Correlation between gene mutation status and molecular subtypes

Prostate Adenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1X63KVW

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, 5 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'.

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, 5 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	1e-05 (0.00338)	1e-05 (0.00338)	0.336 (1.00)	0.284 (1.00)	1e-05 (0.00338)	1e-05 (0.00338)	0.966 (1.00)	0.0514 (1.00)	0.126 (1.00)	0.353 (1.00)
TP53	23 (9%)	238	1e-05 (0.00338)	0.327 (1.00)	0.00805 (1.00)	0.00633 (1.00)	0.0108 (1.00)	0.0109 (1.00)	0.737 (1.00)	0.412 (1.00)	0.0852 (1.00)	0.0396 (1.00)
PTEN	13 (5%)	248	0.619 (1.00)	0.406 (1.00)	0.2 (1.00)	0.305 (1.00)	0.078 (1.00)	0.0644 (1.00)	0.278 (1.00)	0.287 (1.00)	0.151 (1.00)	0.0746 (1.00)
CTNNB1	9 (3%)	252	0.443 (1.00)	0.0622 (1.00)	0.0396 (1.00)	0.0384 (1.00)	0.329 (1.00)	0.143 (1.00)	0.126 (1.00)	0.0461 (1.00)	0.187 (1.00)	0.127 (1.00)
TCEB3	4 (2%)	257	0.644 (1.00)	0.391 (1.00)	0.116 (1.00)	0.629 (1.00)	0.392 (1.00)	0.327 (1.00)	0.154 (1.00)	0.16 (1.00)	0.181 (1.00)	0.439 (1.00)
FOXA1	12 (5%)	249	0.0037 (1.00)	0.0161 (1.00)	1 (1.00)	0.492 (1.00)	0.238 (1.00)	0.0271 (1.00)	0.19 (1.00)	0.135 (1.00)	0.199 (1.00)	0.677 (1.00)
BRAF	6 (2%)	255	0.735 (1.00)	0.273 (1.00)	0.833 (1.00)	1 (1.00)	0.252 (1.00)	0.00907 (1.00)	0.518 (1.00)	0.523 (1.00)	0.511 (1.00)	0.663 (1.00)
PIK3CA	9 (3%)	252	0.309 (1.00)	0.00411 (1.00)	0.041 (1.00)	0.0383 (1.00)	0.0557 (1.00)	0.00207 (0.689)	0.104 (1.00)	0.0741 (1.00)	0.948 (1.00)	0.214 (1.00)
IDH1	4 (2%)	257	0.0402 (1.00)	0.0143 (1.00)	0.0619 (1.00)	0.0512 (1.00)	0.00754 (1.00)	0.00902 (1.00)	0.392 (1.00)	0.0356 (1.00)	0.523 (1.00)	0.0754 (1.00)
FAM47C	8 (3%)	253	0.417 (1.00)	0.222 (1.00)	1 (1.00)	1 (1.00)	0.907 (1.00)	0.602 (1.00)	0.497 (1.00)	0.548 (1.00)	0.367 (1.00)	0.267 (1.00)
TP53BP1	5 (2%)	256	0.0337 (1.00)	0.105 (1.00)	0.12 (1.00)	0.15 (1.00)	0.446 (1.00)	0.026 (1.00)	1 (1.00)	0.289 (1.00)	0.72 (1.00)	0.0792 (1.00)
CNTNAP1	5 (2%)	256	0.168 (1.00)	0.0765 (1.00)			0.266 (1.00)	0.392 (1.00)	0.738 (1.00)	0.0202 (1.00)
MLLT10	4 (2%)	257	0.645 (1.00)	0.471 (1.00)	0.559 (1.00)	0.689 (1.00)	1 (1.00)	0.69 (1.00)	0.0722 (1.00)	0.416 (1.00)
ZMYM3	6 (2%)	255	0.535 (1.00)	0.00622 (1.00)	0.443 (1.00)	0.392 (1.00)	0.0402 (1.00)	0.146 (1.00)	0.0278 (1.00)	0.14 (1.00)	0.0452 (1.00)	0.0939 (1.00)
SMG7	4 (2%)	257	0.643 (1.00)	0.628 (1.00)	1 (1.00)	1 (1.00)	0.113 (1.00)	0.00866 (1.00)	0.556 (1.00)	0.239 (1.00)	0.524 (1.00)	0.452 (1.00)
EDC4	3 (1%)	258	0.059 (1.00)	0.27 (1.00)			0.403 (1.00)	0.309 (1.00)	0.518 (1.00)	0.0326 (1.00)	0.601 (1.00)	1 (1.00)
ZNF709	4 (2%)	257	0.822 (1.00)	0.0593 (1.00)	0.452 (1.00)	0.389 (1.00)	0.394 (1.00)	1 (1.00)	0.556 (1.00)	0.0716 (1.00)	0.882 (1.00)	0.852 (1.00)
CDK12	7 (3%)	254	0.00222 (0.737)	0.378 (1.00)	0.0398 (1.00)	0.0396 (1.00)	1 (1.00)	0.255 (1.00)	0.304 (1.00)	0.0449 (1.00)	0.441 (1.00)	0.922 (1.00)
RPTN	6 (2%)	255	0.115 (1.00)	0.0766 (1.00)	0.115 (1.00)	0.115 (1.00)	0.875 (1.00)	0.451 (1.00)	0.518 (1.00)	0.161 (1.00)	0.712 (1.00)	0.96 (1.00)
TNRC18	4 (2%)	257	0.169 (1.00)	0.697 (1.00)			1 (1.00)	1 (1.00)	0.555 (1.00)	0.594 (1.00)	1 (1.00)	1 (1.00)
MED15	5 (2%)	256	0.688 (1.00)	0.0941 (1.00)	0.444 (1.00)	0.735 (1.00)	0.631 (1.00)	0.449 (1.00)	0.527 (1.00)	0.844 (1.00)	0.523 (1.00)	0.618 (1.00)
NKX3-1	5 (2%)	256	0.472 (1.00)	0.227 (1.00)	0.0283 (1.00)	0.0512 (1.00)	0.864 (1.00)	0.866 (1.00)	0.326 (1.00)	0.794 (1.00)
KDM6A	6 (2%)	255	0.0101 (1.00)	0.291 (1.00)	0.832 (1.00)	0.691 (1.00)	0.0135 (1.00)	0.253 (1.00)	0.876 (1.00)	0.0965 (1.00)	0.6 (1.00)	0.106 (1.00)
RNF31	4 (2%)	257	1 (1.00)	0.28 (1.00)	0.68 (1.00)	0.559 (1.00)	0.519 (1.00)	1 (1.00)	0.553 (1.00)	0.0992 (1.00)	0.512 (1.00)	0.662 (1.00)
ESCO1	4 (2%)	257	0.821 (1.00)	0.282 (1.00)	0.475 (1.00)	0.378 (1.00)	0.207 (1.00)	0.549 (1.00)	0.0738 (1.00)	0.779 (1.00)
LMOD2	3 (1%)	258	1 (1.00)	0.832 (1.00)			1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.296 (1.00)	0.41 (1.00)
FAM120B	3 (1%)	258	0.198 (1.00)	0.272 (1.00)			0.399 (1.00)	0.532 (1.00)	0.778 (1.00)	0.0889 (1.00)
CLEC1A	4 (2%)	257	0.82 (1.00)	0.313 (1.00)			0.156 (1.00)	0.214 (1.00)	0.47 (1.00)	1 (1.00)
ITGA2B	3 (1%)	258	1 (1.00)	0.327 (1.00)	0.784 (1.00)	0.781 (1.00)	0.643 (1.00)	0.309 (1.00)	0.515 (1.00)	0.443 (1.00)	0.432 (1.00)	0.664 (1.00)
RNF17	3 (1%)	258	1 (1.00)	0.725 (1.00)	0.0161 (1.00)	0.0252 (1.00)	0.11 (1.00)	0.111 (1.00)	0.2 (1.00)	0.92 (1.00)
RP1L1	7 (3%)	254	0.751 (1.00)	0.762 (1.00)	0.444 (1.00)	0.39 (1.00)	0.712 (1.00)	0.4 (1.00)	0.0689 (1.00)	0.352 (1.00)	0.0633 (1.00)	0.105 (1.00)
EOMES	4 (2%)	257	0.25 (1.00)	0.782 (1.00)	0.783 (1.00)	0.781 (1.00)	0.267 (1.00)	0.162 (1.00)	1 (1.00)	0.439 (1.00)	0.0181 (1.00)	0.29 (1.00)
MTF1	3 (1%)	258	0.128 (1.00)	0.63 (1.00)			0.202 (1.00)	0.206 (1.00)	0.643 (1.00)	0.368 (1.00)
NTM	5 (2%)	256	1 (1.00)	0.442 (1.00)	0.122 (1.00)	0.331 (1.00)	0.326 (1.00)	0.376 (1.00)	0.736 (1.00)	0.579 (1.00)
FNBP4	3 (1%)	258	0.337 (1.00)	0.00676 (1.00)			0.399 (1.00)	0.308 (1.00)	0.515 (1.00)	0.136 (1.00)
CDKN1B	4 (2%)	257	0.645 (1.00)	0.14 (1.00)	0.242 (1.00)	0.31 (1.00)	0.463 (1.00)	0.118 (1.00)	0.555 (1.00)	0.0617 (1.00)	0.511 (1.00)	0.177 (1.00)
EIF2AK3	4 (2%)	257	0.647 (1.00)	0.352 (1.00)			1 (1.00)	0.843 (1.00)	0.392 (1.00)	0.949 (1.00)	0.791 (1.00)	0.498 (1.00)
LARP1	3 (1%)	258	0.552 (1.00)	0.268 (1.00)			0.779 (1.00)	1 (1.00)	1 (1.00)	0.792 (1.00)

