Correlation between gene mutation status and molecular subtypes

Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1QC02BP

Overview

Introduction

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

Summary

Testing the association between mutation status of 38 genes and 8 molecular subtypes across 194 patients, 5 significant findings detected with P value < 0.05 and Q value < 0.25.

KRAS mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
ARID1A mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 38 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 5 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	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
KRAS	11 (6%)	183	0.565 (1.00)	4e-05 (0.012)	8e-05 (0.024)	0.00119 (0.352)	0.00262 (0.773)	0.00077 (0.229)	0.036 (1.00)	0.00019 (0.0568)
ARID1A	14 (7%)	180	0.00639 (1.00)	0.00334 (0.982)	0.0121 (1.00)	0.00078 (0.232)	0.103 (1.00)	0.00445 (1.00)	0.702 (1.00)	0.00447 (1.00)
HLA-A	16 (8%)	178	0.26 (1.00)	0.105 (1.00)	0.0086 (1.00)	0.128 (1.00)	0.434 (1.00)	0.00771 (1.00)	0.696 (1.00)	0.418 (1.00)
FBXW7	19 (10%)	175	0.494 (1.00)	0.29 (1.00)	1 (1.00)	0.574 (1.00)	0.4 (1.00)	0.458 (1.00)	0.226 (1.00)	0.541 (1.00)
HLA-B	11 (6%)	183	0.519 (1.00)	0.152 (1.00)	0.0335 (1.00)	0.0997 (1.00)	0.0192 (1.00)	0.135 (1.00)	0.0128 (1.00)	0.0484 (1.00)
PTEN	15 (8%)	179	0.567 (1.00)	0.557 (1.00)	0.0508 (1.00)	0.221 (1.00)	0.433 (1.00)	0.192 (1.00)	1 (1.00)	0.418 (1.00)
MAPK1	9 (5%)	185	0.552 (1.00)	0.257 (1.00)	0.0302 (1.00)	0.0634 (1.00)	0.185 (1.00)	0.0818 (1.00)	0.0211 (1.00)	0.0223 (1.00)
EP300	21 (11%)	173	1 (1.00)	0.158 (1.00)	0.0595 (1.00)	0.0811 (1.00)	0.84 (1.00)	0.00893 (1.00)	1 (1.00)	0.247 (1.00)
PIK3CA	53 (27%)	141	0.0346 (1.00)	0.195 (1.00)	0.19 (1.00)	0.0327 (1.00)	0.328 (1.00)	0.344 (1.00)	0.48 (1.00)	0.227 (1.00)
NFE2L2	12 (6%)	182	0.927 (1.00)	0.0666 (1.00)	0.134 (1.00)	0.0666 (1.00)	0.0351 (1.00)	0.0182 (1.00)	0.385 (1.00)	0.0733 (1.00)
FAT2	11 (6%)	183	0.613 (1.00)	0.3 (1.00)	0.0856 (1.00)	0.423 (1.00)	0.583 (1.00)	0.764 (1.00)	0.0702 (1.00)	0.0907 (1.00)
ZNF750	10 (5%)	184	0.085 (1.00)	0.218 (1.00)	0.653 (1.00)	0.103 (1.00)	0.182 (1.00)	0.191 (1.00)	0.47 (1.00)	0.0723 (1.00)
BAP1	4 (2%)	190	0.139 (1.00)	0.0852 (1.00)	0.0853 (1.00)	0.75 (1.00)	0.69 (1.00)	0.352 (1.00)	0.26 (1.00)	0.172 (1.00)
RAB35	4 (2%)	190	0.26 (1.00)	0.141 (1.00)	1 (1.00)	0.751 (1.00)	0.474 (1.00)	0.107 (1.00)	0.296 (1.00)	0.0308 (1.00)
ERBB3	11 (6%)	183	0.0747 (1.00)	0.604 (1.00)	0.0152 (1.00)	0.00923 (1.00)	0.0798 (1.00)	0.0287 (1.00)	0.929 (1.00)	0.335 (1.00)
SMAD4	7 (4%)	187	0.49 (1.00)	0.25 (1.00)	0.484 (1.00)	0.87 (1.00)	0.725 (1.00)	0.599 (1.00)	1 (1.00)	0.946 (1.00)
TCTE1	5 (3%)	189	0.18 (1.00)	0.378 (1.00)	0.0155 (1.00)	0.397 (1.00)	0.0242 (1.00)	0.101 (1.00)	0.201 (1.00)	0.338 (1.00)
NHS	12 (6%)	182	0.861 (1.00)	0.863 (1.00)	0.643 (1.00)	0.264 (1.00)	0.931 (1.00)	0.834 (1.00)	0.424 (1.00)	0.436 (1.00)
LIN9	7 (4%)	187	0.158 (1.00)	0.164 (1.00)	0.894 (1.00)	1 (1.00)	0.886 (1.00)	0.271 (1.00)	0.3 (1.00)	0.892 (1.00)
C12ORF43	4 (2%)	190	0.197 (1.00)	0.802 (1.00)	1 (1.00)	0.75 (1.00)	0.473 (1.00)	0.206 (1.00)	0.295 (1.00)	0.161 (1.00)
MED1	11 (6%)	183	0.922 (1.00)	0.0195 (1.00)	0.0325 (1.00)	0.0887 (1.00)	0.188 (1.00)	0.242 (1.00)	0.507 (1.00)	0.124 (1.00)
USP28	4 (2%)	190	0.198 (1.00)	0.665 (1.00)	0.453 (1.00)	1 (1.00)	0.392 (1.00)	0.937 (1.00)	0.201 (1.00)	0.819 (1.00)
IDS	7 (4%)	187	0.188 (1.00)	0.566 (1.00)	0.792 (1.00)	1 (1.00)	0.495 (1.00)	0.22 (1.00)	0.439 (1.00)	0.715 (1.00)
TRIM9	8 (4%)	186	0.33 (1.00)	0.815 (1.00)	0.0938 (1.00)	0.565 (1.00)	0.544 (1.00)	0.0378 (1.00)	0.567 (1.00)	0.358 (1.00)
SEMA4B	7 (4%)	187	1 (1.00)	0.911 (1.00)	0.427 (1.00)	0.12 (1.00)	0.0607 (1.00)	0.288 (1.00)	0.39 (1.00)	0.128 (1.00)
ARHGAP4	6 (3%)	188	1 (1.00)	0.589 (1.00)	0.327 (1.00)	0.702 (1.00)	0.509 (1.00)	0.227 (1.00)	0.692 (1.00)	1 (1.00)
POU2F1	3 (2%)	191	0.453 (1.00)	0.387 (1.00)	0.461 (1.00)	0.698 (1.00)	0.63 (1.00)	0.489 (1.00)	0.293 (1.00)	0.161 (1.00)
IFNGR1	6 (3%)	188	1 (1.00)	0.4 (1.00)	0.764 (1.00)	1 (1.00)	0.323 (1.00)	0.033 (1.00)	0.0529 (1.00)	0.785 (1.00)
IGFN1	11 (6%)	183	0.215 (1.00)	0.807 (1.00)	0.727 (1.00)	0.59 (1.00)	0.356 (1.00)	0.966 (1.00)	0.331 (1.00)	0.849 (1.00)
RPGR	9 (5%)	185	1 (1.00)	0.872 (1.00)	0.906 (1.00)	0.876 (1.00)	0.916 (1.00)	0.952 (1.00)	0.759 (1.00)	0.8 (1.00)
CASP8	9 (5%)	185	0.674 (1.00)	0.706 (1.00)	0.308 (1.00)	0.455 (1.00)	0.571 (1.00)	0.449 (1.00)	0.124 (1.00)	0.434 (1.00)
GAS6	4 (2%)	190	0.817 (1.00)	0.137 (1.00)	0.357 (1.00)	0.75 (1.00)	1 (1.00)	0.392 (1.00)	0.292 (1.00)	0.755 (1.00)
ABCD1	7 (4%)	187	0.603 (1.00)	0.863 (1.00)	0.324 (1.00)	0.135 (1.00)	0.493 (1.00)	0.52 (1.00)	0.0568 (1.00)	0.374 (1.00)
RPAP1	4 (2%)	190	0.682 (1.00)	0.72 (1.00)	0.453 (1.00)	1 (1.00)	1 (1.00)	0.742 (1.00)	1 (1.00)	0.903 (1.00)
HIST1H4E	4 (2%)	190	0.199 (1.00)	0.801 (1.00)	0.357 (1.00)	0.3 (1.00)	0.473 (1.00)	0.828 (1.00)	0.401 (1.00)	0.379 (1.00)
NLRC5	7 (4%)	187	0.68 (1.00)	0.0993 (1.00)	0.258 (1.00)	0.156 (1.00)	0.138 (1.00)	0.275 (1.00)	0.565 (1.00)	0.159 (1.00)
DDX41	5 (3%)	189	0.0293 (1.00)	0.123 (1.00)	0.17 (1.00)	0.4 (1.00)	0.331 (1.00)	0.784 (1.00)	1 (1.00)	0.546 (1.00)
MCM7	3 (2%)	191		0.0719 (1.00)			1 (1.00)	0.49 (1.00)	0.0571 (1.00)	0.163 (1.00)

