Correlation between gene mutation status and molecular subtypes

Kidney Renal Clear Cell Carcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C18914MR

Overview

Introduction

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

Summary

Testing the association between mutation status of 29 genes and 12 molecular subtypes across 417 patients, 15 significant findings detected with P value < 0.05 and Q value < 0.25.

SETD2 mutation correlated to 'METHLYATION_CNMF'.
BAP1 mutation correlated to 'MRNA_CHIERARCHICAL', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
PTEN mutation correlated to 'MRNASEQ_CNMF'.
PBRM1 mutation correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.
KDM5C mutation correlated to 'MRNASEQ_CHIERARCHICAL'.
MTOR mutation correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 29 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 15 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	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	Fisher's exact test	Fisher's exact test
BAP1	41 (10%)	376	0.0315 (1.00)	0.00055 (0.143)	0.011 (1.00)	0.00012 (0.0314)	0.00085 (0.218)	0.066 (1.00)	4e-05 (0.0106)	1e-05 (0.00269)	7e-05 (0.0184)	1e-05 (0.00269)	0.351 (1.00)	0.0371 (1.00)
PBRM1	136 (33%)	281	0.153 (1.00)	0.059 (1.00)	0.138 (1.00)	3e-05 (0.00795)	0.00071 (0.183)	0.253 (1.00)	0.00642 (1.00)	0.027 (1.00)	0.00379 (0.947)	0.0599 (1.00)	1e-05 (0.00269)	0.0545 (1.00)
MTOR	23 (6%)	394			0.565 (1.00)	0.154 (1.00)	0.00047 (0.123)	0.00076 (0.195)	0.657 (1.00)	0.447 (1.00)	0.345 (1.00)	0.0326 (1.00)	0.0647 (1.00)	0.0033 (0.828)
SETD2	44 (11%)	373	1 (1.00)	0.499 (1.00)	0.668 (1.00)	1e-05 (0.00269)	0.639 (1.00)	0.161 (1.00)	0.464 (1.00)	0.08 (1.00)	0.778 (1.00)	0.762 (1.00)	0.621 (1.00)	0.0592 (1.00)
PTEN	18 (4%)	399	0.107 (1.00)	0.0319 (1.00)	0.212 (1.00)	0.168 (1.00)	0.259 (1.00)	0.156 (1.00)	0.00098 (0.25)	0.00111 (0.282)	0.00867 (1.00)	0.041 (1.00)	0.0157 (1.00)	0.0552 (1.00)
KDM5C	26 (6%)	391			0.188 (1.00)	0.0891 (1.00)	0.436 (1.00)	0.756 (1.00)	0.109 (1.00)	0.00069 (0.179)	0.00426 (1.00)	0.635 (1.00)	0.374 (1.00)	0.137 (1.00)
VHL	166 (40%)	251	0.113 (1.00)	0.226 (1.00)	0.114 (1.00)	0.748 (1.00)	0.774 (1.00)	0.393 (1.00)	0.014 (1.00)	0.513 (1.00)	0.161 (1.00)	0.00267 (0.673)	0.672 (1.00)	0.159 (1.00)
FAM200A	5 (1%)	412			0.0014 (0.354)		0.031 (1.00)	0.318 (1.00)	0.159 (1.00)	0.412 (1.00)	0.207 (1.00)	0.586 (1.00)
TP53	9 (2%)	408			0.767 (1.00)	0.511 (1.00)	0.515 (1.00)	0.648 (1.00)	0.456 (1.00)	0.311 (1.00)	0.464 (1.00)	0.173 (1.00)	0.227 (1.00)	0.271 (1.00)
NEFH	5 (1%)	412			0.858 (1.00)	0.54 (1.00)	0.978 (1.00)	0.116 (1.00)	0.0124 (1.00)	0.0162 (1.00)	0.618 (1.00)	0.405 (1.00)	0.683 (1.00)	1 (1.00)
CCDC120	4 (1%)	413			0.183 (1.00)		0.564 (1.00)	0.794 (1.00)	0.675 (1.00)	0.816 (1.00)	0.822 (1.00)	1 (1.00)	0.613 (1.00)	0.163 (1.00)
GUSB	4 (1%)	413			0.684 (1.00)		0.449 (1.00)	0.446 (1.00)	0.185 (1.00)	0.195 (1.00)	0.459 (1.00)	0.516 (1.00)
PIK3CA	12 (3%)	405			0.294 (1.00)	0.655 (1.00)	0.889 (1.00)	0.73 (1.00)	0.287 (1.00)	0.537 (1.00)	0.751 (1.00)	0.8 (1.00)	0.612 (1.00)	0.605 (1.00)
PCK1	5 (1%)	412			0.227 (1.00)	0.615 (1.00)	1 (1.00)	0.685 (1.00)	0.848 (1.00)	0.682 (1.00)	0.724 (1.00)	0.488 (1.00)
ARID1A	12 (3%)	405			0.656 (1.00)	0.261 (1.00)	0.969 (1.00)	0.93 (1.00)	0.308 (1.00)	0.646 (1.00)	0.116 (1.00)	0.071 (1.00)	0.283 (1.00)	0.848 (1.00)
ATM	11 (3%)	406			0.508 (1.00)	0.476 (1.00)	0.512 (1.00)	0.707 (1.00)	0.217 (1.00)	0.616 (1.00)	0.114 (1.00)	0.526 (1.00)	0.0782 (1.00)	0.0454 (1.00)
DPCR1	6 (1%)	411			0.453 (1.00)	0.515 (1.00)	0.101 (1.00)	0.495 (1.00)	0.108 (1.00)	0.00854 (1.00)	0.675 (1.00)	0.407 (1.00)	0.654 (1.00)	0.867 (1.00)
FGFR3	4 (1%)	413			0.572 (1.00)	0.839 (1.00)	0.95 (1.00)	0.792 (1.00)	0.828 (1.00)	0.479 (1.00)	0.821 (1.00)	0.313 (1.00)
PTCH1	7 (2%)	410			0.633 (1.00)	0.0549 (1.00)	0.281 (1.00)	0.119 (1.00)	0.877 (1.00)	0.101 (1.00)	0.796 (1.00)	0.217 (1.00)
RBMX	4 (1%)	413			0.571 (1.00)	0.619 (1.00)	0.0985 (1.00)	0.599 (1.00)	0.407 (1.00)	0.484 (1.00)	0.251 (1.00)	0.173 (1.00)
ARAP3	3 (1%)	414			0.625 (1.00)		1 (1.00)	0.795 (1.00)	0.784 (1.00)	1 (1.00)	0.796 (1.00)	1 (1.00)
GPR172B	4 (1%)	413			1 (1.00)		0.0778 (1.00)	1 (1.00)	0.529 (1.00)	1 (1.00)	0.611 (1.00)	0.433 (1.00)
EGFR	7 (2%)	410			1 (1.00)	0.683 (1.00)	0.623 (1.00)	0.378 (1.00)	0.465 (1.00)	0.888 (1.00)	1 (1.00)	0.752 (1.00)
IL1RAP	4 (1%)	413			1 (1.00)	0.616 (1.00)	0.294 (1.00)	0.0739 (1.00)	0.829 (1.00)	0.814 (1.00)	0.566 (1.00)	0.823 (1.00)
BCL6	5 (1%)	412			0.229 (1.00)	0.616 (1.00)	0.724 (1.00)	0.144 (1.00)	1 (1.00)	0.804 (1.00)	0.726 (1.00)	0.855 (1.00)	1 (1.00)	1 (1.00)
NFAT5	6 (1%)	411			0.768 (1.00)	0.877 (1.00)	0.27 (1.00)	0.718 (1.00)	0.297 (1.00)	0.431 (1.00)	0.243 (1.00)	1 (1.00)
LARP1	5 (1%)	412			0.857 (1.00)	0.438 (1.00)	0.179 (1.00)	0.719 (1.00)	0.848 (1.00)	0.864 (1.00)	0.617 (1.00)	0.27 (1.00)
KIAA1751	6 (1%)	411			0.675 (1.00)	0.639 (1.00)	0.532 (1.00)	0.0535 (1.00)	0.405 (1.00)	0.93 (1.00)	0.496 (1.00)	0.169 (1.00)	0.792 (1.00)	0.161 (1.00)
INSRR	4 (1%)	413			0.571 (1.00)	0.12 (1.00)	0.348 (1.00)	0.685 (1.00)	0.406 (1.00)	0.239 (1.00)	0.46 (1.00)	0.249 (1.00)