'SPOP MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0034

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
SPOP MUTATED	4	5	16
SPOP WILD-TYPE	153	46	34

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 = 0.0034

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
SPOP MUTATED	5	19	1	1
SPOP WILD-TYPE	84	50	79	22

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 = 0.336 (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 = 0.284 (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 = 0.0034

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
SPOP MUTATED	6	18	1
SPOP WILD-TYPE	79	60	94

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 = 0.0034

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
SPOP MUTATED	8	17	0
SPOP WILD-TYPE	78	63	92

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 = 0.966 (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
ALL	79	97	83
SPOP MUTATED	8	9	9
SPOP WILD-TYPE	71	88	74

'SPOP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0514 (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	CLUS_4	CLUS_5
ALL	86	50	30	41	52
SPOP MUTATED	8	3	0	8	7
SPOP WILD-TYPE	78	47	30	33	45

'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.126 (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	CLUS_4
ALL	33	40	18	74
SPOP MUTATED	1	5	0	11
SPOP WILD-TYPE	32	35	18	63

'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.353 (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	CLUS_6
ALL	26	16	4	37	25	57
SPOP MUTATED	2	2	0	6	0	7
SPOP WILD-TYPE	24	14	4	31	25	50

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0034

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
TP53 MUTATED	4	18	1
TP53 WILD-TYPE	153	33	49

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 = 0.327 (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	CLUS_4
ALL	89	69	80	23
TP53 MUTATED	5	5	10	3
TP53 WILD-TYPE	84	64	70	20

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00805 (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 = 0.00633 (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 = 0.0108 (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	85	78	95
TP53 MUTATED	3	5	15
TP53 WILD-TYPE	82	73	80

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 = 0.0109 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
TP53 MUTATED	5	3	15
TP53 WILD-TYPE	81	77	77

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 = 0.737 (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
ALL	79	97	83
TP53 MUTATED	6	8	9
TP53 WILD-TYPE	73	89	74

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.412 (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	CLUS_4	CLUS_5
ALL	86	50	30	41	52
TP53 MUTATED	6	2	4	5	6
TP53 WILD-TYPE	80	48	26	36	46

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0852 (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	CLUS_4
ALL	33	40	18	74
TP53 MUTATED	0	6	2	9
TP53 WILD-TYPE	33	34	16	65

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0396 (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	CLUS_6
ALL	26	16	4	37	25	57
TP53 MUTATED	3	0	2	5	0	7
TP53 WILD-TYPE	23	16	2	32	25	50

Figure S10. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.619 (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	51	50
PTEN MUTATED	7	4	2
PTEN WILD-TYPE	150	47	48

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.406 (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	CLUS_4
ALL	89	69	80	23
PTEN MUTATED	2	4	6	1
PTEN WILD-TYPE	87	65	74	22

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.2 (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 = 0.305 (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 = 0.078 (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	85	78	95
PTEN MUTATED	1	4	8
PTEN WILD-TYPE	84	74	87

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0644 (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	86	80	92
PTEN MUTATED	1	4	8
PTEN WILD-TYPE	85	76	84

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.278 (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
ALL	79	97	83
PTEN MUTATED	3	3	7
PTEN WILD-TYPE	76	94	76

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.287 (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	CLUS_4	CLUS_5
ALL	86	50	30	41	52
PTEN MUTATED	4	1	0	4	4
PTEN WILD-TYPE	82	49	30	37	48

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.151 (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	CLUS_4
ALL	33	40	18	74
PTEN MUTATED	1	5	1	2
PTEN WILD-TYPE	32	35	17	72

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0746 (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	CLUS_6
ALL	26	16	4	37	25	57
PTEN MUTATED	0	0	0	6	0	3
PTEN WILD-TYPE	26	16	4	31	25	54

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.443 (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	51	50
CTNNB1 MUTATED	4	2	3
CTNNB1 WILD-TYPE	153	49	47

'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0622 (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	CLUS_4
ALL	89	69	80	23
CTNNB1 MUTATED	0	3	5	1
CTNNB1 WILD-TYPE	89	66	75	22

'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0396 (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 S11. Get High-res Image Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0384 (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 S12. Get High-res Image Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.329 (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	85	78	95
CTNNB1 MUTATED	1	3	5
CTNNB1 WILD-TYPE	84	75	90

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.143 (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	86	80	92
CTNNB1 MUTATED	1	2	6
CTNNB1 WILD-TYPE	85	78	86

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.126 (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
ALL	79	97	83
CTNNB1 MUTATED	1	2	6
CTNNB1 WILD-TYPE	78	95	77

