

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.376 (Fisher's exact test), Q value = 1

Table S220. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
KDM6A MUTATED	4	1	1
KDM6A WILD-TYPE	86	82	84

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.767 (Fisher's exact test), Q value = 1

Table S221. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
KDM6A MUTATED	0	0	2	1	3
KDM6A WILD-TYPE	48	18	57	54	76

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S222. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
KDM6A MUTATED	1	4	1
KDM6A WILD-TYPE	91	42	120

Figure S50. Get High-res Image Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S223. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
KDM6A MUTATED	2	3	1
KDM6A WILD-TYPE	68	88	97

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.673 (Fisher's exact test), Q value = 1

Table S224. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
KDM6A MUTATED	0	1	1	1	3
KDM6A WILD-TYPE	42	20	50	61	80

'RNF31 MUTATION STATUS' versus 'CN_CNMF'

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

Table S225. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
RNF31 MUTATED	3	0	0
RNF31 WILD-TYPE	154	59	42

'RNF31 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 1

Table S226. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
RNF31 MUTATED	2	2	0
RNF31 WILD-TYPE	73	87	97

'RNF31 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 1

Table S227. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
RNF31 MUTATED	0	2	2
RNF31 WILD-TYPE	42	57	61

'RNF31 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.561 (Fisher's exact test), Q value = 1

Table S228. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
RNF31 MUTATED	0	2	2
RNF31 WILD-TYPE	48	64	48

'RNF31 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 1

Table S229. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
RNF31 MUTATED	1	2	0
RNF31 WILD-TYPE	80	82	93

'RNF31 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S230. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
RNF31 MUTATED	0	2	1
RNF31 WILD-TYPE	90	81	84

'RNF31 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S231. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
RNF31 MUTATED	0	0	2	0	2
RNF31 WILD-TYPE	48	18	57	55	77

'RNF31 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.174 (Fisher's exact test), Q value = 1

Table S232. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
RNF31 MUTATED	0	0	4
RNF31 WILD-TYPE	92	46	117

'RNF31 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.196 (Fisher's exact test), Q value = 1

Table S233. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
RNF31 MUTATED	2	2	0
RNF31 WILD-TYPE	68	89	98

'RNF31 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.457 (Fisher's exact test), Q value = 1

Table S234. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
RNF31 MUTATED	0	0	2	0	2
RNF31 WILD-TYPE	42	21	49	62	81

'ESCO1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S235. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
ESCO1 MUTATED	3	0	1
ESCO1 WILD-TYPE	154	59	41

'ESCO1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S236. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
ESCO1 MUTATED	1	2	1
ESCO1 WILD-TYPE	74	87	96

'ESCO1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S237. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
ESCO1 MUTATED	1	0	2
ESCO1 WILD-TYPE	41	59	61

'ESCO1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.378 (Fisher's exact test), Q value = 1

Table S238. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
ESCO1 MUTATED	2	1	0
ESCO1 WILD-TYPE	46	65	50

'ESCO1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 1

Table S239. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
ESCO1 MUTATED	0	3	1
ESCO1 WILD-TYPE	81	81	92

'ESCO1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0785 (Fisher's exact test), Q value = 1

Table S240. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
ESCO1 MUTATED	0	3	1
ESCO1 WILD-TYPE	90	80	84

'ESCO1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S241. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
ESCO1 MUTATED	2	0	0	2	0
ESCO1 WILD-TYPE	46	18	59	53	79

'ESCO1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.394 (Fisher's exact test), Q value = 1

Table S242. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
ESCO1 MUTATED	3	0	1
ESCO1 WILD-TYPE	89	46	120

'ESCO1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S243. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
ESCO1 MUTATED	1	1	2
ESCO1 WILD-TYPE	69	90	96

'ESCO1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 1

Table S244. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
ESCO1 MUTATED	1	0	0	3	0
ESCO1 WILD-TYPE	41	21	51	59	83

'LMOD2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S245. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
LMOD2 MUTATED	3	0	0
LMOD2 WILD-TYPE	154	59	42

'LMOD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S246. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
LMOD2 MUTATED	0	2	1
LMOD2 WILD-TYPE	75	87	96

'LMOD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S247. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
LMOD2 MUTATED	1	1	1
LMOD2 WILD-TYPE	80	83	92

'LMOD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S248. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
LMOD2 MUTATED	1	1	1
LMOD2 WILD-TYPE	89	82	84