'SETD2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S1. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	21	3
SETD2 MUTATED	2	2	0
SETD2 WILD-TYPE	20	19	3

'SETD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.499 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	4	10	3	10	10	8	1
SETD2 MUTATED	1	2	0	0	1	0	0
SETD2 WILD-TYPE	3	8	3	10	9	8	1

'SETD2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S3. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
SETD2 MUTATED	17	10	17
SETD2 WILD-TYPE	151	101	119

'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S4. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
SETD2 MUTATED	6	0	22
SETD2 WILD-TYPE	90	53	72

Figure S1. Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
SETD2 MUTATED	14	6	7	5	3	6
SETD2 WILD-TYPE	74	69	67	54	35	46

'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S6. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
SETD2 MUTATED	11	13	17
SETD2 WILD-TYPE	71	162	112

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
SETD2 MUTATED	15	9	20
SETD2 WILD-TYPE	162	64	145

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.08 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
SETD2 MUTATED	18	10	14	2	0	0
SETD2 WILD-TYPE	90	134	99	20	24	4

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S9. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
SETD2 MUTATED	8	19	15
SETD2 WILD-TYPE	89	159	117

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S10. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
SETD2 MUTATED	13	23	6
SETD2 WILD-TYPE	117	180	68

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S11. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
SETD2 MUTATED	3	10	9
SETD2 WILD-TYPE	38	64	59

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0592 (Fisher's exact test), Q value = 1

Table S12. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
SETD2 MUTATED	3	12	7
SETD2 WILD-TYPE	61	67	33

'BAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0315 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	21	3
BAP1 MUTATED	1	7	0
BAP1 WILD-TYPE	21	14	3

Figure S2. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.14

Table S14. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	4	10	3	10	10	8	1
BAP1 MUTATED	0	0	0	7	1	0	0
BAP1 WILD-TYPE	4	10	3	3	9	8	1

Figure S3. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S15. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
BAP1 MUTATED	10	9	22
BAP1 WILD-TYPE	158	102	114

Figure S4. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.031

Table S16. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
BAP1 MUTATED	1	6	16
BAP1 WILD-TYPE	95	47	78

Figure S5. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.22

Table S17. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
BAP1 MUTATED	2	11	9	1	2	10
BAP1 WILD-TYPE	86	64	65	58	36	42

Figure S6. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.066 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
BAP1 MUTATED	6	11	18
BAP1 WILD-TYPE	76	164	111

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.011

Table S19. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
BAP1 MUTATED	5	8	28
BAP1 WILD-TYPE	172	65	137

Figure S7. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S20. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
BAP1 MUTATED	5	4	17	0	15	0
BAP1 WILD-TYPE	103	140	96	22	9	4

Figure S8. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.018

Table S21. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
BAP1 MUTATED	9	7	25
BAP1 WILD-TYPE	88	171	107

Figure S9. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S22. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
BAP1 MUTATED	19	6	16
BAP1 WILD-TYPE	111	197	58

Figure S10. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.351 (Fisher's exact test), Q value = 1

Table S23. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
BAP1 MUTATED	3	3	7
BAP1 WILD-TYPE	38	71	61

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 1

Table S24. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
BAP1 MUTATED	5	2	6
BAP1 WILD-TYPE	59	77	34