'KRAS MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
KRAS MUTATED	7	1	3
KRAS WILD-TYPE	83	39	58

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.012

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
KRAS MUTATED	10	0	0	0	0	1
KRAS WILD-TYPE	38	34	37	35	28	11

Figure S1. Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.024

Table S3. Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
KRAS MUTATED	10	0	1
KRAS WILD-TYPE	56	80	44

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

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.35

Table S4. Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
KRAS MUTATED	8	2	1
KRAS WILD-TYPE	40	118	22

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

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.77

Table S5. Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
KRAS MUTATED	7	4	0
KRAS WILD-TYPE	52	52	79

Figure S4. Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.23

Table S6. Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
KRAS MUTATED	8	0	2	1	0
KRAS WILD-TYPE	33	50	56	14	30

Figure S5. Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
KRAS MUTATED	6	5	0
KRAS WILD-TYPE	63	52	58

Figure S6. Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.057

Table S8. Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
KRAS MUTATED	9	1	0	1
KRAS WILD-TYPE	33	31	28	81

Figure S7. Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 1

Table S9. Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
HLA-A MUTATED	9	4	2
HLA-A WILD-TYPE	81	36	59

'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S10. Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
HLA-A MUTATED	1	3	5	6	1	0
HLA-A WILD-TYPE	47	31	32	29	27	12

'HLA-A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0086 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
HLA-A MUTATED	1	6	8
HLA-A WILD-TYPE	65	74	37

Figure S8. Get High-res Image Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S12. Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
HLA-A MUTATED	1	11	3
HLA-A WILD-TYPE	47	109	20

'HLA-A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
HLA-A MUTATED	3	4	9
HLA-A WILD-TYPE	56	52	70

'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00771 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
HLA-A MUTATED	0	4	3	3	6
HLA-A WILD-TYPE	41	46	55	12	24

Figure S9. Get High-res Image Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
HLA-A MUTATED	4	4	6
HLA-A WILD-TYPE	65	53	52

'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S16. Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
HLA-A MUTATED	1	2	2	9
HLA-A WILD-TYPE	41	30	26	73

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

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

Table S17. Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
FBXW7 MUTATED	11	3	4
FBXW7 WILD-TYPE	79	37	57

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S18. Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
FBXW7 MUTATED	6	4	4	5	0	0
FBXW7 WILD-TYPE	42	30	33	30	28	12

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S19. Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
FBXW7 MUTATED	6	8	4
FBXW7 WILD-TYPE	60	72	41

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S20. Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
FBXW7 MUTATED	6	11	1
FBXW7 WILD-TYPE	42	109	22

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S21. Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
FBXW7 MUTATED	6	3	10
FBXW7 WILD-TYPE	53	53	69

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S22. Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
FBXW7 MUTATED	4	8	3	1	3
FBXW7 WILD-TYPE	37	42	55	14	27

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S23. Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
FBXW7 MUTATED	10	3	6
FBXW7 WILD-TYPE	59	54	52

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
FBXW7 MUTATED	5	1	3	10
FBXW7 WILD-TYPE	37	31	25	72

'HLA-B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 1

Table S25. Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
HLA-B MUTATED	7	2	2
HLA-B WILD-TYPE	83	38	59

'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 1

Table S26. Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
HLA-B MUTATED	0	4	3	2	1	1
HLA-B WILD-TYPE	48	30	34	33	27	11

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 1

Table S27. Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
HLA-B MUTATED	1	4	6
HLA-B WILD-TYPE	65	76	39

Figure S10. Get High-res Image Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0997 (Fisher's exact test), Q value = 1

Table S28. Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
HLA-B MUTATED	0	10	1
HLA-B WILD-TYPE	48	110	22

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 1

Table S29. Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
HLA-B MUTATED	1	1	9
HLA-B WILD-TYPE	58	55	70

Figure S11. Get High-res Image Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 1

Table S30. Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
HLA-B MUTATED	0	5	2	1	3
HLA-B WILD-TYPE	41	45	56	14	27

'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
HLA-B MUTATED	3	0	7
HLA-B WILD-TYPE	66	57	51