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0461 (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	CLUS_4	CLUS_5
ALL	86	50	30	41	52
CTNNB1 MUTATED	1	0	1	4	3
CTNNB1 WILD-TYPE	85	50	29	37	49

Figure S13. Get High-res Image Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.187 (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	CLUS_4
ALL	33	40	18	74
CTNNB1 MUTATED	0	4	0	3
CTNNB1 WILD-TYPE	33	36	18	71

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.127 (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	CLUS_6
ALL	26	16	4	37	25	57
CTNNB1 MUTATED	0	0	0	5	0	2
CTNNB1 WILD-TYPE	26	16	4	32	25	55

'TCEB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.644 (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	51	50
TCEB3 MUTATED	2	1	1
TCEB3 WILD-TYPE	155	50	49

'TCEB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.391 (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	CLUS_4
ALL	89	69	80	23
TCEB3 MUTATED	1	0	3	0
TCEB3 WILD-TYPE	88	69	77	23

'TCEB3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.116 (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 = 0.629 (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 = 0.392 (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	85	78	95
TCEB3 MUTATED	1	0	3
TCEB3 WILD-TYPE	84	78	92

'TCEB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.327 (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	86	80	92
TCEB3 MUTATED	1	0	3
TCEB3 WILD-TYPE	85	80	89

'TCEB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.154 (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
ALL	79	97	83
TCEB3 MUTATED	3	1	0
TCEB3 WILD-TYPE	76	96	83

'TCEB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.16 (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	CLUS_4	CLUS_5
ALL	86	50	30	41	52
TCEB3 MUTATED	1	1	2	0	0
TCEB3 WILD-TYPE	85	49	28	41	52

'TCEB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.181 (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	CLUS_4
ALL	33	40	18	74
TCEB3 MUTATED	1	2	0	0
TCEB3 WILD-TYPE	32	38	18	74

'TCEB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.439 (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	CLUS_6
ALL	26	16	4	37	25	57
TCEB3 MUTATED	1	0	0	1	1	0
TCEB3 WILD-TYPE	25	16	4	36	24	57

'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0037 (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	51	50
FOXA1 MUTATED	3	2	7
FOXA1 WILD-TYPE	154	49	43

Figure S14. Get High-res Image Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
FOXA1 MUTATED	2	8	1	1
FOXA1 WILD-TYPE	87	61	79	22

Figure S15. 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 = 0.492 (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 = 0.238 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
FOXA1 MUTATED	4	6	2
FOXA1 WILD-TYPE	81	72	93

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0271 (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	86	80	92
FOXA1 MUTATED	3	8	1
FOXA1 WILD-TYPE	83	72	91

Figure S16. Get High-res Image Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.19 (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
ALL	79	97	83
FOXA1 MUTATED	2	3	7
FOXA1 WILD-TYPE	77	94	76

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.135 (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	CLUS_4	CLUS_5
ALL	86	50	30	41	52
FOXA1 MUTATED	1	2	1	4	4
FOXA1 WILD-TYPE	85	48	29	37	48

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.199 (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	CLUS_4
ALL	33	40	18	74
FOXA1 MUTATED	2	0	0	6
FOXA1 WILD-TYPE	31	40	18	68

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.677 (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	CLUS_6
ALL	26	16	4	37	25	57
FOXA1 MUTATED	1	0	0	2	0	5
FOXA1 WILD-TYPE	25	16	4	35	25	52

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.735 (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	51	50
BRAF MUTATED	3	1	2
BRAF WILD-TYPE	154	50	48

'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.273 (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	CLUS_4
ALL	89	69	80	23
BRAF MUTATED	3	2	0	1
BRAF WILD-TYPE	86	67	80	22

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.833 (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 = 0.252 (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	85	78	95
BRAF MUTATED	1	4	1
BRAF WILD-TYPE	84	74	94

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00907 (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	86	80	92
BRAF MUTATED	1	5	0
BRAF WILD-TYPE	85	75	92

Figure S17. Get High-res Image Gene #7: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.518 (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
ALL	79	97	83
BRAF MUTATED	2	1	3
BRAF WILD-TYPE	77	96	80

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.523 (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	CLUS_4	CLUS_5
ALL	86	50	30	41	52
BRAF MUTATED	3	1	0	2	0
BRAF WILD-TYPE	83	49	30	39	52

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.511 (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	CLUS_4
ALL	33	40	18	74
BRAF MUTATED	0	2	0	1
BRAF WILD-TYPE	33	38	18	73

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.663 (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	CLUS_6
ALL	26	16	4	37	25	57
BRAF MUTATED	0	0	0	2	0	1
BRAF WILD-TYPE	26	16	4	35	25	56

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.309 (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	51	50
PIK3CA MUTATED	6	3	0
PIK3CA WILD-TYPE	151	48	50

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00411 (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	CLUS_4
ALL	89	69	80	23
PIK3CA MUTATED	0	1	5	3
PIK3CA WILD-TYPE	89	68	75	20

Figure S18. Get High-res Image Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.041 (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 S19. Get High-res Image Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0383 (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 S20. Get High-res Image Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0557 (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	85	78	95
PIK3CA MUTATED	1	1	7
PIK3CA WILD-TYPE	84	77	88

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00207 (Fisher's exact test), Q value = 0.69

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
PIK3CA MUTATED	0	1	8
PIK3CA WILD-TYPE	86	79	84

Figure S21. Get High-res Image Gene #8: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.104 (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
ALL	79	97	83
PIK3CA MUTATED	2	1	6
PIK3CA WILD-TYPE	77	96	77

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0741 (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	CLUS_4	CLUS_5
ALL	86	50	30	41	52
PIK3CA MUTATED	1	0	2	3	3
PIK3CA WILD-TYPE	85	50	28	38	49

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.948 (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	CLUS_4
ALL	33	40	18	74
PIK3CA MUTATED	1	2	0	4
PIK3CA WILD-TYPE	32	38	18	70

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.214 (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	CLUS_6
ALL	26	16	4	37	25	57
PIK3CA MUTATED	0	0	1	3	1	2
PIK3CA WILD-TYPE	26	16	3	34	24	55

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0402 (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	51	50
IDH1 MUTATED	1	0	3
IDH1 WILD-TYPE	156	51	47

Figure S22. Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0143 (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	CLUS_4
ALL	89	69	80	23
IDH1 MUTATED	0	4	0	0
IDH1 WILD-TYPE	89	65	80	23

Figure S23. Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0619 (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 = 0.0512 (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 = 0.00754 (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	85	78	95
IDH1 MUTATED	0	4	0
IDH1 WILD-TYPE	85	74	95

Figure S24. Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00902 (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	86	80	92
IDH1 MUTATED	0	4	0
IDH1 WILD-TYPE	86	76	92

Figure S25. Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.392 (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
ALL	79	97	83
IDH1 MUTATED	0	3	1
IDH1 WILD-TYPE	79	94	82

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0356 (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	CLUS_4	CLUS_5
ALL	86	50	30	41	52
IDH1 MUTATED	0	3	0	1	0
IDH1 WILD-TYPE	86	47	30	40	52

Figure S26. Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.523 (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	CLUS_4
ALL	33	40	18	74
IDH1 MUTATED	1	1	1	1
IDH1 WILD-TYPE	32	39	17	73