Figure S11. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S25. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	21	3
PTEN MUTATED	0	4	0
PTEN WILD-TYPE	22	17	3

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 1

Table S26. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	4	10	3	10	10	8	1
PTEN MUTATED	0	4	0	0	0	0	0
PTEN WILD-TYPE	4	6	3	10	10	8	1

Figure S12. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
PTEN MUTATED	5	3	9
PTEN WILD-TYPE	163	108	127

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S28. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
PTEN MUTATED	1	3	5
PTEN WILD-TYPE	95	50	89

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S29. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
PTEN MUTATED	2	6	2	2	1	5
PTEN WILD-TYPE	86	69	72	57	37	47

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S30. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
PTEN MUTATED	1	8	9
PTEN WILD-TYPE	81	167	120

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.25

Table S31. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
PTEN MUTATED	1	4	13
PTEN WILD-TYPE	176	69	152

Figure S13. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.28

Table S32. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
PTEN MUTATED	5	0	12	1	0	0
PTEN WILD-TYPE	103	144	101	21	24	4

Figure S14. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00867 (Fisher's exact test), Q value = 1

Table S33. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
PTEN MUTATED	7	2	9
PTEN WILD-TYPE	90	176	123

Figure S15. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 1

Table S34. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
PTEN MUTATED	9	4	5
PTEN WILD-TYPE	121	199	69

Figure S16. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 1

Table S35. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
PTEN MUTATED	0	0	5
PTEN WILD-TYPE	41	74	63

Figure S17. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0552 (Fisher's exact test), Q value = 1

Table S36. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
PTEN MUTATED	4	0	1
PTEN WILD-TYPE	60	79	39

'PBRM1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 1

Table S37. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	21	3
PBRM1 MUTATED	10	4	1
PBRM1 WILD-TYPE	12	17	2

'PBRM1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S38. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	4	10	3	10	10	8	1
PBRM1 MUTATED	2	4	0	0	4	4	1
PBRM1 WILD-TYPE	2	6	3	10	6	4	0

'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S39. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
PBRM1 MUTATED	60	28	48
PBRM1 WILD-TYPE	108	83	88

'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0079

Table S40. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
PBRM1 MUTATED	42	6	42
PBRM1 WILD-TYPE	54	47	52

Figure S18. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.18

Table S41. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
PBRM1 MUTATED	46	16	22	17	9	16
PBRM1 WILD-TYPE	42	59	52	42	29	36

Figure S19. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S42. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
PBRM1 MUTATED	33	54	39
PBRM1 WILD-TYPE	49	121	90

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S43. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
PBRM1 MUTATED	71	15	49
PBRM1 WILD-TYPE	106	58	116

Figure S20. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 1

Table S44. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
PBRM1 MUTATED	40	57	29	5	3	1
PBRM1 WILD-TYPE	68	87	84	17	21	3

Figure S21. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00379 (Fisher's exact test), Q value = 0.95

Table S45. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
PBRM1 MUTATED	22	73	37
PBRM1 WILD-TYPE	75	105	95

Figure S22. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0599 (Fisher's exact test), Q value = 1

Table S46. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
PBRM1 MUTATED	34	77	21
PBRM1 WILD-TYPE	96	126	53

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S47. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
PBRM1 MUTATED	2	37	22
PBRM1 WILD-TYPE	39	37	46

Figure S23. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0545 (Fisher's exact test), Q value = 1

Table S48. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
PBRM1 MUTATED	14	31	16
PBRM1 WILD-TYPE	50	48	24

'KDM5C MUTATION STATUS' versus 'CN_CNMF'

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

Table S49. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
KDM5C MUTATED	8	5	13
KDM5C WILD-TYPE	160	106	123

'KDM5C MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S50. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
KDM5C MUTATED	4	2	11
KDM5C WILD-TYPE	92	51	83

'KDM5C MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S51. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
KDM5C MUTATED	5	3	6	2	1	6
KDM5C WILD-TYPE	83	72	68	57	37	46

'KDM5C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.756 (Fisher's exact test), Q value = 1

Table S52. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
KDM5C MUTATED	6	9	8
KDM5C WILD-TYPE	76	166	121

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S53. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
KDM5C MUTATED	8	2	15
KDM5C WILD-TYPE	169	71	150

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.18

Table S54. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
KDM5C MUTATED	15	1	8	1	0	0
KDM5C WILD-TYPE	93	143	105	21	24	4

Figure S24. Get High-res Image Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00426 (Fisher's exact test), Q value = 1

Table S55. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
KDM5C MUTATED	2	8	16
KDM5C WILD-TYPE	95	170	116

Figure S25. Get High-res Image Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.635 (Fisher's exact test), Q value = 1

Table S56. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
KDM5C MUTATED	9	11	6
KDM5C WILD-TYPE	121	192	68

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S57. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
KDM5C MUTATED	0	4	4
KDM5C WILD-TYPE	41	70	64

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S58. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
KDM5C MUTATED	4	1	3
KDM5C WILD-TYPE	60	78	37

'VHL MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 1

Table S59. Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	21	3
VHL MUTATED	13	6	1
VHL WILD-TYPE	9	15	2

'VHL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.226 (Fisher's exact test), Q value = 1

Table S60. Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	4	10	3	10	10	8	1
VHL MUTATED	2	2	0	4	6	5	1
VHL WILD-TYPE	2	8	3	6	4	3	0

'VHL MUTATION STATUS' versus 'CN_CNMF'

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

Table S61. Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
VHL MUTATED	68	52	46
VHL WILD-TYPE	100	59	90

'VHL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.748 (Fisher's exact test), Q value = 1

Table S62. Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
VHL MUTATED	46	23	40
VHL WILD-TYPE	50	30	54

'VHL MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S63. Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
VHL MUTATED	40	30	28	20	17	20
VHL WILD-TYPE	48	45	46	39	21	32

'VHL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.393 (Fisher's exact test), Q value = 1

Table S64. Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
VHL MUTATED	33	76	46
VHL WILD-TYPE	49	99	83