Figure S12. Get High-res Image Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0484 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
HLA-B MUTATED	0	0	2	8
HLA-B WILD-TYPE	42	32	26	74

Figure S13. Get High-res Image Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S33. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
PTEN MUTATED	9	3	3
PTEN WILD-TYPE	81	37	58

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 1

Table S34. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
PTEN MUTATED	5	2	3	1	4	0
PTEN WILD-TYPE	43	32	34	34	24	12

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0508 (Fisher's exact test), Q value = 1

Table S35. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
PTEN MUTATED	6	9	0
PTEN WILD-TYPE	60	71	45

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 1

Table S36. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
PTEN MUTATED	6	9	0
PTEN WILD-TYPE	42	111	23

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S37. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
PTEN MUTATED	7	3	5
PTEN WILD-TYPE	52	53	74

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S38. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
PTEN MUTATED	4	6	3	2	0
PTEN WILD-TYPE	37	44	55	13	30

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S39. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
PTEN MUTATED	6	4	5
PTEN WILD-TYPE	63	53	53

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S40. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
PTEN MUTATED	4	4	3	4
PTEN WILD-TYPE	38	28	25	78

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00639 (Fisher's exact test), Q value = 1

Table S41. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
ARID1A MUTATED	11	3	0
ARID1A WILD-TYPE	79	37	61

Figure S14. Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.98

Table S42. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
ARID1A MUTATED	10	2	2	0	0	0
ARID1A WILD-TYPE	38	32	35	35	28	12

Figure S15. Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 1

Table S43. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
ARID1A MUTATED	10	2	2
ARID1A WILD-TYPE	56	78	43

Figure S16. Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.23

Table S44. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
ARID1A MUTATED	10	4	0
ARID1A WILD-TYPE	38	116	23

Figure S17. Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 1

Table S45. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
ARID1A MUTATED	8	2	4
ARID1A WILD-TYPE	51	54	75

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00445 (Fisher's exact test), Q value = 1

Table S46. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
ARID1A MUTATED	7	1	1	3	2
ARID1A WILD-TYPE	34	49	57	12	28

Figure S18. Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S47. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
ARID1A MUTATED	6	3	3
ARID1A WILD-TYPE	63	54	55

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00447 (Fisher's exact test), Q value = 1

Table S48. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
ARID1A MUTATED	7	0	3	2
ARID1A WILD-TYPE	35	32	25	80

Figure S19. Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MAPK1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S49. Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
MAPK1 MUTATED	6	1	2
MAPK1 WILD-TYPE	84	39	59

'MAPK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 1

Table S50. Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
MAPK1 MUTATED	0	2	3	1	2	1
MAPK1 WILD-TYPE	48	32	34	34	26	11

'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 1

Table S51. Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
MAPK1 MUTATED	0	7	2
MAPK1 WILD-TYPE	66	73	43

Figure S20. Get High-res Image Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0634 (Fisher's exact test), Q value = 1

Table S52. Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
MAPK1 MUTATED	0	9	0
MAPK1 WILD-TYPE	48	111	23

'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S53. Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
MAPK1 MUTATED	1	5	3
MAPK1 WILD-TYPE	58	51	76

'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0818 (Fisher's exact test), Q value = 1

Table S54. Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
MAPK1 MUTATED	0	2	6	1	0
MAPK1 WILD-TYPE	41	48	52	14	30

'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 1

Table S55. Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
MAPK1 MUTATED	0	5	4
MAPK1 WILD-TYPE	69	52	54

Figure S21. Get High-res Image Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 1

Table S56. Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
MAPK1 MUTATED	0	5	1	3
MAPK1 WILD-TYPE	42	27	27	79

Figure S22. Get High-res Image Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'CN_CNMF'

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

Table S57. Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
EP300 MUTATED	10	4	6
EP300 WILD-TYPE	80	36	55

'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S58. Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
EP300 MUTATED	3	7	5	1	3	2
EP300 WILD-TYPE	45	27	32	34	25	10

'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0595 (Fisher's exact test), Q value = 1

Table S59. Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
EP300 MUTATED	4	14	3
EP300 WILD-TYPE	62	66	42

'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0811 (Fisher's exact test), Q value = 1

Table S60. Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
EP300 MUTATED	2	18	1
EP300 WILD-TYPE	46	102	22

'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 1

Table S61. Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
EP300 MUTATED	6	5	10
EP300 WILD-TYPE	53	51	69

'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00893 (Fisher's exact test), Q value = 1

Table S62. Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
EP300 MUTATED	1	9	10	1	0
EP300 WILD-TYPE	40	41	48	14	30

Figure S23. Get High-res Image Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S63. Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
EP300 MUTATED	7	5	6
EP300 WILD-TYPE	62	52	52

'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S64. Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
EP300 MUTATED	2	3	1	12
EP300 WILD-TYPE	40	29	27	70

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 1

Table S65. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
PIK3CA MUTATED	33	7	13
PIK3CA WILD-TYPE	57	33	48

Figure S24. Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S66. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
PIK3CA MUTATED	17	10	11	5	9	1
PIK3CA WILD-TYPE	31	24	26	30	19	11

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S67. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
PIK3CA MUTATED	22	22	8
PIK3CA WILD-TYPE	44	58	37

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 1

Table S68. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
PIK3CA MUTATED	18	32	2
PIK3CA WILD-TYPE	30	88	21

Figure S25. Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S69. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
PIK3CA MUTATED	20	12	21
PIK3CA WILD-TYPE	39	44	58

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 1

Table S70. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
PIK3CA MUTATED	14	17	13	4	5
PIK3CA WILD-TYPE	27	33	45	11	25

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S71. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
PIK3CA MUTATED	22	13	14
PIK3CA WILD-TYPE	47	44	44

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S72. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
PIK3CA MUTATED	16	9	7	17
PIK3CA WILD-TYPE	26	23	21	65

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.927 (Fisher's exact test), Q value = 1

Table S73. Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
NFE2L2 MUTATED	5	3	4
NFE2L2 WILD-TYPE	85	37	57

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0666 (Fisher's exact test), Q value = 1

Table S74. Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
NFE2L2 MUTATED	0	5	2	2	3	0
NFE2L2 WILD-TYPE	48	29	35	33	25	12

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S75. Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
NFE2L2 MUTATED	1	7	4
NFE2L2 WILD-TYPE	65	73	41

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0666 (Fisher's exact test), Q value = 1

Table S76. Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
NFE2L2 MUTATED	0	11	1
NFE2L2 WILD-TYPE	48	109	22

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 1

Table S77. Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
NFE2L2 MUTATED	0	5	7
NFE2L2 WILD-TYPE	59	51	72