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0754 (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	CLUS_6
ALL	26	16	4	37	25	57
IDH1 MUTATED	0	2	0	1	1	0
IDH1 WILD-TYPE	26	14	4	36	24	57

'FAM47C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.417 (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	51	50
FAM47C MUTATED	6	0	2
FAM47C WILD-TYPE	151	51	48

'FAM47C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.222 (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	CLUS_4
ALL	89	69	80	23
FAM47C MUTATED	4	0	4	0
FAM47C WILD-TYPE	85	69	76	23

'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 = 0.907 (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	85	78	95
FAM47C MUTATED	2	3	3
FAM47C WILD-TYPE	83	75	92

'FAM47C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.602 (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	86	80	92
FAM47C MUTATED	2	4	2
FAM47C WILD-TYPE	84	76	90

'FAM47C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.497 (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
ALL	79	97	83
FAM47C MUTATED	3	4	1
FAM47C WILD-TYPE	76	93	82

'FAM47C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.548 (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	CLUS_4	CLUS_5
ALL	86	50	30	41	52
FAM47C MUTATED	3	2	0	0	3
FAM47C WILD-TYPE	83	48	30	41	49

'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.367 (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	CLUS_4
ALL	33	40	18	74
FAM47C MUTATED	1	2	2	2
FAM47C WILD-TYPE	32	38	16	72

'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.267 (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	CLUS_6
ALL	26	16	4	37	25	57
FAM47C MUTATED	2	2	0	0	1	2
FAM47C WILD-TYPE	24	14	4	37	24	55

'TP53BP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0337 (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	51	50
TP53BP1 MUTATED	1	1	3
TP53BP1 WILD-TYPE	156	50	47

Figure S27. Get High-res Image Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53BP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.105 (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	CLUS_4
ALL	89	69	80	23
TP53BP1 MUTATED	1	3	0	1
TP53BP1 WILD-TYPE	88	66	80	22

'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 = 0.446 (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	85	78	95
TP53BP1 MUTATED	1	3	1
TP53BP1 WILD-TYPE	84	75	94

'TP53BP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.026 (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	86	80	92
TP53BP1 MUTATED	1	4	0
TP53BP1 WILD-TYPE	85	76	92

Figure S28. Get High-res Image Gene #11: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53BP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (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
ALL	79	97	83
TP53BP1 MUTATED	1	2	2
TP53BP1 WILD-TYPE	78	95	81

'TP53BP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.289 (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	CLUS_4	CLUS_5
ALL	86	50	30	41	52
TP53BP1 MUTATED	1	2	0	2	0
TP53BP1 WILD-TYPE	85	48	30	39	52

'TP53BP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.72 (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	CLUS_4
ALL	33	40	18	74
TP53BP1 MUTATED	0	2	0	2
TP53BP1 WILD-TYPE	33	38	18	72

'TP53BP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0792 (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	CLUS_6
ALL	26	16	4	37	25	57
TP53BP1 MUTATED	1	2	0	1	0	0
TP53BP1 WILD-TYPE	25	14	4	36	25	57

'CNTNAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.168 (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	51	50
CNTNAP1 MUTATED	1	2	1
CNTNAP1 WILD-TYPE	156	49	49

'CNTNAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0765 (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	CLUS_4
ALL	89	69	80	23
CNTNAP1 MUTATED	1	4	0	0
CNTNAP1 WILD-TYPE	88	65	80	23

'CNTNAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.266 (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	85	78	95
CNTNAP1 MUTATED	2	2	0
CNTNAP1 WILD-TYPE	83	76	95

'CNTNAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.392 (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	86	80	92
CNTNAP1 MUTATED	2	2	0
CNTNAP1 WILD-TYPE	84	78	92

'CNTNAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.738 (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
ALL	79	97	83
CNTNAP1 MUTATED	2	1	2
CNTNAP1 WILD-TYPE	77	96	81

'CNTNAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0202 (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	CLUS_4	CLUS_5
ALL	86	50	30	41	52
CNTNAP1 MUTATED	0	0	0	3	2
CNTNAP1 WILD-TYPE	86	50	30	38	50

Figure S29. Get High-res Image Gene #12: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MLLT10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S117. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
MLLT10 MUTATED	2	1	1
MLLT10 WILD-TYPE	155	50	49

'MLLT10 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S118. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
MLLT10 MUTATED	3	1	0	0
MLLT10 WILD-TYPE	86	68	80	23

'MLLT10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.559 (Fisher's exact test), Q value = 1

Table S119. 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 = 0.689 (Fisher's exact test), Q value = 1

Table S120. 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 S121. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
MLLT10 MUTATED	1	1	2
MLLT10 WILD-TYPE	84	77	93

'MLLT10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S122. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
MLLT10 MUTATED	1	2	1
MLLT10 WILD-TYPE	85	78	91

'MLLT10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0722 (Fisher's exact test), Q value = 1

Table S123. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
MLLT10 MUTATED	3	0	1
MLLT10 WILD-TYPE	76	97	82

'MLLT10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 1

Table S124. Gene #13: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
MLLT10 MUTATED	3	0	0	1	0
MLLT10 WILD-TYPE	83	50	30	40	52

'ZMYM3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S125. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
ZMYM3 MUTATED	5	0	1
ZMYM3 WILD-TYPE	152	51	49

'ZMYM3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00622 (Fisher's exact test), Q value = 1

Table S126. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
ZMYM3 MUTATED	0	1	2	3
ZMYM3 WILD-TYPE	89	68	78	20

Figure S30. Get High-res Image Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ZMYM3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S127. 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 = 0.392 (Fisher's exact test), Q value = 1

Table S128. 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 = 0.0402 (Fisher's exact test), Q value = 1

Table S129. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
ZMYM3 MUTATED	0	1	5
ZMYM3 WILD-TYPE	85	77	90

Figure S31. Get High-res Image Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S130. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
ZMYM3 MUTATED	0	2	4
ZMYM3 WILD-TYPE	86	78	88

'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 1

Table S131. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
ZMYM3 MUTATED	0	1	5
ZMYM3 WILD-TYPE	79	96	78

Figure S32. Get High-res Image Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.14 (Fisher's exact test), Q value = 1

Table S132. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
ZMYM3 MUTATED	1	1	1	3	0
ZMYM3 WILD-TYPE	85	49	29	38	52

'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 1

Table S133. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
ZMYM3 MUTATED	2	3	0	0
ZMYM3 WILD-TYPE	31	37	18	74

Figure S33. 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 = 0.0939 (Fisher's exact test), Q value = 1

Table S134. Gene #14: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
ZMYM3 MUTATED	0	0	0	3	2	0
ZMYM3 WILD-TYPE	26	16	4	34	23	57

'SMG7 MUTATION STATUS' versus 'CN_CNMF'

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

Table S135. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
SMG7 MUTATED	2	1	1
SMG7 WILD-TYPE	155	50	49

'SMG7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.628 (Fisher's exact test), Q value = 1

Table S136. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
SMG7 MUTATED	1	1	1	1
SMG7 WILD-TYPE	88	68	79	22

'SMG7 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S137. 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 S138. 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 = 0.113 (Fisher's exact test), Q value = 1