'VHL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 1

Table S65. Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
VHL MUTATED	85	23	58
VHL WILD-TYPE	92	50	107

Figure S26. Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VHL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.513 (Fisher's exact test), Q value = 1

Table S66. Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
VHL MUTATED	46	64	41	6	8	1
VHL WILD-TYPE	62	80	72	16	16	3

'VHL MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S67. Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
VHL MUTATED	40	78	44
VHL WILD-TYPE	57	100	88

'VHL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.67

Table S68. Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
VHL MUTATED	41	98	23
VHL WILD-TYPE	89	105	51

Figure S27. Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.672 (Fisher's exact test), Q value = 1

Table S69. Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
VHL MUTATED	18	36	28
VHL WILD-TYPE	23	38	40

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 1

Table S70. Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
VHL MUTATED	23	41	18
VHL WILD-TYPE	41	38	22

'FAM200A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.35

Table S71. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
FAM200A MUTATED	0	5	0
FAM200A WILD-TYPE	168	106	136

Figure S28. Get High-res Image Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FAM200A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 1

Table S72. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
FAM200A MUTATED	0	1	0	0	2	0
FAM200A WILD-TYPE	88	74	74	59	36	52

Figure S29. Get High-res Image Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'FAM200A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 1

Table S73. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
FAM200A MUTATED	0	3	0
FAM200A WILD-TYPE	82	172	129

'FAM200A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 1

Table S74. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
FAM200A MUTATED	4	1	0
FAM200A WILD-TYPE	173	72	165

'FAM200A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S75. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
FAM200A MUTATED	1	4	0	0	0	0
FAM200A WILD-TYPE	107	140	113	22	24	4

'FAM200A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 1

Table S76. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
FAM200A MUTATED	1	4	0
FAM200A WILD-TYPE	96	174	132

'FAM200A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S77. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
FAM200A MUTATED	1	4	0
FAM200A WILD-TYPE	129	199	74

'TP53 MUTATION STATUS' versus 'CN_CNMF'

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

Table S78. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
TP53 MUTATED	3	2	4
TP53 WILD-TYPE	165	109	132

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S79. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
TP53 MUTATED	1	2	3
TP53 WILD-TYPE	95	51	91

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S80. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
TP53 MUTATED	0	2	2	1	1	2
TP53 WILD-TYPE	88	73	72	58	37	50

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S81. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
TP53 MUTATED	1	3	4
TP53 WILD-TYPE	81	172	125

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.456 (Fisher's exact test), Q value = 1

Table S82. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
TP53 MUTATED	2	2	5
TP53 WILD-TYPE	175	71	160

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 1

Table S83. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
TP53 MUTATED	1	2	6	0	0	0
TP53 WILD-TYPE	107	142	107	22	24	4

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 1

Table S84. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
TP53 MUTATED	3	2	4
TP53 WILD-TYPE	94	176	128

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 1

Table S85. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
TP53 MUTATED	5	2	2
TP53 WILD-TYPE	125	201	72

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S86. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
TP53 MUTATED	3	2	1
TP53 WILD-TYPE	38	72	67

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.271 (Fisher's exact test), Q value = 1

Table S87. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
TP53 MUTATED	4	2	0
TP53 WILD-TYPE	60	77	40

'NEFH MUTATION STATUS' versus 'CN_CNMF'

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

Table S88. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
NEFH MUTATED	3	1	1
NEFH WILD-TYPE	165	110	135

'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 1

Table S89. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
NEFH MUTATED	3	0	1
NEFH WILD-TYPE	93	53	93

'NEFH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.978 (Fisher's exact test), Q value = 1

Table S90. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
NEFH MUTATED	2	1	1	1	0	0
NEFH WILD-TYPE	86	74	73	58	38	52

'NEFH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S91. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
NEFH MUTATED	0	1	4
NEFH WILD-TYPE	82	174	125

'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 1

Table S92. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
NEFH MUTATED	0	3	2
NEFH WILD-TYPE	177	70	163

Figure S30. Get High-res Image Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 1

Table S93. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
NEFH MUTATED	1	0	1	2	1	0
NEFH WILD-TYPE	107	144	112	20	23	4

Figure S31. Get High-res Image Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S94. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
NEFH MUTATED	0	3	2
NEFH WILD-TYPE	97	175	130

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S95. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
NEFH MUTATED	1	2	2
NEFH WILD-TYPE	129	201	72

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 1

Table S96. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
NEFH MUTATED	0	2	2
NEFH WILD-TYPE	41	72	66

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S97. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
NEFH MUTATED	1	2	1
NEFH WILD-TYPE	63	77	39

'CCDC120 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 1

Table S98. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
CCDC120 MUTATED	0	2	2
CCDC120 WILD-TYPE	168	109	134

'CCDC120 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 1

Table S99. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
CCDC120 MUTATED	1	0	2	0	0	0
CCDC120 WILD-TYPE	87	75	72	59	38	52

'CCDC120 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S100. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
CCDC120 MUTATED	1	1	1
CCDC120 WILD-TYPE	81	174	128

'CCDC120 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 1

Table S101. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
CCDC120 MUTATED	1	1	2
CCDC120 WILD-TYPE	176	72	163

'CCDC120 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.816 (Fisher's exact test), Q value = 1

Table S102. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
CCDC120 MUTATED	2	1	1	0	0	0
CCDC120 WILD-TYPE	106	143	112	22	24	4

'CCDC120 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S103. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
CCDC120 MUTATED	1	1	2
CCDC120 WILD-TYPE	96	177	130

'CCDC120 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S104. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
CCDC120 MUTATED	1	2	1
CCDC120 WILD-TYPE	129	201	73

'CCDC120 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S105. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
CCDC120 MUTATED	0	1	2
CCDC120 WILD-TYPE	41	73	66

'CCDC120 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.163 (Fisher's exact test), Q value = 1

Table S106. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
CCDC120 MUTATED	0	1	2
CCDC120 WILD-TYPE	64	78	38

'MTOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 1

Table S107. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
MTOR MUTATED	8	5	10
MTOR WILD-TYPE	160	106	126

'MTOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 1

Table S108. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
MTOR MUTATED	5	2	11
MTOR WILD-TYPE	91	51	83

'MTOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.12

Table S109. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
MTOR MUTATED	4	1	8	0	0	8
MTOR WILD-TYPE	84	74	66	59	38	44

Figure S32. Get High-res Image Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MTOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.2

Table S110. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
MTOR MUTATED	6	2	13
MTOR WILD-TYPE	76	173	116

Figure S33. Get High-res Image Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MTOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S111. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
MTOR MUTATED	8	5	10
MTOR WILD-TYPE	169	68	155

'MTOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S112. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
MTOR MUTATED	5	7	7	2	1	1
MTOR WILD-TYPE	103	137	106	20	23	3

'MTOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S113. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
MTOR MUTATED	6	7	10
MTOR WILD-TYPE	91	171	122

'MTOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S114. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
MTOR MUTATED	9	6	8
MTOR WILD-TYPE	121	197	66

Figure S34. Get High-res Image Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0647 (Fisher's exact test), Q value = 1

Table S115. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
MTOR MUTATED	1	3	9
MTOR WILD-TYPE	40	71	59

'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0033 (Fisher's exact test), Q value = 0.83

Table S116. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
MTOR MUTATED	5	1	7
MTOR WILD-TYPE	59	78	33

Figure S35. Get High-res Image Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GUSB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.684 (Fisher's exact test), Q value = 1

Table S117. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
GUSB MUTATED	1	2	1
GUSB WILD-TYPE	167	109	135

'GUSB MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S118. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
GUSB MUTATED	0	2	1	0	0	0
GUSB WILD-TYPE	88	73	73	59	38	52

'GUSB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S119. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
GUSB MUTATED	1	2	0
GUSB WILD-TYPE	81	173	129

'GUSB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 1

Table S120. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
GUSB MUTATED	0	1	3
GUSB WILD-TYPE	177	72	162

'GUSB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S121. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
GUSB MUTATED	1	0	2	0	1	0
GUSB WILD-TYPE	107	144	111	22	23	4

'GUSB MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S122. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
GUSB MUTATED	2	1	1
GUSB WILD-TYPE	95	177	131

'GUSB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.516 (Fisher's exact test), Q value = 1

Table S123. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
GUSB MUTATED	2	1	1
GUSB WILD-TYPE	128	202	73

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

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

Table S124. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
PIK3CA MUTATED	7	1	4
PIK3CA WILD-TYPE	161	110	132

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S125. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
PIK3CA MUTATED	3	0	3
PIK3CA WILD-TYPE	93	53	91

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S126. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
PIK3CA MUTATED	2	4	2	1	1	1
PIK3CA WILD-TYPE	86	71	72	58	37	51

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S127. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
PIK3CA MUTATED	2	4	5
PIK3CA WILD-TYPE	80	171	124

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S128. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
PIK3CA MUTATED	6	0	6
PIK3CA WILD-TYPE	171	73	159

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.537 (Fisher's exact test), Q value = 1

Table S129. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
PIK3CA MUTATED	1	5	5	0	1	0
PIK3CA WILD-TYPE	107	139	108	22	23	4

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S130. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
PIK3CA MUTATED	3	4	5
PIK3CA WILD-TYPE	94	174	127

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S131. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
PIK3CA MUTATED	5	5	2
PIK3CA WILD-TYPE	125	198	72

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S132. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
PIK3CA MUTATED	0	1	2
PIK3CA WILD-TYPE	41	73	66

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S133. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
PIK3CA MUTATED	2	1	0
PIK3CA WILD-TYPE	62	78	40

'PCK1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S134. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
PCK1 MUTATED	4	0	1
PCK1 WILD-TYPE	164	111	135

'PCK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.615 (Fisher's exact test), Q value = 1

Table S135. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
PCK1 MUTATED	1	0	2
PCK1 WILD-TYPE	95	53	92

'PCK1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S136. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
PCK1 MUTATED	1	1	1	1	0	0
PCK1 WILD-TYPE	87	74	73	58	38	52

'PCK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S137. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
PCK1 MUTATED	1	1	2
PCK1 WILD-TYPE	81	174	127

'PCK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.848 (Fisher's exact test), Q value = 1

Table S138. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
PCK1 MUTATED	3	0	2
PCK1 WILD-TYPE	174	73	163

'PCK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.682 (Fisher's exact test), Q value = 1

Table S139. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
PCK1 MUTATED	0	3	2	0	0	0
PCK1 WILD-TYPE	108	141	111	22	24	4

'PCK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S140. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
PCK1 MUTATED	2	2	1
PCK1 WILD-TYPE	95	176	131

'PCK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.488 (Fisher's exact test), Q value = 1

Table S141. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
PCK1 MUTATED	3	2	0
PCK1 WILD-TYPE	127	201	74

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.656 (Fisher's exact test), Q value = 1

Table S142. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
ARID1A MUTATED	5	2	5
ARID1A WILD-TYPE	163	109	131

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S143. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
ARID1A MUTATED	5	1	1
ARID1A WILD-TYPE	91	52	93

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.969 (Fisher's exact test), Q value = 1

Table S144. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
ARID1A MUTATED	3	2	2	3	1	1
ARID1A WILD-TYPE	85	73	72	56	37	51

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S145. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
ARID1A MUTATED	3	5	4
ARID1A WILD-TYPE	79	170	125

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S146. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
ARID1A MUTATED	8	1	3
ARID1A WILD-TYPE	169	72	162

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.646 (Fisher's exact test), Q value = 1

Table S147. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
ARID1A MUTATED	2	7	3	0	0	0
ARID1A WILD-TYPE	106	137	110	22	24	4

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S148. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
ARID1A MUTATED	1	9	2
ARID1A WILD-TYPE	96	169	130