Figure S26. Get High-res Image Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 1

Table S78. Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
NFE2L2 MUTATED	0	1	6	3	2
NFE2L2 WILD-TYPE	41	49	52	12	28

Figure S27. Get High-res Image Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S79. Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
NFE2L2 MUTATED	2	4	5
NFE2L2 WILD-TYPE	67	53	53

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0733 (Fisher's exact test), Q value = 1

Table S80. Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
NFE2L2 MUTATED	0	2	4	5
NFE2L2 WILD-TYPE	42	30	24	77

'FAT2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S81. Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
FAT2 MUTATED	6	3	2
FAT2 WILD-TYPE	84	37	59

'FAT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S82. Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
FAT2 MUTATED	1	5	2	2	1	0
FAT2 WILD-TYPE	47	29	35	33	27	12

'FAT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0856 (Fisher's exact test), Q value = 1

Table S83. Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
FAT2 MUTATED	1	5	5
FAT2 WILD-TYPE	65	75	40

'FAT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.423 (Fisher's exact test), Q value = 1

Table S84. Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
FAT2 MUTATED	1	9	1
FAT2 WILD-TYPE	47	111	22

'FAT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 1

Table S85. Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
FAT2 MUTATED	2	3	6
FAT2 WILD-TYPE	57	53	73

'FAT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.764 (Fisher's exact test), Q value = 1

Table S86. Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
FAT2 MUTATED	1	4	4	0	2
FAT2 WILD-TYPE	40	46	54	15	28

'FAT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0702 (Fisher's exact test), Q value = 1

Table S87. Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
FAT2 MUTATED	3	1	7
FAT2 WILD-TYPE	66	56	51

'FAT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0907 (Fisher's exact test), Q value = 1

Table S88. Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
FAT2 MUTATED	1	0	1	9
FAT2 WILD-TYPE	41	32	27	73

'ZNF750 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.085 (Fisher's exact test), Q value = 1

Table S89. Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
ZNF750 MUTATED	8	0	2
ZNF750 WILD-TYPE	82	40	59

'ZNF750 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S90. Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
ZNF750 MUTATED	1	3	4	1	0	1
ZNF750 WILD-TYPE	47	31	33	34	28	11

'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.653 (Fisher's exact test), Q value = 1

Table S91. Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
ZNF750 MUTATED	2	5	3
ZNF750 WILD-TYPE	64	75	42

'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 1

Table S92. Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
ZNF750 MUTATED	0	9	1
ZNF750 WILD-TYPE	48	111	22

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S93. Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
ZNF750 MUTATED	2	1	7
ZNF750 WILD-TYPE	57	55	72

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 1

Table S94. Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
ZNF750 MUTATED	0	5	2	1	2
ZNF750 WILD-TYPE	41	45	56	14	28

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S95. Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
ZNF750 MUTATED	4	1	4
ZNF750 WILD-TYPE	65	56	54

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0723 (Fisher's exact test), Q value = 1

Table S96. Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
ZNF750 MUTATED	0	0	2	7
ZNF750 WILD-TYPE	42	32	26	75

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S97. Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
BAP1 MUTATED	4	0	0
BAP1 WILD-TYPE	86	40	61

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0852 (Fisher's exact test), Q value = 1

Table S98. Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
BAP1 MUTATED	0	3	1	0	0	0
BAP1 WILD-TYPE	48	31	36	35	28	12

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0853 (Fisher's exact test), Q value = 1

Table S99. Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
BAP1 MUTATED	0	4	0
BAP1 WILD-TYPE	66	76	45

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.75 (Fisher's exact test), Q value = 1

Table S100. Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
BAP1 MUTATED	0	4	0
BAP1 WILD-TYPE	48	116	23

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S101. Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
BAP1 MUTATED	1	2	1
BAP1 WILD-TYPE	58	54	78

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S102. Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
BAP1 MUTATED	0	2	1	1	0
BAP1 WILD-TYPE	41	48	57	14	30

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 1

Table S103. Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
BAP1 MUTATED	0	2	2
BAP1 WILD-TYPE	69	55	56

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 1

Table S104. Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
BAP1 MUTATED	0	2	1	1
BAP1 WILD-TYPE	42	30	27	81

'RAB35 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 1

Table S105. Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
RAB35 MUTATED	1	0	3
RAB35 WILD-TYPE	89	40	58

'RAB35 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 1

Table S106. Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
RAB35 MUTATED	0	0	2	1	0	1
RAB35 WILD-TYPE	48	34	35	34	28	11

'RAB35 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S107. Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
RAB35 MUTATED	1	2	1
RAB35 WILD-TYPE	65	78	44

'RAB35 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S108. Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
RAB35 MUTATED	0	4	0
RAB35 WILD-TYPE	48	116	23

'RAB35 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S109. Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
RAB35 MUTATED	0	2	2
RAB35 WILD-TYPE	59	54	77

'RAB35 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S110. Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
RAB35 MUTATED	0	0	3	1	0
RAB35 WILD-TYPE	41	50	55	14	30

'RAB35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S111. Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
RAB35 MUTATED	0	1	2
RAB35 WILD-TYPE	69	56	56

'RAB35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 1

Table S112. Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
RAB35 MUTATED	0	1	2	0
RAB35 WILD-TYPE	42	31	26	82

Figure S28. Get High-res Image Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ERBB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0747 (Fisher's exact test), Q value = 1

Table S113. Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
ERBB3 MUTATED	5	5	1
ERBB3 WILD-TYPE	85	35	60

'ERBB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.604 (Fisher's exact test), Q value = 1

Table S114. Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
ERBB3 MUTATED	5	3	1	1	1	0
ERBB3 WILD-TYPE	43	31	36	34	27	12

'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 1

Table S115. Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
ERBB3 MUTATED	8	1	2
ERBB3 WILD-TYPE	58	79	43

Figure S29. Get High-res Image Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00923 (Fisher's exact test), Q value = 1

Table S116. Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
ERBB3 MUTATED	7	3	1
ERBB3 WILD-TYPE	41	117	22

Figure S30. Get High-res Image Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S117. Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
ERBB3 MUTATED	5	5	1
ERBB3 WILD-TYPE	54	51	78

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S118. Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
ERBB3 MUTATED	7	2	1	0	1
ERBB3 WILD-TYPE	34	48	57	15	29

Figure S31. Get High-res Image Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.929 (Fisher's exact test), Q value = 1

Table S119. Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
ERBB3 MUTATED	4	4	3
ERBB3 WILD-TYPE	65	53	55

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S120. Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
ERBB3 MUTATED	5	2	1	3
ERBB3 WILD-TYPE	37	30	27	79

'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S121. Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
SMAD4 MUTATED	4	0	2
SMAD4 WILD-TYPE	86	40	59