'LMOD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.211 (Fisher's exact test), Q value = 1

Table S249. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
LMOD2 MUTATED	1	1	0	0	1
LMOD2 WILD-TYPE	47	17	59	55	78

'LMOD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.767 (Fisher's exact test), Q value = 1

Table S250. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
LMOD2 MUTATED	1	1	1
LMOD2 WILD-TYPE	91	45	120

'LMOD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S251. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
LMOD2 MUTATED	0	1	2
LMOD2 WILD-TYPE	70	90	96

'LMOD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S252. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
LMOD2 MUTATED	1	1	0	0	1
LMOD2 WILD-TYPE	41	20	51	62	82

'FAM120B MUTATION STATUS' versus 'CN_CNMF'

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

Table S253. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
FAM120B MUTATED	1	1	1
FAM120B WILD-TYPE	156	58	41

'FAM120B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S254. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
FAM120B MUTATED	1	1	1
FAM120B WILD-TYPE	74	88	96

'FAM120B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S255. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
FAM120B MUTATED	2	0	1
FAM120B WILD-TYPE	79	84	92

'FAM120B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.539 (Fisher's exact test), Q value = 1

Table S256. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
FAM120B MUTATED	1	0	2
FAM120B WILD-TYPE	89	83	83

'FAM120B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S257. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
FAM120B MUTATED	0	0	0	0	3
FAM120B WILD-TYPE	48	18	59	55	76

'FAM120B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S258. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
FAM120B MUTATED	0	0	3
FAM120B WILD-TYPE	92	46	118

'FAM120B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0621 (Fisher's exact test), Q value = 1

Table S259. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
FAM120B MUTATED	0	3	0
FAM120B WILD-TYPE	70	88	98

'FAM120B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 1

Table S260. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
FAM120B MUTATED	0	0	0	0	3
FAM120B WILD-TYPE	42	21	51	62	80

'CLEC1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.628 (Fisher's exact test), Q value = 1

Table S261. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
CLEC1A MUTATED	3	0	1
CLEC1A WILD-TYPE	154	59	41

'CLEC1A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S262. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
CLEC1A MUTATED	0	1	3
CLEC1A WILD-TYPE	75	88	94

'CLEC1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 1

Table S263. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
CLEC1A MUTATED	0	3	1
CLEC1A WILD-TYPE	81	81	92

'CLEC1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.844 (Fisher's exact test), Q value = 1

Table S264. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
CLEC1A MUTATED	1	1	2
CLEC1A WILD-TYPE	89	82	83

'CLEC1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S265. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
CLEC1A MUTATED	0	1	1	1	1
CLEC1A WILD-TYPE	48	17	58	54	78

'CLEC1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.523 (Fisher's exact test), Q value = 1

Table S266. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
CLEC1A MUTATED	2	1	1
CLEC1A WILD-TYPE	90	45	120

'CLEC1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 1

Table S267. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
CLEC1A MUTATED	0	1	3
CLEC1A WILD-TYPE	70	90	95

'CLEC1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S268. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
CLEC1A MUTATED	1	1	0	1	1
CLEC1A WILD-TYPE	41	20	51	61	82

'ITGA2B MUTATION STATUS' versus 'CN_CNMF'

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

Table S269. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
ITGA2B MUTATED	3	0	0
ITGA2B WILD-TYPE	154	59	42

'ITGA2B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S270. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
ITGA2B MUTATED	1	1	1
ITGA2B WILD-TYPE	74	88	96

'ITGA2B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.78 (Fisher's exact test), Q value = 1

Table S271. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
ITGA2B MUTATED	0	1	2
ITGA2B WILD-TYPE	42	58	61

'ITGA2B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.779 (Fisher's exact test), Q value = 1

Table S272. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
ITGA2B MUTATED	0	2	1
ITGA2B WILD-TYPE	48	64	49

'ITGA2B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.416 (Fisher's exact test), Q value = 1

Table S273. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
ITGA2B MUTATED	2	0	1
ITGA2B WILD-TYPE	79	84	92

'ITGA2B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.538 (Fisher's exact test), Q value = 1

Table S274. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
ITGA2B MUTATED	1	0	2
ITGA2B WILD-TYPE	89	83	83

'ITGA2B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 1

Table S275. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
ITGA2B MUTATED	0	1	1	0	1
ITGA2B WILD-TYPE	48	17	58	55	78