Table S139. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
SMG7 MUTATED	0	3	1
SMG7 WILD-TYPE	85	75	94

'SMG7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00866 (Fisher's exact test), Q value = 1

Table S140. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
SMG7 MUTATED	0	4	0
SMG7 WILD-TYPE	86	76	92

Figure S34. Get High-res Image Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SMG7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S141. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
SMG7 MUTATED	0	2	2
SMG7 WILD-TYPE	79	95	81

'SMG7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.239 (Fisher's exact test), Q value = 1

Table S142. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
SMG7 MUTATED	0	1	0	2	1
SMG7 WILD-TYPE	86	49	30	39	51

'SMG7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S143. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
SMG7 MUTATED	1	1	1	1
SMG7 WILD-TYPE	32	39	17	73

'SMG7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S144. Gene #15: 'SMG7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
SMG7 MUTATED	0	1	0	2	0	1
SMG7 WILD-TYPE	26	15	4	35	25	56

'EDC4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.059 (Fisher's exact test), Q value = 1

Table S145. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
EDC4 MUTATED	0	2	1
EDC4 WILD-TYPE	157	49	49

'EDC4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 1

Table S146. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
EDC4 MUTATED	1	1	0	1
EDC4 WILD-TYPE	88	68	80	22

'EDC4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 1

Table S147. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
EDC4 MUTATED	0	2	1
EDC4 WILD-TYPE	85	76	94

'EDC4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.309 (Fisher's exact test), Q value = 1

Table S148. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
EDC4 MUTATED	0	2	1
EDC4 WILD-TYPE	86	78	91

'EDC4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S149. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
EDC4 MUTATED	0	1	2
EDC4 WILD-TYPE	79	96	81

'EDC4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 1

Table S150. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
EDC4 MUTATED	0	0	0	0	3
EDC4 WILD-TYPE	86	50	30	41	49

Figure S35. Get High-res Image Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'EDC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S151. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
EDC4 MUTATED	0	0	0	3
EDC4 WILD-TYPE	33	40	18	71

'EDC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S152. Gene #16: 'EDC4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
EDC4 MUTATED	0	0	0	1	0	2
EDC4 WILD-TYPE	26	16	4	36	25	55

'ZNF709 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.822 (Fisher's exact test), Q value = 1

Table S153. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
ZNF709 MUTATED	3	0	1
ZNF709 WILD-TYPE	154	51	49

'ZNF709 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0593 (Fisher's exact test), Q value = 1

Table S154. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
ZNF709 MUTATED	1	0	1	2
ZNF709 WILD-TYPE	88	69	79	21

'ZNF709 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S155. 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 S156. 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 = 0.394 (Fisher's exact test), Q value = 1

Table S157. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
ZNF709 MUTATED	1	0	3
ZNF709 WILD-TYPE	84	78	92

'ZNF709 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S158. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
ZNF709 MUTATED	1	1	2
ZNF709 WILD-TYPE	85	79	90

'ZNF709 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S159. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
ZNF709 MUTATED	0	2	2
ZNF709 WILD-TYPE	79	95	81

'ZNF709 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0716 (Fisher's exact test), Q value = 1

Table S160. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
ZNF709 MUTATED	0	0	0	2	2
ZNF709 WILD-TYPE	86	50	30	39	50

'ZNF709 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S161. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
ZNF709 MUTATED	0	1	0	3
ZNF709 WILD-TYPE	33	39	18	71

'ZNF709 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S162. Gene #17: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
ZNF709 MUTATED	0	0	0	1	0	3
ZNF709 WILD-TYPE	26	16	4	36	25	54

'CDK12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.74

Table S163. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
CDK12 MUTATED	0	4	2
CDK12 WILD-TYPE	157	47	48

Figure S36. Get High-res Image Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CDK12 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S164. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
CDK12 MUTATED	1	4	2	0
CDK12 WILD-TYPE	88	65	78	23

'CDK12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 1

Table S165. 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 S37. Get High-res Image Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CDK12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 1

Table S166. 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 S38. Get High-res Image Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CDK12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S167. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
CDK12 MUTATED	2	2	2
CDK12 WILD-TYPE	83	76	93

'CDK12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S168. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
CDK12 MUTATED	1	4	1
CDK12 WILD-TYPE	85	76	91

'CDK12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 1

Table S169. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
CDK12 MUTATED	2	1	4
CDK12 WILD-TYPE	77	96	79

'CDK12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0449 (Fisher's exact test), Q value = 1

Table S170. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
CDK12 MUTATED	1	0	1	4	1
CDK12 WILD-TYPE	85	50	29	37	51

Figure S39. Get High-res Image Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 1

Table S171. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
CDK12 MUTATED	0	3	0	3
CDK12 WILD-TYPE	33	37	18	71

'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.922 (Fisher's exact test), Q value = 1

Table S172. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
CDK12 MUTATED	1	0	0	2	0	3
CDK12 WILD-TYPE	25	16	4	35	25	54

'RPTN MUTATION STATUS' versus 'CN_CNMF'

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

Table S173. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
RPTN MUTATED	3	0	3
RPTN WILD-TYPE	154	51	47

'RPTN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0766 (Fisher's exact test), Q value = 1

Table S174. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
RPTN MUTATED	2	2	0	2
RPTN WILD-TYPE	87	67	80	21

'RPTN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S175. 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 = 0.115 (Fisher's exact test), Q value = 1

Table S176. 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 = 0.875 (Fisher's exact test), Q value = 1

Table S177. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
RPTN MUTATED	2	1	3
RPTN WILD-TYPE	83	77	92

'RPTN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.451 (Fisher's exact test), Q value = 1

Table S178. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
RPTN MUTATED	2	3	1
RPTN WILD-TYPE	84	77	91

'RPTN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S179. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
RPTN MUTATED	2	1	3
RPTN WILD-TYPE	77	96	80

'RPTN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S180. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
RPTN MUTATED	1	0	0	2	3
RPTN WILD-TYPE	85	50	30	39	49

'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.712 (Fisher's exact test), Q value = 1

Table S181. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
RPTN MUTATED	0	2	0	3
RPTN WILD-TYPE	33	38	18	71

'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.96 (Fisher's exact test), Q value = 1

Table S182. Gene #19: 'RPTN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
RPTN MUTATED	1	0	0	1	0	3
RPTN WILD-TYPE	25	16	4	36	25	54

'TNRC18 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 1

Table S183. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
TNRC18 MUTATED	1	2	1
TNRC18 WILD-TYPE	156	49	49

'TNRC18 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 1

Table S184. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
TNRC18 MUTATED	2	0	2	0
TNRC18 WILD-TYPE	87	69	78	23

'TNRC18 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S185. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
TNRC18 MUTATED	1	1	2
TNRC18 WILD-TYPE	84	77	93

'TNRC18 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S186. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
TNRC18 MUTATED	1	1	2
TNRC18 WILD-TYPE	85	79	90

'TNRC18 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S187. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
TNRC18 MUTATED	0	2	2
TNRC18 WILD-TYPE	79	95	81

'TNRC18 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.594 (Fisher's exact test), Q value = 1

Table S188. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
TNRC18 MUTATED	1	1	1	1	0
TNRC18 WILD-TYPE	85	49	29	40	52