'SMAD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S122. Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
SMAD4 MUTATED	2	0	3	0	1	1
SMAD4 WILD-TYPE	46	34	34	35	27	11

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S123. Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
SMAD4 MUTATED	2	2	3
SMAD4 WILD-TYPE	64	78	42

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.87 (Fisher's exact test), Q value = 1

Table S124. Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
SMAD4 MUTATED	2	4	1
SMAD4 WILD-TYPE	46	116	22

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S125. Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
SMAD4 MUTATED	2	1	4
SMAD4 WILD-TYPE	57	55	75

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S126. Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
SMAD4 MUTATED	1	3	1	0	2
SMAD4 WILD-TYPE	40	47	57	15	28

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S127. Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
SMAD4 MUTATED	3	2	2
SMAD4 WILD-TYPE	66	55	56

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.946 (Fisher's exact test), Q value = 1

Table S128. Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
SMAD4 MUTATED	1	1	1	4
SMAD4 WILD-TYPE	41	31	27	78

'TCTE1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S129. Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
TCTE1 MUTATED	3	2	0
TCTE1 WILD-TYPE	87	38	61

'TCTE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S130. Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
TCTE1 MUTATED	0	2	1	2	0	0
TCTE1 WILD-TYPE	48	32	36	33	28	12

'TCTE1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 1

Table S131. Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
TCTE1 MUTATED	0	1	4
TCTE1 WILD-TYPE	66	79	41

Figure S32. Get High-res Image Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TCTE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 1

Table S132. Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
TCTE1 MUTATED	0	4	1
TCTE1 WILD-TYPE	48	116	22

'TCTE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S133. Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
TCTE1 MUTATED	0	0	5
TCTE1 WILD-TYPE	59	56	74

Figure S33. Get High-res Image Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TCTE1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S134. Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
TCTE1 MUTATED	0	1	1	2	1
TCTE1 WILD-TYPE	41	49	57	13	29

'TCTE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 1

Table S135. Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
TCTE1 MUTATED	1	0	3
TCTE1 WILD-TYPE	68	57	55

'TCTE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S136. Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
TCTE1 MUTATED	0	0	0	4
TCTE1 WILD-TYPE	42	32	28	78

'NHS MUTATION STATUS' versus 'CN_CNMF'

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

Table S137. Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
NHS MUTATED	6	3	3
NHS WILD-TYPE	84	37	58

'NHS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S138. Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
NHS MUTATED	4	3	1	2	2	0
NHS WILD-TYPE	44	31	36	33	26	12

'NHS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S139. Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
NHS MUTATED	3	5	4
NHS WILD-TYPE	63	75	41

'NHS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.264 (Fisher's exact test), Q value = 1

Table S140. Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
NHS MUTATED	3	6	3
NHS WILD-TYPE	45	114	20

'NHS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.931 (Fisher's exact test), Q value = 1

Table S141. Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
NHS MUTATED	3	4	5
NHS WILD-TYPE	56	52	74

'NHS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S142. Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
NHS MUTATED	3	3	3	0	3
NHS WILD-TYPE	38	47	55	15	27

'NHS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 1

Table S143. Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
NHS MUTATED	6	3	2
NHS WILD-TYPE	63	54	56

'NHS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S144. Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
NHS MUTATED	3	1	0	7
NHS WILD-TYPE	39	31	28	75

'LIN9 MUTATION STATUS' versus 'CN_CNMF'

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

Table S145. Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
LIN9 MUTATED	1	1	4
LIN9 WILD-TYPE	89	39	57

'LIN9 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S146. Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
LIN9 MUTATED	1	1	2	0	1	2
LIN9 WILD-TYPE	47	33	35	35	27	10

'LIN9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.894 (Fisher's exact test), Q value = 1

Table S147. Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
LIN9 MUTATED	3	3	1
LIN9 WILD-TYPE	63	77	44

'LIN9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S148. Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
LIN9 MUTATED	2	5	0
LIN9 WILD-TYPE	46	115	23

'LIN9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.886 (Fisher's exact test), Q value = 1

Table S149. Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
LIN9 MUTATED	3	2	2
LIN9 WILD-TYPE	56	54	77

'LIN9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S150. Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
LIN9 MUTATED	0	2	4	1	0
LIN9 WILD-TYPE	41	48	54	14	30

'LIN9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S151. Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
LIN9 MUTATED	1	2	4
LIN9 WILD-TYPE	68	55	54

'LIN9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.892 (Fisher's exact test), Q value = 1

Table S152. Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
LIN9 MUTATED	1	2	1	3
LIN9 WILD-TYPE	41	30	27	79

'C12ORF43 MUTATION STATUS' versus 'CN_CNMF'

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

Table S153. Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
C12ORF43 MUTATED	2	2	0
C12ORF43 WILD-TYPE	88	38	61

'C12ORF43 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S154. Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
C12ORF43 MUTATED	0	1	1	1	1	0
C12ORF43 WILD-TYPE	48	33	36	34	27	12

'C12ORF43 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S155. Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
C12ORF43 MUTATED	1	2	1
C12ORF43 WILD-TYPE	65	78	44

'C12ORF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.75 (Fisher's exact test), Q value = 1

Table S156. Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
C12ORF43 MUTATED	0	4	0
C12ORF43 WILD-TYPE	48	116	23

'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S157. Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
C12ORF43 MUTATED	0	2	2
C12ORF43 WILD-TYPE	59	54	77

'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S158. Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
C12ORF43 MUTATED	0	0	2	1	1
C12ORF43 WILD-TYPE	41	50	56	14	29

'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S159. Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
C12ORF43 MUTATED	0	1	2
C12ORF43 WILD-TYPE	69	56	56

'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S160. Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
C12ORF43 MUTATED	0	0	2	1
C12ORF43 WILD-TYPE	42	32	26	81

'MED1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S161. Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
MED1 MUTATED	6	2	3
MED1 WILD-TYPE	84	38	58

'MED1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 1

Table S162. Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
MED1 MUTATED	0	1	3	3	1	3
MED1 WILD-TYPE	48	33	34	32	27	9

Figure S34. Get High-res Image Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MED1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 1

Table S163. Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
MED1 MUTATED	1	4	6
MED1 WILD-TYPE	65	76	39

Figure S35. Get High-res Image Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'MED1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0887 (Fisher's exact test), Q value = 1

Table S164. Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
MED1 MUTATED	0	9	2
MED1 WILD-TYPE	48	111	21

'MED1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S165. Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
MED1 MUTATED	1	3	7
MED1 WILD-TYPE	58	53	72

'MED1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S166. Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
MED1 MUTATED	0	4	4	0	3
MED1 WILD-TYPE	41	46	54	15	27

'MED1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.507 (Fisher's exact test), Q value = 1