'ITGA2B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S276. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
ITGA2B MUTATED	0	1	2
ITGA2B WILD-TYPE	92	45	119

'ITGA2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S277. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
ITGA2B MUTATED	1	1	1
ITGA2B WILD-TYPE	69	90	97

'ITGA2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.447 (Fisher's exact test), Q value = 1

Table S278. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
ITGA2B MUTATED	0	0	2	0	1
ITGA2B WILD-TYPE	42	21	49	62	82

'RNF17 MUTATION STATUS' versus 'CN_CNMF'

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

Table S279. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
RNF17 MUTATED	1	1	1
RNF17 WILD-TYPE	156	58	41

'RNF17 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.778 (Fisher's exact test), Q value = 1

Table S280. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
RNF17 MUTATED	0	1	2
RNF17 WILD-TYPE	75	88	95

'RNF17 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 1

Table S281. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
RNF17 MUTATED	3	0	0
RNF17 WILD-TYPE	39	59	63

Figure S51. Get High-res Image Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'RNF17 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 1

Table S282. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
RNF17 MUTATED	3	0	0
RNF17 WILD-TYPE	45	66	50

Figure S52. Get High-res Image Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'RNF17 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 1

Table S283. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
RNF17 MUTATED	0	0	3
RNF17 WILD-TYPE	81	84	90

'RNF17 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 1

Table S284. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
RNF17 MUTATED	0	1	2
RNF17 WILD-TYPE	90	82	83

'RNF17 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.831 (Fisher's exact test), Q value = 1

Table S285. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
RNF17 MUTATED	1	0	0	1	1
RNF17 WILD-TYPE	47	18	59	54	78

'RNF17 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 1

Table S286. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
RNF17 MUTATED	2	0	1
RNF17 WILD-TYPE	90	46	120

'RNF17 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S287. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
RNF17 MUTATED	1	1	1
RNF17 WILD-TYPE	69	90	97

'RNF17 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.058 (Fisher's exact test), Q value = 1

Table S288. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
RNF17 MUTATED	0	0	0	3	0
RNF17 WILD-TYPE	42	21	51	59	83

'RP1L1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S289. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
RP1L1 MUTATED	5	1	1
RP1L1 WILD-TYPE	152	58	41

'RP1L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.895 (Fisher's exact test), Q value = 1

Table S290. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
RP1L1 MUTATED	2	3	2
RP1L1 WILD-TYPE	73	86	95

'RP1L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S291. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
RP1L1 MUTATED	0	2	3
RP1L1 WILD-TYPE	42	57	60

'RP1L1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S292. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
RP1L1 MUTATED	0	3	2
RP1L1 WILD-TYPE	48	63	48

'RP1L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.893 (Fisher's exact test), Q value = 1

Table S293. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
RP1L1 MUTATED	2	3	2
RP1L1 WILD-TYPE	79	81	91

'RP1L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.704 (Fisher's exact test), Q value = 1

Table S294. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
RP1L1 MUTATED	3	1	3
RP1L1 WILD-TYPE	87	82	82

'RP1L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0775 (Fisher's exact test), Q value = 1

Table S295. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
RP1L1 MUTATED	0	0	5	1	1
RP1L1 WILD-TYPE	48	18	54	54	78

'RP1L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.883 (Fisher's exact test), Q value = 1

Table S296. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
RP1L1 MUTATED	2	1	4
RP1L1 WILD-TYPE	90	45	117

'RP1L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 1

Table S297. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
RP1L1 MUTATED	5	1	1
RP1L1 WILD-TYPE	65	90	97

Figure S53. Get High-res Image Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'RP1L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0707 (Fisher's exact test), Q value = 1

Table S298. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
RP1L1 MUTATED	3	0	3	0	1
RP1L1 WILD-TYPE	39	21	48	62	82

'EOMES MUTATION STATUS' versus 'CN_CNMF'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S299. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
EOMES MUTATED	3	0	1
EOMES WILD-TYPE	154	59	41

'EOMES MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S300. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
EOMES MUTATED	2	1	1
EOMES WILD-TYPE	73	88	96

'EOMES MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.784 (Fisher's exact test), Q value = 1

Table S301. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
EOMES MUTATED	0	1	2
EOMES WILD-TYPE	42	58	61

'EOMES MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.78 (Fisher's exact test), Q value = 1

Table S302. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
EOMES MUTATED	0	2	1
EOMES WILD-TYPE	48	64	49