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.071 (Fisher's exact test), Q value = 1

Table S149. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
ARID1A MUTATED	1	10	1
ARID1A WILD-TYPE	129	193	73

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S150. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
ARID1A MUTATED	0	4	1
ARID1A WILD-TYPE	41	70	67

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.848 (Fisher's exact test), Q value = 1

Table S151. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
ARID1A MUTATED	1	3	1
ARID1A WILD-TYPE	63	76	39

'ATM MUTATION STATUS' versus 'CN_CNMF'

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

Table S152. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
ATM MUTATED	5	4	2
ATM WILD-TYPE	163	107	134

'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S153. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
ATM MUTATED	5	1	2
ATM WILD-TYPE	91	52	92

'ATM MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S154. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
ATM MUTATED	3	2	0	3	1	1
ATM WILD-TYPE	85	73	74	56	37	51

'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.707 (Fisher's exact test), Q value = 1

Table S155. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
ATM MUTATED	1	6	3
ATM WILD-TYPE	81	169	126

'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S156. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
ATM MUTATED	7	0	4
ATM WILD-TYPE	170	73	161

'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.616 (Fisher's exact test), Q value = 1

Table S157. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
ATM MUTATED	2	7	2	0	0	0
ATM WILD-TYPE	106	137	111	22	24	4

'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S158. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
ATM MUTATED	0	7	3
ATM WILD-TYPE	97	171	129

'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.526 (Fisher's exact test), Q value = 1

Table S159. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
ATM MUTATED	2	5	3
ATM WILD-TYPE	128	198	71

'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0782 (Fisher's exact test), Q value = 1

Table S160. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
ATM MUTATED	0	4	0
ATM WILD-TYPE	41	70	68

'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0454 (Fisher's exact test), Q value = 1

Table S161. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
ATM MUTATED	0	1	3
ATM WILD-TYPE	64	78	37

Figure S36. Get High-res Image Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'DPCR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S162. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
DPCR1 MUTATED	1	2	3
DPCR1 WILD-TYPE	167	109	133

'DPCR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S163. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
DPCR1 MUTATED	1	2	3
DPCR1 WILD-TYPE	95	51	91

'DPCR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 1

Table S164. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
DPCR1 MUTATED	0	1	1	0	2	2
DPCR1 WILD-TYPE	88	74	73	59	36	50

'DPCR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.495 (Fisher's exact test), Q value = 1

Table S165. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
DPCR1 MUTATED	0	4	2
DPCR1 WILD-TYPE	82	171	127

'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S166. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
DPCR1 MUTATED	1	3	2
DPCR1 WILD-TYPE	176	70	163

'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00854 (Fisher's exact test), Q value = 1

Table S167. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
DPCR1 MUTATED	1	0	2	1	1	1
DPCR1 WILD-TYPE	107	144	111	21	23	3

Figure S37. Get High-res Image Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 1

Table S168. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
DPCR1 MUTATED	2	3	1
DPCR1 WILD-TYPE	95	175	131

'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.407 (Fisher's exact test), Q value = 1

Table S169. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
DPCR1 MUTATED	2	2	2
DPCR1 WILD-TYPE	128	201	72

'DPCR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S170. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
DPCR1 MUTATED	2	3	1
DPCR1 WILD-TYPE	39	71	67

'DPCR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S171. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
DPCR1 MUTATED	3	2	1
DPCR1 WILD-TYPE	61	77	39

'FGFR3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S172. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
FGFR3 MUTATED	2	0	2
FGFR3 WILD-TYPE	166	111	134

'FGFR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S173. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
FGFR3 MUTATED	1	1	2
FGFR3 WILD-TYPE	95	52	92

'FGFR3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.95 (Fisher's exact test), Q value = 1

Table S174. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
FGFR3 MUTATED	1	1	0	1	0	0
FGFR3 WILD-TYPE	87	74	74	58	38	52

'FGFR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S175. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
FGFR3 MUTATED	1	1	1
FGFR3 WILD-TYPE	81	174	128

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S176. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
FGFR3 MUTATED	2	1	1
FGFR3 WILD-TYPE	175	72	164

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.479 (Fisher's exact test), Q value = 1

Table S177. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
FGFR3 MUTATED	2	0	2	0	0	0
FGFR3 WILD-TYPE	106	144	111	22	24	4

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S178. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
FGFR3 MUTATED	1	1	2
FGFR3 WILD-TYPE	96	177	130

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S179. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
FGFR3 MUTATED	3	1	0
FGFR3 WILD-TYPE	127	202	74

'PTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.633 (Fisher's exact test), Q value = 1

Table S180. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
PTCH1 MUTATED	2	3	2
PTCH1 WILD-TYPE	166	108	134

'PTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0549 (Fisher's exact test), Q value = 1

Table S181. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
PTCH1 MUTATED	0	0	4
PTCH1 WILD-TYPE	96	53	90

'PTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 1

Table S182. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
PTCH1 MUTATED	2	1	0	1	0	3
PTCH1 WILD-TYPE	86	74	74	58	38	49

'PTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 1

Table S183. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
PTCH1 MUTATED	0	2	5
PTCH1 WILD-TYPE	82	173	124

'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S184. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
PTCH1 MUTATED	4	1	2
PTCH1 WILD-TYPE	173	72	163

'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 1

Table S185. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
PTCH1 MUTATED	3	2	0	0	2	0
PTCH1 WILD-TYPE	105	142	113	22	22	4

'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S186. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
PTCH1 MUTATED	1	3	3
PTCH1 WILD-TYPE	96	175	129

'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S187. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
PTCH1 MUTATED	1	3	3
PTCH1 WILD-TYPE	129	200	71

'RBMX MUTATION STATUS' versus 'CN_CNMF'

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

Table S188. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
RBMX MUTATED	2	0	2
RBMX WILD-TYPE	166	111	134