'TNRC18 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S189. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
TNRC18 MUTATED	0	1	0	2
TNRC18 WILD-TYPE	33	39	18	72

'TNRC18 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S190. Gene #20: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
TNRC18 MUTATED	0	0	0	1	0	2
TNRC18 WILD-TYPE	26	16	4	36	25	55

'MED15 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 1

Table S191. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
MED15 MUTATED	4	0	1
MED15 WILD-TYPE	153	51	49

'MED15 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0941 (Fisher's exact test), Q value = 1

Table S192. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
MED15 MUTATED	0	3	1	1
MED15 WILD-TYPE	89	66	79	22

'MED15 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S193. 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 = 0.735 (Fisher's exact test), Q value = 1

Table S194. 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 = 0.631 (Fisher's exact test), Q value = 1

Table S195. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
MED15 MUTATED	1	1	3
MED15 WILD-TYPE	84	77	92

'MED15 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S196. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
MED15 MUTATED	1	3	1
MED15 WILD-TYPE	85	77	91

'MED15 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 1

Table S197. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
MED15 MUTATED	1	1	3
MED15 WILD-TYPE	78	96	80

'MED15 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.844 (Fisher's exact test), Q value = 1

Table S198. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
MED15 MUTATED	1	1	0	1	2
MED15 WILD-TYPE	85	49	30	40	50

'MED15 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 1

Table S199. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
MED15 MUTATED	1	1	1	1
MED15 WILD-TYPE	32	39	17	73

'MED15 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.618 (Fisher's exact test), Q value = 1

Table S200. Gene #21: 'MED15 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
MED15 MUTATED	0	1	0	1	1	1
MED15 WILD-TYPE	26	15	4	36	24	56

'NKX3-1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.472 (Fisher's exact test), Q value = 1

Table S201. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
NKX3-1 MUTATED	4	0	0
NKX3-1 WILD-TYPE	153	51	50

'NKX3-1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 1

Table S202. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
NKX3-1 MUTATED	0	2	2	1
NKX3-1 WILD-TYPE	89	67	78	22

'NKX3-1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 1

Table S203. 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 S40. 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 = 0.0512 (Fisher's exact test), Q value = 1

Table S204. 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

'NKX3-1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.864 (Fisher's exact test), Q value = 1

Table S205. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
NKX3-1 MUTATED	1	2	2
NKX3-1 WILD-TYPE	84	76	93

'NKX3-1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S206. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
NKX3-1 MUTATED	1	2	2
NKX3-1 WILD-TYPE	85	78	90

'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S207. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
NKX3-1 MUTATED	2	3	0
NKX3-1 WILD-TYPE	77	94	83

'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S208. Gene #22: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
NKX3-1 MUTATED	2	2	0	0	1
NKX3-1 WILD-TYPE	84	48	30	41	51

'KDM6A MUTATION STATUS' versus 'CN_CNMF'

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

Table S209. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
KDM6A MUTATED	1	1	4
KDM6A WILD-TYPE	156	50	46

Figure S41. Get High-res Image Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S210. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
KDM6A MUTATED	1	4	1	0
KDM6A WILD-TYPE	88	65	79	23

'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S211. 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 = 0.691 (Fisher's exact test), Q value = 1

Table S212. 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 = 0.0135 (Fisher's exact test), Q value = 1

Table S213. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
KDM6A MUTATED	0	5	1
KDM6A WILD-TYPE	85	73	94

Figure S42. Get High-res Image Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 1

Table S214. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
KDM6A MUTATED	1	4	1
KDM6A WILD-TYPE	85	76	91

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S215. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
KDM6A MUTATED	1	3	2
KDM6A WILD-TYPE	78	94	81

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0965 (Fisher's exact test), Q value = 1

Table S216. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
KDM6A MUTATED	1	4	0	0	1
KDM6A WILD-TYPE	85	46	30	41	51

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S217. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
KDM6A MUTATED	0	0	0	3
KDM6A WILD-TYPE	33	40	18	71

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S218. Gene #23: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
KDM6A MUTATED	0	2	0	0	0	1
KDM6A WILD-TYPE	26	14	4	37	25	56

'RNF31 MUTATION STATUS' versus 'CN_CNMF'

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

Table S219. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
RNF31 MUTATED	3	0	0
RNF31 WILD-TYPE	154	51	50

'RNF31 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S220. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
RNF31 MUTATED	2	1	0	1
RNF31 WILD-TYPE	87	68	80	22

'RNF31 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S221. 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 = 0.559 (Fisher's exact test), Q value = 1

Table S222. 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 = 0.519 (Fisher's exact test), Q value = 1

Table S223. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
RNF31 MUTATED	2	0	1
RNF31 WILD-TYPE	83	78	94

'RNF31 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S224. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
RNF31 MUTATED	1	1	1
RNF31 WILD-TYPE	85	79	91

'RNF31 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S225. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
RNF31 MUTATED	0	2	2
RNF31 WILD-TYPE	79	95	81

'RNF31 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0992 (Fisher's exact test), Q value = 1

Table S226. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
RNF31 MUTATED	0	0	1	2	1
RNF31 WILD-TYPE	86	50	29	39	51

'RNF31 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.512 (Fisher's exact test), Q value = 1

Table S227. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
RNF31 MUTATED	0	2	0	1
RNF31 WILD-TYPE	33	38	18	73

'RNF31 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S228. Gene #24: 'RNF31 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
RNF31 MUTATED	0	0	0	2	0	1
RNF31 WILD-TYPE	26	16	4	35	25	56

'ESCO1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 1

Table S229. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
ESCO1 MUTATED	3	0	1
ESCO1 WILD-TYPE	154	51	49

'ESCO1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 1

Table S230. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
ESCO1 MUTATED	2	1	0	1
ESCO1 WILD-TYPE	87	68	80	22

'ESCO1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.475 (Fisher's exact test), Q value = 1

Table S231. 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 S232. 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 = 0.207 (Fisher's exact test), Q value = 1

Table S233. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
ESCO1 MUTATED	3	0	1
ESCO1 WILD-TYPE	82	78	94

'ESCO1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.549 (Fisher's exact test), Q value = 1

Table S234. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
ESCO1 MUTATED	2	0	2
ESCO1 WILD-TYPE	84	80	90

'ESCO1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0738 (Fisher's exact test), Q value = 1

Table S235. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
ESCO1 MUTATED	3	0	1
ESCO1 WILD-TYPE	76	97	82

'ESCO1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.779 (Fisher's exact test), Q value = 1

Table S236. Gene #25: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
ESCO1 MUTATED	2	0	1	0	1
ESCO1 WILD-TYPE	84	50	29	41	51

'LMOD2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S237. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
LMOD2 MUTATED	3	0	0
LMOD2 WILD-TYPE	154	51	50

'LMOD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S238. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
LMOD2 MUTATED	2	0	1	0
LMOD2 WILD-TYPE	87	69	79	23

'LMOD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S239. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
LMOD2 MUTATED	1	1	1
LMOD2 WILD-TYPE	84	77	94

'LMOD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S240. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
LMOD2 MUTATED	1	1	1
LMOD2 WILD-TYPE	85	79	91