'EOMES MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 1

Table S303. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
EOMES MUTATED	2	2	0
EOMES WILD-TYPE	79	82	93

'EOMES MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S304. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
EOMES MUTATED	3	0	1
EOMES WILD-TYPE	87	83	84

'EOMES MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00566 (Fisher's exact test), Q value = 1

Table S305. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
EOMES MUTATED	0	2	2	0	0
EOMES WILD-TYPE	48	16	57	55	79

Figure S54. Get High-res Image Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'EOMES MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.059 (Fisher's exact test), Q value = 1

Table S306. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
EOMES MUTATED	2	2	0
EOMES WILD-TYPE	90	44	121

'EOMES MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S307. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
EOMES MUTATED	1	1	2
EOMES WILD-TYPE	69	90	96

'EOMES MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00346 (Fisher's exact test), Q value = 1

Table S308. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
EOMES MUTATED	2	2	0	0	0
EOMES WILD-TYPE	40	19	51	62	83

Figure S55. Get High-res Image Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MTF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.743 (Fisher's exact test), Q value = 1

Table S309. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
MTF1 MUTATED	3	0	0
MTF1 WILD-TYPE	154	59	42

'MTF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 1

Table S310. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
MTF1 MUTATED	1	2	0
MTF1 WILD-TYPE	74	87	97

'MTF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 1

Table S311. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
MTF1 MUTATED	2	1	0
MTF1 WILD-TYPE	79	83	93

'MTF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.11 (Fisher's exact test), Q value = 1

Table S312. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
MTF1 MUTATED	3	0	0
MTF1 WILD-TYPE	87	83	85

'MTF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0535 (Fisher's exact test), Q value = 1

Table S313. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
MTF1 MUTATED	0	1	2	0	0
MTF1 WILD-TYPE	48	17	57	55	79

'MTF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 1

Table S314. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
MTF1 MUTATED	1	2	0
MTF1 WILD-TYPE	91	44	121

Figure S56. Get High-res Image Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MTF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S315. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
MTF1 MUTATED	1	1	1
MTF1 WILD-TYPE	69	90	97

'MTF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00355 (Fisher's exact test), Q value = 1

Table S316. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
MTF1 MUTATED	1	2	0	0	0
MTF1 WILD-TYPE	41	19	51	62	83

Figure S57. Get High-res Image Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NTM MUTATION STATUS' versus 'CN_CNMF'

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

Table S317. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
NTM MUTATED	3	1	1
NTM WILD-TYPE	154	58	41

'NTM MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S318. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
NTM MUTATED	0	2	3
NTM WILD-TYPE	75	87	94

'NTM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 1

Table S319. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
NTM MUTATED	1	0	4
NTM WILD-TYPE	41	59	59

'NTM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 1

Table S320. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
NTM MUTATED	2	3	0
NTM WILD-TYPE	46	63	50

'NTM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S321. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
NTM MUTATED	0	2	3
NTM WILD-TYPE	81	82	90

'NTM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 1

Table S322. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
NTM MUTATED	0	3	2
NTM WILD-TYPE	90	80	83

'NTM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 1

Table S323. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
NTM MUTATED	1	0	0	2	2
NTM WILD-TYPE	47	18	59	53	77

'NTM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.72 (Fisher's exact test), Q value = 1

Table S324. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
NTM MUTATED	2	0	3
NTM WILD-TYPE	90	46	118

'NTM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S325. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
NTM MUTATED	1	2	2
NTM WILD-TYPE	69	89	96

'NTM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.404 (Fisher's exact test), Q value = 1

Table S326. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
NTM MUTATED	0	0	0	3	2
NTM WILD-TYPE	42	21	51	59	81

'FNBP4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S327. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
FNBP4 MUTATED	1	1	1
FNBP4 WILD-TYPE	156	58	41

'FNBP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S328. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
FNBP4 MUTATED	2	0	1
FNBP4 WILD-TYPE	73	89	96

'FNBP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S329. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
FNBP4 MUTATED	2	0	1
FNBP4 WILD-TYPE	79	84	92

'FNBP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S330. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
FNBP4 MUTATED	2	0	1
FNBP4 WILD-TYPE	88	83	84

'FNBP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S331. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
FNBP4 MUTATED	0	1	1	0	1
FNBP4 WILD-TYPE	48	17	58	55	78

'FNBP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.41 (Fisher's exact test), Q value = 1