'RBMX MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S189. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
RBMX MUTATED	1	0	2
RBMX WILD-TYPE	95	53	92

'RBMX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0985 (Fisher's exact test), Q value = 1

Table S190. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
RBMX MUTATED	0	1	0	0	0	2
RBMX WILD-TYPE	88	74	74	59	38	50

'RBMX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.599 (Fisher's exact test), Q value = 1

Table S191. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
RBMX MUTATED	0	1	2
RBMX WILD-TYPE	82	174	127

'RBMX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.407 (Fisher's exact test), Q value = 1

Table S192. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
RBMX MUTATED	1	0	3
RBMX WILD-TYPE	176	73	162

'RBMX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 1

Table S193. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
RBMX MUTATED	2	0	2	0	0	0
RBMX WILD-TYPE	106	144	111	22	24	4

'RBMX MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S194. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
RBMX MUTATED	1	0	2
RBMX WILD-TYPE	96	178	130

'RBMX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 1

Table S195. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
RBMX MUTATED	2	0	1
RBMX WILD-TYPE	128	203	73

'ARAP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S196. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
ARAP3 MUTATED	2	1	0
ARAP3 WILD-TYPE	166	110	136

'ARAP3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S197. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
ARAP3 MUTATED	1	1	1	0	0	0
ARAP3 WILD-TYPE	87	74	73	59	38	52

'ARAP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S198. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
ARAP3 MUTATED	1	1	1
ARAP3 WILD-TYPE	81	174	128

'ARAP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S199. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
ARAP3 MUTATED	1	0	2
ARAP3 WILD-TYPE	176	73	163

'ARAP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S200. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
ARAP3 MUTATED	1	1	1	0	0	0
ARAP3 WILD-TYPE	107	143	112	22	24	4

'ARAP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S201. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
ARAP3 MUTATED	0	2	1
ARAP3 WILD-TYPE	97	176	131

'ARAP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S202. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
ARAP3 MUTATED	1	2	0
ARAP3 WILD-TYPE	129	201	74

'GPR172B MUTATION STATUS' versus 'CN_CNMF'

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

Table S203. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
GPR172B MUTATED	2	1	1
GPR172B WILD-TYPE	166	110	135

'GPR172B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0778 (Fisher's exact test), Q value = 1

Table S204. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
GPR172B MUTATED	0	0	0	2	0	1
GPR172B WILD-TYPE	88	75	74	57	38	51

'GPR172B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S205. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
GPR172B MUTATED	0	2	1
GPR172B WILD-TYPE	82	173	128

'GPR172B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S206. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
GPR172B MUTATED	3	0	1
GPR172B WILD-TYPE	174	73	164

'GPR172B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S207. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
GPR172B MUTATED	1	2	1	0	0	0
GPR172B WILD-TYPE	107	142	112	22	24	4

'GPR172B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 1

Table S208. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
GPR172B MUTATED	0	1	2
GPR172B WILD-TYPE	97	177	130

'GPR172B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.433 (Fisher's exact test), Q value = 1

Table S209. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
GPR172B MUTATED	0	2	1
GPR172B WILD-TYPE	130	201	73

'EGFR MUTATION STATUS' versus 'CN_CNMF'

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

Table S210. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
EGFR MUTATED	3	2	2
EGFR WILD-TYPE	165	109	134

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 1

Table S211. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
EGFR MUTATED	2	0	2
EGFR WILD-TYPE	94	53	92

'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.623 (Fisher's exact test), Q value = 1

Table S212. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
EGFR MUTATED	2	1	0	1	1	2
EGFR WILD-TYPE	86	74	74	58	37	50

'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S213. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
EGFR MUTATED	3	2	2
EGFR WILD-TYPE	79	173	127

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S214. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
EGFR MUTATED	3	0	4
EGFR WILD-TYPE	174	73	161

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.888 (Fisher's exact test), Q value = 1

Table S215. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
EGFR MUTATED	1	3	3	0	0	0
EGFR WILD-TYPE	107	141	110	22	24	4

'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S216. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
EGFR MUTATED	1	3	2
EGFR WILD-TYPE	96	175	130

'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.752 (Fisher's exact test), Q value = 1

Table S217. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
EGFR MUTATED	2	4	0
EGFR WILD-TYPE	128	199	74

'IL1RAP MUTATION STATUS' versus 'CN_CNMF'

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

Table S218. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
IL1RAP MUTATED	2	1	1
IL1RAP WILD-TYPE	166	110	135

'IL1RAP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 1

Table S219. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
IL1RAP MUTATED	1	0	2
IL1RAP WILD-TYPE	95	53	92

'IL1RAP MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S220. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
IL1RAP MUTATED	2	0	0	0	1	1
IL1RAP WILD-TYPE	86	75	74	59	37	51

'IL1RAP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0739 (Fisher's exact test), Q value = 1

Table S221. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
IL1RAP MUTATED	2	0	2
IL1RAP WILD-TYPE	80	175	127

'IL1RAP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S222. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
IL1RAP MUTATED	2	1	1
IL1RAP WILD-TYPE	175	72	164

'IL1RAP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.814 (Fisher's exact test), Q value = 1

Table S223. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
IL1RAP MUTATED	2	1	1	0	0	0
IL1RAP WILD-TYPE	106	143	112	22	24	4

'IL1RAP MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S224. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
IL1RAP MUTATED	0	3	1
IL1RAP WILD-TYPE	97	175	131

'IL1RAP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S225. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
IL1RAP MUTATED	1	3	0
IL1RAP WILD-TYPE	129	200	74

'BCL6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S226. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
BCL6 MUTATED	4	0	1
BCL6 WILD-TYPE	164	111	135

'BCL6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 1

Table S227. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
BCL6 MUTATED	1	0	2
BCL6 WILD-TYPE	95	53	92

'BCL6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S228. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
BCL6 MUTATED	1	2	2	0	0	0
BCL6 WILD-TYPE	87	73	72	59	38	52