Table S167. Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
MED1 MUTATED	3	2	5
MED1 WILD-TYPE	66	55	53

'MED1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S168. Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
MED1 MUTATED	0	1	3	6
MED1 WILD-TYPE	42	31	25	76

'USP28 MUTATION STATUS' versus 'CN_CNMF'

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

Table S169. Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
USP28 MUTATED	2	2	0
USP28 WILD-TYPE	88	38	61

'USP28 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.665 (Fisher's exact test), Q value = 1

Table S170. Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
USP28 MUTATED	1	2	1	0	0	0
USP28 WILD-TYPE	47	32	36	35	28	12

'USP28 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S171. Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
USP28 MUTATED	1	1	2
USP28 WILD-TYPE	65	79	43

'USP28 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S172. Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
USP28 MUTATED	1	3	0
USP28 WILD-TYPE	47	117	23

'USP28 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S173. Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
USP28 MUTATED	1	0	3
USP28 WILD-TYPE	58	56	76

'USP28 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S174. Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
USP28 MUTATED	1	1	2	0	0
USP28 WILD-TYPE	40	49	56	15	30

'USP28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 1

Table S175. Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
USP28 MUTATED	1	0	3
USP28 WILD-TYPE	68	57	55

'USP28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.819 (Fisher's exact test), Q value = 1

Table S176. Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
USP28 MUTATED	1	0	0	3
USP28 WILD-TYPE	41	32	28	79

'IDS MUTATION STATUS' versus 'CN_CNMF'

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

Table S177. Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
IDS MUTATED	4	2	0
IDS WILD-TYPE	86	38	61

'IDS MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S178. Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
IDS MUTATED	2	3	1	0	1	0
IDS WILD-TYPE	46	31	36	35	27	12

'IDS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S179. Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
IDS MUTATED	2	4	1
IDS WILD-TYPE	64	76	44

'IDS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S180. Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
IDS MUTATED	2	5	0
IDS WILD-TYPE	46	115	23

'IDS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S181. Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
IDS MUTATED	1	3	3
IDS WILD-TYPE	58	53	76

'IDS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 1

Table S182. Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
IDS MUTATED	1	1	3	2	0
IDS WILD-TYPE	40	49	55	13	30

'IDS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S183. Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
IDS MUTATED	1	3	3
IDS WILD-TYPE	68	54	55

'IDS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.715 (Fisher's exact test), Q value = 1

Table S184. Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
IDS MUTATED	2	2	0	3
IDS WILD-TYPE	40	30	28	79

'TRIM9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 1

Table S185. Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
TRIM9 MUTATED	6	1	1
TRIM9 WILD-TYPE	84	39	60

'TRIM9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.815 (Fisher's exact test), Q value = 1

Table S186. Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
TRIM9 MUTATED	3	2	1	2	0	0
TRIM9 WILD-TYPE	45	32	36	33	28	12

'TRIM9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0938 (Fisher's exact test), Q value = 1

Table S187. Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
TRIM9 MUTATED	3	1	4
TRIM9 WILD-TYPE	63	79	41

'TRIM9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S188. Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
TRIM9 MUTATED	3	4	1
TRIM9 WILD-TYPE	45	116	22

'TRIM9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 1

Table S189. Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
TRIM9 MUTATED	2	1	5
TRIM9 WILD-TYPE	57	55	74

'TRIM9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 1

Table S190. Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
TRIM9 MUTATED	3	1	0	2	2
TRIM9 WILD-TYPE	38	49	58	13	28

Figure S36. Get High-res Image Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'TRIM9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S191. Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
TRIM9 MUTATED	4	1	2
TRIM9 WILD-TYPE	65	56	56

'TRIM9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S192. Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
TRIM9 MUTATED	3	0	0	4
TRIM9 WILD-TYPE	39	32	28	78

'SEMA4B MUTATION STATUS' versus 'CN_CNMF'

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

Table S193. Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
SEMA4B MUTATED	4	1	2
SEMA4B WILD-TYPE	86	39	59

'SEMA4B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.911 (Fisher's exact test), Q value = 1

Table S194. Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
SEMA4B MUTATED	1	2	1	2	1	0
SEMA4B WILD-TYPE	47	32	36	33	27	12

'SEMA4B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 1

Table S195. Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
SEMA4B MUTATED	1	3	3
SEMA4B WILD-TYPE	65	77	42

'SEMA4B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S196. Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
SEMA4B MUTATED	0	5	2
SEMA4B WILD-TYPE	48	115	21

'SEMA4B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0607 (Fisher's exact test), Q value = 1

Table S197. Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
SEMA4B MUTATED	1	0	6
SEMA4B WILD-TYPE	58	56	73

'SEMA4B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S198. Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
SEMA4B MUTATED	0	2	2	0	3
SEMA4B WILD-TYPE	41	48	56	15	27

'SEMA4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S199. Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
SEMA4B MUTATED	2	1	4
SEMA4B WILD-TYPE	67	56	54

'SEMA4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S200. Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
SEMA4B MUTATED	0	0	1	6
SEMA4B WILD-TYPE	42	32	27	76

'ARHGAP4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S201. Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
ARHGAP4 MUTATED	3	1	2
ARHGAP4 WILD-TYPE	87	39	59

'ARHGAP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S202. Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
ARHGAP4 MUTATED	2	2	0	2	0	0
ARHGAP4 WILD-TYPE	46	32	37	33	28	12

'ARHGAP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S203. Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
ARHGAP4 MUTATED	1	2	3
ARHGAP4 WILD-TYPE	65	78	42

'ARHGAP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S204. Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
ARHGAP4 MUTATED	1	4	1
ARHGAP4 WILD-TYPE	47	116	22

'ARHGAP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S205. Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
ARHGAP4 MUTATED	1	1	4
ARHGAP4 WILD-TYPE	58	55	75

'ARHGAP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S206. Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
ARHGAP4 MUTATED	1	1	2	2	0
ARHGAP4 WILD-TYPE	40	49	56	13	30

'ARHGAP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 1

Table S207. Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
ARHGAP4 MUTATED	1	2	1
ARHGAP4 WILD-TYPE	68	55	57

'ARHGAP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S208. Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
ARHGAP4 MUTATED	1	1	0	2
ARHGAP4 WILD-TYPE	41	31	28	80

'POU2F1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S209. Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
POU2F1 MUTATED	2	1	0
POU2F1 WILD-TYPE	88	39	61

'POU2F1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S210. Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
POU2F1 MUTATED	0	1	2	0	0	0
POU2F1 WILD-TYPE	48	33	35	35	28	12

'POU2F1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S211. Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
POU2F1 MUTATED	0	2	1
POU2F1 WILD-TYPE	66	78	44