Table S332. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
FNBP4 MUTATED	0	1	2
FNBP4 WILD-TYPE	92	45	119

'FNBP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 1

Table S333. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
FNBP4 MUTATED	1	2	0
FNBP4 WILD-TYPE	69	89	98

'FNBP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0453 (Fisher's exact test), Q value = 1

Table S334. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
FNBP4 MUTATED	0	1	2	0	0
FNBP4 WILD-TYPE	42	20	49	62	83

Figure S58. Get High-res Image Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDKN1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S335. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
CDKN1B MUTATED	2	1	1
CDKN1B WILD-TYPE	155	58	41

'CDKN1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 1

Table S336. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
CDKN1B MUTATED	3	0	1
CDKN1B WILD-TYPE	72	89	96

'CDKN1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 1

Table S337. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
CDKN1B MUTATED	1	0	3
CDKN1B WILD-TYPE	41	59	60

'CDKN1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 1

Table S338. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	66	50
CDKN1B MUTATED	1	3	0
CDKN1B WILD-TYPE	47	63	50

'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 1

Table S339. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
CDKN1B MUTATED	3	0	1
CDKN1B WILD-TYPE	78	84	92

'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S340. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
CDKN1B MUTATED	2	0	2
CDKN1B WILD-TYPE	88	83	83

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.743 (Fisher's exact test), Q value = 1

Table S341. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
CDKN1B MUTATED	0	0	1	2	1
CDKN1B WILD-TYPE	48	18	58	53	78

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S342. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
CDKN1B MUTATED	0	2	2
CDKN1B WILD-TYPE	92	44	119

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 1

Table S343. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
CDKN1B MUTATED	2	1	1
CDKN1B WILD-TYPE	68	90	97

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S344. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
CDKN1B MUTATED	0	1	2	0	1
CDKN1B WILD-TYPE	42	20	49	62	82

'EIF2AK3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S345. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
EIF2AK3 MUTATED	3	1	0
EIF2AK3 WILD-TYPE	154	58	42

'EIF2AK3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 1

Table S346. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
EIF2AK3 MUTATED	0	3	1
EIF2AK3 WILD-TYPE	75	86	96

'EIF2AK3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 1

Table S347. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
EIF2AK3 MUTATED	0	2	2
EIF2AK3 WILD-TYPE	81	82	91

'EIF2AK3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S348. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
EIF2AK3 MUTATED	1	2	1
EIF2AK3 WILD-TYPE	89	81	84

'EIF2AK3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 1

Table S349. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
EIF2AK3 MUTATED	1	0	0	0	3
EIF2AK3 WILD-TYPE	47	18	59	55	76

'EIF2AK3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S350. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
EIF2AK3 MUTATED	1	1	2
EIF2AK3 WILD-TYPE	91	45	119

'EIF2AK3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S351. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
EIF2AK3 MUTATED	0	3	1
EIF2AK3 WILD-TYPE	70	88	97

'EIF2AK3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S352. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
EIF2AK3 MUTATED	0	0	0	1	3
EIF2AK3 WILD-TYPE	42	21	51	61	80

'LARP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.742 (Fisher's exact test), Q value = 1

Table S353. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	59	42
LARP1 MUTATED	3	0	0
LARP1 WILD-TYPE	154	59	42

'LARP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 1

Table S354. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
LARP1 MUTATED	1	2	0
LARP1 WILD-TYPE	74	87	97

'LARP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S355. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	84	93
LARP1 MUTATED	0	1	2
LARP1 WILD-TYPE	81	83	91

'LARP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 1

Table S356. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	83	85
LARP1 MUTATED	0	2	1
LARP1 WILD-TYPE	90	81	84

'LARP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 1

Table S357. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	18	59	55	79
LARP1 MUTATED	2	0	0	1	0
LARP1 WILD-TYPE	46	18	59	54	79

'LARP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S358. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	46	121
LARP1 MUTATED	3	0	0
LARP1 WILD-TYPE	89	46	121

'LARP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 1

Table S359. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	91	98
LARP1 MUTATED	1	0	2
LARP1 WILD-TYPE	69	91	96

'LARP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 1

Table S360. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	21	51	62	83
LARP1 MUTATED	0	0	0	2	1
LARP1 WILD-TYPE	42	21	51	60	82

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = PRAD-TP.transferedmergedcluster.txt
Number of patients = 261
Number of significantly mutated genes = 38
Number of Molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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