'LMOD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S241. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
LMOD2 MUTATED	1	1	1
LMOD2 WILD-TYPE	78	96	82

'LMOD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S242. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
LMOD2 MUTATED	1	1	0	0	1
LMOD2 WILD-TYPE	85	49	30	41	51

'LMOD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S243. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
LMOD2 MUTATED	1	0	1	1
LMOD2 WILD-TYPE	32	40	17	73

'LMOD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.41 (Fisher's exact test), Q value = 1

Table S244. Gene #26: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
LMOD2 MUTATED	1	1	0	0	0	1
LMOD2 WILD-TYPE	25	15	4	37	25	56

'FAM120B MUTATION STATUS' versus 'CN_CNMF'

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

Table S245. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
FAM120B MUTATED	1	2	0
FAM120B WILD-TYPE	156	49	50

'FAM120B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S246. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
FAM120B MUTATED	1	1	0	1
FAM120B WILD-TYPE	88	68	80	22

'FAM120B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.399 (Fisher's exact test), Q value = 1

Table S247. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
FAM120B MUTATED	0	2	1
FAM120B WILD-TYPE	85	76	94

'FAM120B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S248. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
FAM120B MUTATED	0	1	2
FAM120B WILD-TYPE	86	79	90

'FAM120B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.778 (Fisher's exact test), Q value = 1

Table S249. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
FAM120B MUTATED	0	2	1
FAM120B WILD-TYPE	79	95	82

'FAM120B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0889 (Fisher's exact test), Q value = 1

Table S250. Gene #27: 'FAM120B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
FAM120B MUTATED	0	0	1	0	2
FAM120B WILD-TYPE	86	50	29	41	50

'CLEC1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S251. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
CLEC1A MUTATED	3	0	1
CLEC1A WILD-TYPE	154	51	49

'CLEC1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.313 (Fisher's exact test), Q value = 1

Table S252. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
CLEC1A MUTATED	1	0	2	1
CLEC1A WILD-TYPE	88	69	78	22

'CLEC1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 1

Table S253. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
CLEC1A MUTATED	3	1	0
CLEC1A WILD-TYPE	82	77	95

'CLEC1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S254. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
CLEC1A MUTATED	3	0	1
CLEC1A WILD-TYPE	83	80	91

'CLEC1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S255. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
CLEC1A MUTATED	2	2	0
CLEC1A WILD-TYPE	77	95	83

'CLEC1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S256. Gene #28: 'CLEC1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
CLEC1A MUTATED	2	1	0	0	1
CLEC1A WILD-TYPE	84	49	30	41	51

'ITGA2B MUTATION STATUS' versus 'CN_CNMF'

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

Table S257. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
ITGA2B MUTATED	3	0	0
ITGA2B WILD-TYPE	154	51	50

'ITGA2B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 1

Table S258. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
ITGA2B MUTATED	1	0	1	1
ITGA2B WILD-TYPE	88	69	79	22

'ITGA2B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.784 (Fisher's exact test), Q value = 1

Table S259. 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 = 0.781 (Fisher's exact test), Q value = 1

Table S260. 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 = 0.643 (Fisher's exact test), Q value = 1

Table S261. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
ITGA2B MUTATED	0	1	2
ITGA2B WILD-TYPE	85	77	93

'ITGA2B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.309 (Fisher's exact test), Q value = 1

Table S262. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
ITGA2B MUTATED	0	2	1
ITGA2B WILD-TYPE	86	78	91

'ITGA2B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 1

Table S263. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
ITGA2B MUTATED	0	1	2
ITGA2B WILD-TYPE	79	96	81

'ITGA2B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S264. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
ITGA2B MUTATED	0	1	0	1	1
ITGA2B WILD-TYPE	86	49	30	40	51

'ITGA2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.432 (Fisher's exact test), Q value = 1

Table S265. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
ITGA2B MUTATED	0	1	1	1
ITGA2B WILD-TYPE	33	39	17	73

'ITGA2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.664 (Fisher's exact test), Q value = 1

Table S266. Gene #29: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
ITGA2B MUTATED	0	0	0	2	0	1
ITGA2B WILD-TYPE	26	16	4	35	25	56

'RNF17 MUTATION STATUS' versus 'CN_CNMF'

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

Table S267. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
RNF17 MUTATED	3	0	0
RNF17 WILD-TYPE	154	51	50

'RNF17 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S268. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
RNF17 MUTATED	1	0	2	0
RNF17 WILD-TYPE	88	69	78	23

'RNF17 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 1

Table S269. 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 S43. Get High-res Image Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'RNF17 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 1

Table S270. 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 S44. 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 S271. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
RNF17 MUTATED	0	0	3
RNF17 WILD-TYPE	85	78	92

'RNF17 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.111 (Fisher's exact test), Q value = 1

Table S272. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
RNF17 MUTATED	0	0	3
RNF17 WILD-TYPE	86	80	89

'RNF17 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S273. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
RNF17 MUTATED	2	0	1
RNF17 WILD-TYPE	77	97	82

'RNF17 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.92 (Fisher's exact test), Q value = 1

Table S274. Gene #30: 'RNF17 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
RNF17 MUTATED	2	0	0	0	1
RNF17 WILD-TYPE	84	50	30	41	51

'RP1L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.751 (Fisher's exact test), Q value = 1

Table S275. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
RP1L1 MUTATED	4	1	2
RP1L1 WILD-TYPE	153	50	48

'RP1L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S276. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
RP1L1 MUTATED	3	1	2	1
RP1L1 WILD-TYPE	86	68	78	22

'RP1L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S277. 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 S278. 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 = 0.712 (Fisher's exact test), Q value = 1

Table S279. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
RP1L1 MUTATED	3	1	3
RP1L1 WILD-TYPE	82	77	92

'RP1L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S280. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
RP1L1 MUTATED	4	1	2
RP1L1 WILD-TYPE	82	79	90

'RP1L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0689 (Fisher's exact test), Q value = 1

Table S281. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
RP1L1 MUTATED	3	0	4
RP1L1 WILD-TYPE	76	97	79

'RP1L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 1

Table S282. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
RP1L1 MUTATED	1	1	2	2	1
RP1L1 WILD-TYPE	85	49	28	39	51

'RP1L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0633 (Fisher's exact test), Q value = 1

Table S283. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
RP1L1 MUTATED	0	4	0	1
RP1L1 WILD-TYPE	33	36	18	73

'RP1L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 1

Table S284. Gene #31: 'RP1L1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
RP1L1 MUTATED	2	0	0	3	0	0
RP1L1 WILD-TYPE	24	16	4	34	25	57

'EOMES MUTATION STATUS' versus 'CN_CNMF'

P value = 0.25 (Fisher's exact test), Q value = 1

Table S285. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
EOMES MUTATED	2	0	2
EOMES WILD-TYPE	155	51	48

'EOMES MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.782 (Fisher's exact test), Q value = 1

Table S286. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
EOMES MUTATED	1	2	1	0
EOMES WILD-TYPE	88	67	79	23

'EOMES MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.783 (Fisher's exact test), Q value = 1

Table S287. 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 = 0.781 (Fisher's exact test), Q value = 1

Table S288. 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 = 0.267 (Fisher's exact test), Q value = 1