'POU2F1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.698 (Fisher's exact test), Q value = 1

Table S212. Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
POU2F1 MUTATED	0	3	0
POU2F1 WILD-TYPE	48	117	23

'POU2F1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S213. Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
POU2F1 MUTATED	0	1	2
POU2F1 WILD-TYPE	59	55	77

'POU2F1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S214. Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
POU2F1 MUTATED	0	0	2	0	1
POU2F1 WILD-TYPE	41	50	56	15	29

'POU2F1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S215. Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
POU2F1 MUTATED	0	1	2
POU2F1 WILD-TYPE	69	56	56

'POU2F1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S216. Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
POU2F1 MUTATED	0	0	2	1
POU2F1 WILD-TYPE	42	32	26	81

'IFNGR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S217. Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
IFNGR1 MUTATED	3	1	2
IFNGR1 WILD-TYPE	87	39	59

'IFNGR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S218. Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
IFNGR1 MUTATED	2	2	0	1	0	1
IFNGR1 WILD-TYPE	46	32	37	34	28	11

'IFNGR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.764 (Fisher's exact test), Q value = 1

Table S219. Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
IFNGR1 MUTATED	3	2	1
IFNGR1 WILD-TYPE	63	78	44

'IFNGR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S220. Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
IFNGR1 MUTATED	2	4	0
IFNGR1 WILD-TYPE	46	116	23

'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S221. Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
IFNGR1 MUTATED	3	0	3
IFNGR1 WILD-TYPE	56	56	76

'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 1

Table S222. Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
IFNGR1 MUTATED	1	3	0	2	0
IFNGR1 WILD-TYPE	40	47	58	13	30

Figure S37. Get High-res Image Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0529 (Fisher's exact test), Q value = 1

Table S223. Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
IFNGR1 MUTATED	5	0	1
IFNGR1 WILD-TYPE	64	57	57

'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.785 (Fisher's exact test), Q value = 1

Table S224. Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
IFNGR1 MUTATED	2	0	1	3
IFNGR1 WILD-TYPE	40	32	27	79

'IGFN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 1

Table S225. Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
IGFN1 MUTATED	7	0	4
IGFN1 WILD-TYPE	83	40	57

'IGFN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.807 (Fisher's exact test), Q value = 1

Table S226. Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
IGFN1 MUTATED	2	3	3	1	2	0
IGFN1 WILD-TYPE	46	31	34	34	26	12

'IGFN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 1

Table S227. Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
IGFN1 MUTATED	3	6	2
IGFN1 WILD-TYPE	63	74	43

'IGFN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S228. Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
IGFN1 MUTATED	3	8	0
IGFN1 WILD-TYPE	45	112	23

'IGFN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.356 (Fisher's exact test), Q value = 1

Table S229. Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
IGFN1 MUTATED	4	1	6
IGFN1 WILD-TYPE	55	55	73

'IGFN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.966 (Fisher's exact test), Q value = 1

Table S230. Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
IGFN1 MUTATED	3	3	3	1	1
IGFN1 WILD-TYPE	38	47	55	14	29

'IGFN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 1

Table S231. Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
IGFN1 MUTATED	5	1	4
IGFN1 WILD-TYPE	64	56	54

'IGFN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S232. Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
IGFN1 MUTATED	2	1	1	6
IGFN1 WILD-TYPE	40	31	27	76

'RPGR MUTATION STATUS' versus 'CN_CNMF'

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

Table S233. Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
RPGR MUTATED	4	2	3
RPGR WILD-TYPE	86	38	58

'RPGR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S234. Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
RPGR MUTATED	3	2	1	1	1	1
RPGR WILD-TYPE	45	32	36	34	27	11

'RPGR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S235. Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
RPGR MUTATED	4	3	2
RPGR WILD-TYPE	62	77	43

'RPGR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S236. Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
RPGR MUTATED	3	5	1
RPGR WILD-TYPE	45	115	22

'RPGR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S237. Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
RPGR MUTATED	3	3	3
RPGR WILD-TYPE	56	53	76

'RPGR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.952 (Fisher's exact test), Q value = 1

Table S238. Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
RPGR MUTATED	2	2	4	0	1
RPGR WILD-TYPE	39	48	54	15	29

'RPGR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S239. Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
RPGR MUTATED	3	2	4
RPGR WILD-TYPE	66	55	54

'RPGR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S240. Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
RPGR MUTATED	3	2	1	3
RPGR WILD-TYPE	39	30	27	79

'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 1

Table S241. Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
CASP8 MUTATED	3	2	4
CASP8 WILD-TYPE	87	38	57

'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S242. Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
CASP8 MUTATED	1	1	3	2	1	1
CASP8 WILD-TYPE	47	33	34	33	27	11

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S243. Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
CASP8 MUTATED	1	5	3
CASP8 WILD-TYPE	65	75	42

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 1

Table S244. Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
CASP8 MUTATED	1	6	2
CASP8 WILD-TYPE	47	114	21

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S245. Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
CASP8 MUTATED	3	1	5
CASP8 WILD-TYPE	56	55	74

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S246. Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
CASP8 MUTATED	0	3	3	1	2
CASP8 WILD-TYPE	41	47	55	14	28

'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S247. Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
CASP8 MUTATED	4	0	4
CASP8 WILD-TYPE	65	57	54

'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.434 (Fisher's exact test), Q value = 1

Table S248. Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
CASP8 MUTATED	1	0	1	6
CASP8 WILD-TYPE	41	32	27	76

'GAS6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S249. Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
GAS6 MUTATED	2	0	2
GAS6 WILD-TYPE	88	40	59

'GAS6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S250. Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
GAS6 MUTATED	0	0	3	1	0	0
GAS6 WILD-TYPE	48	34	34	34	28	12

'GAS6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S251. Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
GAS6 MUTATED	0	3	1
GAS6 WILD-TYPE	66	77	44

'GAS6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.75 (Fisher's exact test), Q value = 1

Table S252. Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
GAS6 MUTATED	0	4	0
GAS6 WILD-TYPE	48	116	23

'GAS6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S253. Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
GAS6 MUTATED	1	1	2
GAS6 WILD-TYPE	58	55	77

'GAS6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S254. Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
GAS6 MUTATED	0	3	1	0	0
GAS6 WILD-TYPE	41	47	57	15	30

'GAS6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S255. Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
GAS6 MUTATED	0	1	2
GAS6 WILD-TYPE	69	56	56

'GAS6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S256. Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
GAS6 MUTATED	0	1	0	2
GAS6 WILD-TYPE	42	31	28	80

'ABCD1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S257. Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
ABCD1 MUTATED	2	2	1
ABCD1 WILD-TYPE	88	38	60

'ABCD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S258. Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
ABCD1 MUTATED	1	1	1	2	2	0
ABCD1 WILD-TYPE	47	33	36	33	26	12