'BCL6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 1

Table S229. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
BCL6 MUTATED	3	1	1
BCL6 WILD-TYPE	79	174	128

'BCL6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S230. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
BCL6 MUTATED	2	1	2
BCL6 WILD-TYPE	175	72	163

'BCL6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.804 (Fisher's exact test), Q value = 1

Table S231. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
BCL6 MUTATED	2	1	2	0	0	0
BCL6 WILD-TYPE	106	143	111	22	24	4

'BCL6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 1

Table S232. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
BCL6 MUTATED	2	2	1
BCL6 WILD-TYPE	95	176	131

'BCL6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S233. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
BCL6 MUTATED	2	2	1
BCL6 WILD-TYPE	128	201	73

'BCL6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S234. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
BCL6 MUTATED	1	1	1
BCL6 WILD-TYPE	40	73	67

'BCL6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S235. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
BCL6 MUTATED	1	1	1
BCL6 WILD-TYPE	63	78	39

'NFAT5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S236. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
NFAT5 MUTATED	3	2	1
NFAT5 WILD-TYPE	165	109	135

'NFAT5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S237. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
NFAT5 MUTATED	2	1	3
NFAT5 WILD-TYPE	94	52	91

'NFAT5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S238. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
NFAT5 MUTATED	0	1	1	0	1	2
NFAT5 WILD-TYPE	88	74	73	59	37	50

'NFAT5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S239. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
NFAT5 MUTATED	0	3	2
NFAT5 WILD-TYPE	82	172	127

'NFAT5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 1

Table S240. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
NFAT5 MUTATED	1	1	4
NFAT5 WILD-TYPE	176	72	161

'NFAT5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.431 (Fisher's exact test), Q value = 1

Table S241. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
NFAT5 MUTATED	4	1	1	0	0	0
NFAT5 WILD-TYPE	104	143	112	22	24	4

'NFAT5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S242. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
NFAT5 MUTATED	1	1	4
NFAT5 WILD-TYPE	96	177	128

'NFAT5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S243. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
NFAT5 MUTATED	2	3	1
NFAT5 WILD-TYPE	128	200	73

'LARP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S244. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
LARP1 MUTATED	3	1	1
LARP1 WILD-TYPE	165	110	135

'LARP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S245. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
LARP1 MUTATED	2	1	0
LARP1 WILD-TYPE	94	52	94

'LARP1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S246. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
LARP1 MUTATED	1	0	1	3	0	0
LARP1 WILD-TYPE	87	75	73	56	38	52

'LARP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S247. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
LARP1 MUTATED	0	3	2
LARP1 WILD-TYPE	82	172	127

'LARP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.848 (Fisher's exact test), Q value = 1

Table S248. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
LARP1 MUTATED	3	0	2
LARP1 WILD-TYPE	174	73	163

'LARP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S249. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
LARP1 MUTATED	1	3	1	0	0	0
LARP1 WILD-TYPE	107	141	112	22	24	4

'LARP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S250. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
LARP1 MUTATED	0	3	2
LARP1 WILD-TYPE	97	175	130

'LARP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S251. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
LARP1 MUTATED	0	4	1
LARP1 WILD-TYPE	130	199	73

'KIAA1751 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 1

Table S252. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
KIAA1751 MUTATED	2	1	3
KIAA1751 WILD-TYPE	166	110	133

'KIAA1751 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S253. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
KIAA1751 MUTATED	3	0	2
KIAA1751 WILD-TYPE	93	53	92

'KIAA1751 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S254. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
KIAA1751 MUTATED	2	0	1	2	0	0
KIAA1751 WILD-TYPE	86	75	73	57	38	52

'KIAA1751 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0535 (Fisher's exact test), Q value = 1

Table S255. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
KIAA1751 MUTATED	2	0	3
KIAA1751 WILD-TYPE	80	175	126

'KIAA1751 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S256. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
KIAA1751 MUTATED	2	2	1
KIAA1751 WILD-TYPE	175	71	164

'KIAA1751 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S257. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
KIAA1751 MUTATED	2	2	1	0	0	0
KIAA1751 WILD-TYPE	106	142	112	22	24	4

'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 1

Table S258. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
KIAA1751 MUTATED	0	4	2
KIAA1751 WILD-TYPE	97	174	130

'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S259. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
KIAA1751 MUTATED	0	4	2
KIAA1751 WILD-TYPE	130	199	72

'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S260. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	74	68
KIAA1751 MUTATED	0	2	1
KIAA1751 WILD-TYPE	41	72	67

'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S261. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	79	40
KIAA1751 MUTATED	0	1	2
KIAA1751 WILD-TYPE	64	78	38

'INSRR MUTATION STATUS' versus 'CN_CNMF'

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

Table S262. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	111	136
INSRR MUTATED	2	0	2
INSRR WILD-TYPE	166	111	134

'INSRR MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S263. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
INSRR MUTATED	0	2	2
INSRR WILD-TYPE	96	51	92

'INSRR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 1

Table S264. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
INSRR MUTATED	0	0	2	1	0	1
INSRR WILD-TYPE	88	75	72	58	38	51

'INSRR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S265. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	175	129
INSRR MUTATED	1	1	2
INSRR WILD-TYPE	81	174	127

'INSRR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 1

Table S266. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
INSRR MUTATED	1	0	3
INSRR WILD-TYPE	176	73	162

'INSRR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S267. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	144	113	22	24	4
INSRR MUTATED	2	1	0	0	1	0
INSRR WILD-TYPE	106	143	113	22	23	4

'INSRR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S268. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	178	132
INSRR MUTATED	2	1	1
INSRR WILD-TYPE	95	177	131

'INSRR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 1

Table S269. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	203	74
INSRR MUTATED	1	1	2
INSRR WILD-TYPE	129	202	72

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = KIRC-TP.transferedmergedcluster.txt
Number of patients = 417
Number of significantly mutated genes = 29
Number of Molecular subtypes = 12
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)

Made with Nozzle