Table S289. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
EOMES MUTATED	2	2	0
EOMES WILD-TYPE	83	76	95

'EOMES MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S290. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
EOMES MUTATED	3	1	0
EOMES WILD-TYPE	83	79	92

'EOMES MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S291. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
EOMES MUTATED	1	2	1
EOMES WILD-TYPE	78	95	82

'EOMES MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S292. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
EOMES MUTATED	1	2	0	1	0
EOMES WILD-TYPE	85	48	30	40	52

'EOMES MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 1

Table S293. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
EOMES MUTATED	0	2	2	0
EOMES WILD-TYPE	33	38	16	74

Figure S45. Get High-res Image Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'EOMES MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 1

Table S294. Gene #32: 'EOMES MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
EOMES MUTATED	1	1	0	1	1	0
EOMES WILD-TYPE	25	15	4	36	24	57

'MTF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 1

Table S295. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
MTF1 MUTATED	1	0	2
MTF1 WILD-TYPE	156	51	48

'MTF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S296. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
MTF1 MUTATED	2	1	0	0
MTF1 WILD-TYPE	87	68	80	23

'MTF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S297. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
MTF1 MUTATED	1	2	0
MTF1 WILD-TYPE	84	76	95

'MTF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S298. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
MTF1 MUTATED	1	2	0
MTF1 WILD-TYPE	85	78	92

'MTF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S299. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
MTF1 MUTATED	1	2	0
MTF1 WILD-TYPE	78	95	83

'MTF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S300. Gene #33: 'MTF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
MTF1 MUTATED	1	2	0	0	0
MTF1 WILD-TYPE	85	48	30	41	52

'NTM MUTATION STATUS' versus 'CN_CNMF'

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

Table S301. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
NTM MUTATED	3	1	1
NTM WILD-TYPE	154	50	49

'NTM MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S302. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
NTM MUTATED	2	0	3	0
NTM WILD-TYPE	87	69	77	23

'NTM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 1

Table S303. 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 = 0.331 (Fisher's exact test), Q value = 1

Table S304. 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 = 0.326 (Fisher's exact test), Q value = 1

Table S305. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
NTM MUTATED	3	0	2
NTM WILD-TYPE	82	78	93

'NTM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S306. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
NTM MUTATED	2	0	3
NTM WILD-TYPE	84	80	89

'NTM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.736 (Fisher's exact test), Q value = 1

Table S307. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
NTM MUTATED	2	1	2
NTM WILD-TYPE	77	96	81

'NTM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.579 (Fisher's exact test), Q value = 1

Table S308. Gene #34: 'NTM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
NTM MUTATED	3	0	1	0	1
NTM WILD-TYPE	83	50	29	41	51

'FNBP4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S309. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
FNBP4 MUTATED	1	1	1
FNBP4 WILD-TYPE	156	50	49

'FNBP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00676 (Fisher's exact test), Q value = 1

Table S310. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
FNBP4 MUTATED	0	1	0	2
FNBP4 WILD-TYPE	89	68	80	21

Figure S46. Get High-res Image Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FNBP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.399 (Fisher's exact test), Q value = 1

Table S311. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
FNBP4 MUTATED	0	2	1
FNBP4 WILD-TYPE	85	76	94

'FNBP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S312. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
FNBP4 MUTATED	0	2	1
FNBP4 WILD-TYPE	86	78	91

'FNBP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 1

Table S313. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
FNBP4 MUTATED	0	1	2
FNBP4 WILD-TYPE	79	96	81

'FNBP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test), Q value = 1

Table S314. Gene #35: 'FNBP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
FNBP4 MUTATED	0	2	0	1	0
FNBP4 WILD-TYPE	86	48	30	40	52

'CDKN1B MUTATION STATUS' versus 'CN_CNMF'

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

Table S315. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
CDKN1B MUTATED	2	1	1
CDKN1B WILD-TYPE	155	50	49

'CDKN1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 1

Table S316. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
CDKN1B MUTATED	0	2	1	1
CDKN1B WILD-TYPE	89	67	79	22

'CDKN1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 1

Table S317. 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 S318. 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 = 0.463 (Fisher's exact test), Q value = 1

Table S319. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
CDKN1B MUTATED	0	2	2
CDKN1B WILD-TYPE	85	76	93

'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S320. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
CDKN1B MUTATED	0	3	1
CDKN1B WILD-TYPE	86	77	91

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S321. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
CDKN1B MUTATED	0	2	2
CDKN1B WILD-TYPE	79	95	81

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0617 (Fisher's exact test), Q value = 1

Table S322. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
CDKN1B MUTATED	0	2	0	2	0
CDKN1B WILD-TYPE	86	48	30	39	52

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 1

Table S323. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
CDKN1B MUTATED	0	2	0	1
CDKN1B WILD-TYPE	33	38	18	73

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S324. Gene #36: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
CDKN1B MUTATED	0	1	0	2	0	0
CDKN1B WILD-TYPE	26	15	4	35	25	57

'EIF2AK3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S325. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
EIF2AK3 MUTATED	2	1	1
EIF2AK3 WILD-TYPE	155	50	49

'EIF2AK3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 1

Table S326. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
EIF2AK3 MUTATED	2	0	1	1
EIF2AK3 WILD-TYPE	87	69	79	22

'EIF2AK3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S327. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
EIF2AK3 MUTATED	1	1	2
EIF2AK3 WILD-TYPE	84	77	93

'EIF2AK3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S328. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
EIF2AK3 MUTATED	2	1	1
EIF2AK3 WILD-TYPE	84	79	91

'EIF2AK3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 1

Table S329. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
EIF2AK3 MUTATED	0	3	1
EIF2AK3 WILD-TYPE	79	94	82

'EIF2AK3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.949 (Fisher's exact test), Q value = 1

Table S330. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
EIF2AK3 MUTATED	1	1	0	1	1
EIF2AK3 WILD-TYPE	85	49	30	40	51

'EIF2AK3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S331. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	40	18	74
EIF2AK3 MUTATED	1	0	0	3
EIF2AK3 WILD-TYPE	32	40	18	71

'EIF2AK3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.498 (Fisher's exact test), Q value = 1

Table S332. Gene #37: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	26	16	4	37	25	57
EIF2AK3 MUTATED	0	1	0	0	1	2
EIF2AK3 WILD-TYPE	26	15	4	37	24	55

'LARP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S333. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	51	50
LARP1 MUTATED	2	0	1
LARP1 WILD-TYPE	155	51	49

'LARP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 1

Table S334. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	69	80	23
LARP1 MUTATED	1	1	0	1
LARP1 WILD-TYPE	88	68	80	22

'LARP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.779 (Fisher's exact test), Q value = 1

Table S335. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	78	95
LARP1 MUTATED	1	0	2
LARP1 WILD-TYPE	84	78	93

'LARP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S336. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	80	92
LARP1 MUTATED	1	1	1
LARP1 WILD-TYPE	85	79	91

'LARP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S337. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	97	83
LARP1 MUTATED	1	1	1
LARP1 WILD-TYPE	78	96	82

'LARP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S338. Gene #38: 'LARP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	86	50	30	41	52
LARP1 MUTATED	2	1	0	0	0
LARP1 WILD-TYPE	84	49	30	41	52

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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