'ABCD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S259. Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
ABCD1 MUTATED	1	2	3
ABCD1 WILD-TYPE	65	78	42

'ABCD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 1

Table S260. Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
ABCD1 MUTATED	0	4	2
ABCD1 WILD-TYPE	48	116	21

'ABCD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S261. Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
ABCD1 MUTATED	1	3	3
ABCD1 WILD-TYPE	58	53	76

'ABCD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.52 (Fisher's exact test), Q value = 1

Table S262. Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
ABCD1 MUTATED	0	2	3	0	2
ABCD1 WILD-TYPE	41	48	55	15	28

'ABCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0568 (Fisher's exact test), Q value = 1

Table S263. Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
ABCD1 MUTATED	0	4	3
ABCD1 WILD-TYPE	69	53	55

'ABCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S264. Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
ABCD1 MUTATED	0	1	2	4
ABCD1 WILD-TYPE	42	31	26	78

'RPAP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S265. Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
RPAP1 MUTATED	3	0	1
RPAP1 WILD-TYPE	87	40	60

'RPAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.72 (Fisher's exact test), Q value = 1

Table S266. Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
RPAP1 MUTATED	1	1	2	0	0	0
RPAP1 WILD-TYPE	47	33	35	35	28	12

'RPAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S267. Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
RPAP1 MUTATED	1	1	2
RPAP1 WILD-TYPE	65	79	43

'RPAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S268. Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
RPAP1 MUTATED	1	3	0
RPAP1 WILD-TYPE	47	117	23

'RPAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S269. Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
RPAP1 MUTATED	1	1	2
RPAP1 WILD-TYPE	58	55	77

'RPAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S270. Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
RPAP1 MUTATED	0	2	1	0	1
RPAP1 WILD-TYPE	41	48	57	15	29

'RPAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S271. Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
RPAP1 MUTATED	2	1	1
RPAP1 WILD-TYPE	67	56	57

'RPAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S272. Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
RPAP1 MUTATED	1	0	1	2
RPAP1 WILD-TYPE	41	32	27	80

'HIST1H4E MUTATION STATUS' versus 'CN_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 1

Table S273. Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
HIST1H4E MUTATED	2	2	0
HIST1H4E WILD-TYPE	88	38	61

'HIST1H4E MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S274. Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
HIST1H4E MUTATED	0	1	1	1	1	0
HIST1H4E WILD-TYPE	48	33	36	34	27	12

'HIST1H4E MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S275. Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
HIST1H4E MUTATED	0	3	1
HIST1H4E WILD-TYPE	66	77	44

'HIST1H4E MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S276. Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
HIST1H4E MUTATED	0	3	1
HIST1H4E WILD-TYPE	48	117	22

'HIST1H4E MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S277. Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
HIST1H4E MUTATED	0	2	2
HIST1H4E WILD-TYPE	59	54	77

'HIST1H4E MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S278. Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
HIST1H4E MUTATED	0	1	2	0	1
HIST1H4E WILD-TYPE	41	49	56	15	29

'HIST1H4E MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 1

Table S279. Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
HIST1H4E MUTATED	1	2	0
HIST1H4E WILD-TYPE	68	55	58

'HIST1H4E MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S280. Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
HIST1H4E MUTATED	0	1	1	1
HIST1H4E WILD-TYPE	42	31	27	81

'NLRC5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S281. Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
NLRC5 MUTATED	4	2	1
NLRC5 WILD-TYPE	86	38	60

'NLRC5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0993 (Fisher's exact test), Q value = 1

Table S282. Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
NLRC5 MUTATED	4	2	0	0	0	1
NLRC5 WILD-TYPE	44	32	37	35	28	11

'NLRC5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 1

Table S283. Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
NLRC5 MUTATED	4	1	2
NLRC5 WILD-TYPE	62	79	43

'NLRC5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S284. Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
NLRC5 MUTATED	4	3	0
NLRC5 WILD-TYPE	44	117	23

'NLRC5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S285. Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
NLRC5 MUTATED	4	0	3
NLRC5 WILD-TYPE	55	56	76

'NLRC5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 1

Table S286. Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
NLRC5 MUTATED	3	0	2	1	1
NLRC5 WILD-TYPE	38	50	56	14	29

'NLRC5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S287. Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
NLRC5 MUTATED	4	1	2
NLRC5 WILD-TYPE	65	56	56

'NLRC5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S288. Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
NLRC5 MUTATED	4	0	1	2
NLRC5 WILD-TYPE	38	32	27	80

'DDX41 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 1

Table S289. Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	40	61
DDX41 MUTATED	0	1	4
DDX41 WILD-TYPE	90	39	57

Figure S38. Get High-res Image Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'DDX41 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S290. Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
DDX41 MUTATED	0	3	0	1	1	0
DDX41 WILD-TYPE	48	31	37	34	27	12

'DDX41 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 1

Table S291. Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	80	45
DDX41 MUTATED	0	4	1
DDX41 WILD-TYPE	66	76	44

'DDX41 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S292. Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	120	23
DDX41 MUTATED	0	4	1
DDX41 WILD-TYPE	48	116	22

'DDX41 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 1

Table S293. Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
DDX41 MUTATED	0	2	3
DDX41 WILD-TYPE	59	54	76

'DDX41 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S294. Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
DDX41 MUTATED	0	2	2	0	1
DDX41 WILD-TYPE	41	48	56	15	29

'DDX41 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S295. Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
DDX41 MUTATED	2	1	1
DDX41 WILD-TYPE	67	56	57

'DDX41 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S296. Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
DDX41 MUTATED	0	1	0	3
DDX41 WILD-TYPE	42	31	28	79

'MCM7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0719 (Fisher's exact test), Q value = 1

Table S297. Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	48	34	37	35	28	12
MCM7 MUTATED	0	0	0	1	1	1
MCM7 WILD-TYPE	48	34	37	34	27	11

'MCM7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S298. Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	56	79
MCM7 MUTATED	1	1	1
MCM7 WILD-TYPE	58	55	78

'MCM7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S299. Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	41	50	58	15	30
MCM7 MUTATED	0	0	2	0	1
MCM7 WILD-TYPE	41	50	56	15	29

'MCM7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0571 (Fisher's exact test), Q value = 1

Table S300. Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	57	58
MCM7 MUTATED	0	0	3
MCM7 WILD-TYPE	69	57	55

'MCM7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S301. Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	32	28	82
MCM7 MUTATED	0	0	2	1
MCM7 WILD-TYPE	42	32	26	81

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = CESC-TP.transferedmergedcluster.txt
Number of patients = 194
Number of significantly mutated genes = 38
Number of Molecular subtypes = 8
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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