Correlation between gene mutation status and molecular subtypes

Colon 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/C1VT1QZQ

Overview

Introduction

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

Summary

Testing the association between mutation status of 27 genes and 9 molecular subtypes across 154 patients, 10 significant findings detected with P value < 0.05 and Q value < 0.25.

TP53 mutation correlated to 'CN_CNMF'.
BRAF mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
CASP8 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 27 genes and 9 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 10 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
BRAF	20 (13%)	134	1e-05 (0.0023)	1e-05 (0.0023)	9e-05 (0.0202)	0.721 (1.00)	0.523 (1.00)	0.00056 (0.124)	1e-05 (0.0023)	0.462 (1.00)	0.0381 (1.00)
CASP8	10 (6%)	144	0.00046 (0.103)	4e-05 (0.009)	0.00071 (0.157)	0.0154 (1.00)	0.147 (1.00)	0.545 (1.00)	1e-05 (0.0023)	1 (1.00)	0.0771 (1.00)
TP53	73 (47%)	81	0.00509 (1.00)	0.00337 (0.728)	1e-05 (0.0023)	0.198 (1.00)	0.737 (1.00)	0.0886 (1.00)	0.00116 (0.255)	0.621 (1.00)	0.494 (1.00)
APC	107 (69%)	47	0.134 (1.00)	0.0065 (1.00)	0.0256 (1.00)	0.161 (1.00)	0.218 (1.00)	0.493 (1.00)	0.0117 (1.00)	1 (1.00)	0.867 (1.00)
KRAS	59 (38%)	95	0.0337 (1.00)	0.0075 (1.00)	0.718 (1.00)	0.719 (1.00)	0.992 (1.00)	0.134 (1.00)	0.722 (1.00)	0.631 (1.00)	0.524 (1.00)
NRAS	15 (10%)	139	0.0768 (1.00)	0.0919 (1.00)	0.866 (1.00)	0.468 (1.00)	0.954 (1.00)	0.639 (1.00)	0.732 (1.00)	1 (1.00)	1 (1.00)
SMAD4	18 (12%)	136	0.303 (1.00)	0.228 (1.00)	0.008 (1.00)	0.854 (1.00)	0.572 (1.00)	0.468 (1.00)	0.515 (1.00)	1 (1.00)	0.864 (1.00)
FBXW7	29 (19%)	125	0.225 (1.00)	0.056 (1.00)	0.00194 (0.423)	0.00349 (0.75)	0.192 (1.00)	0.851 (1.00)	0.00442 (0.937)	1 (1.00)	0.179 (1.00)
SMAD2	10 (6%)	144	0.0991 (1.00)	0.108 (1.00)	0.0502 (1.00)	1 (1.00)	0.941 (1.00)	0.668 (1.00)	0.806 (1.00)	1 (1.00)	1 (1.00)
FAM123B	19 (12%)	135	0.207 (1.00)	0.182 (1.00)	0.00946 (1.00)	0.287 (1.00)	0.187 (1.00)	0.209 (1.00)	0.351 (1.00)	0.425 (1.00)	0.416 (1.00)
MGC42105	10 (6%)	144	0.00393 (0.841)	0.141 (1.00)	0.224 (1.00)	0.413 (1.00)	0.174 (1.00)	0.144 (1.00)	0.193 (1.00)	1 (1.00)	0.593 (1.00)
ACVR1B	13 (8%)	141	0.366 (1.00)	0.157 (1.00)	0.00614 (1.00)	0.702 (1.00)	0.436 (1.00)	0.0468 (1.00)	0.101 (1.00)	1 (1.00)	0.372 (1.00)
DNMT1	12 (8%)	142	0.0294 (1.00)	0.00816 (1.00)	0.0738 (1.00)	0.0509 (1.00)	0.347 (1.00)	0.327 (1.00)	0.011 (1.00)	1 (1.00)	0.0046 (0.971)
PCBP1	4 (3%)	150	0.33 (1.00)	0.432 (1.00)	0.641 (1.00)			1 (1.00)	0.638 (1.00)	1 (1.00)	0.604 (1.00)
CDC27	10 (6%)	144	0.00215 (0.467)	0.0734 (1.00)	0.00436 (0.929)	1 (1.00)	0.954 (1.00)	0.821 (1.00)	0.0196 (1.00)	0.186 (1.00)	0.015 (1.00)
PIK3CA	26 (17%)	128	0.329 (1.00)	0.58 (1.00)	0.00881 (1.00)	0.117 (1.00)	0.855 (1.00)	0.316 (1.00)	0.559 (1.00)	0.514 (1.00)	0.231 (1.00)
BCOR	6 (4%)	148	0.0339 (1.00)	0.0548 (1.00)	0.0212 (1.00)	0.199 (1.00)	0.604 (1.00)	1 (1.00)	0.12 (1.00)	1 (1.00)	0.0946 (1.00)
ZHX2	8 (5%)	146	0.217 (1.00)	0.226 (1.00)	0.247 (1.00)	0.233 (1.00)	0.579 (1.00)	0.782 (1.00)	0.0846 (1.00)	1 (1.00)	0.194 (1.00)
KLHL5	5 (3%)	149	0.374 (1.00)	0.299 (1.00)	0.357 (1.00)	0.22 (1.00)	0.876 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.161 (1.00)
PCDHGB1	7 (5%)	147	0.108 (1.00)	0.268 (1.00)	0.112 (1.00)	0.432 (1.00)	1 (1.00)	0.531 (1.00)	0.518 (1.00)	1 (1.00)	0.195 (1.00)
UBXN11	3 (2%)	151			0.351 (1.00)			0.233 (1.00)	0.0571 (1.00)	1 (1.00)	0.604 (1.00)
MIER3	10 (6%)	144	0.00136 (0.298)	0.00516 (1.00)	0.00462 (0.971)	0.771 (1.00)	0.784 (1.00)	0.819 (1.00)	0.0119 (1.00)	1 (1.00)	0.177 (1.00)
TBC1D10C	3 (2%)	151	0.238 (1.00)	0.129 (1.00)	1 (1.00)			0.231 (1.00)	0.242 (1.00)	1 (1.00)	0.604 (1.00)
TCF7L2	11 (7%)	143	0.22 (1.00)	1 (1.00)	0.907 (1.00)	0.95 (1.00)	0.86 (1.00)	0.664 (1.00)	1 (1.00)	1 (1.00)	0.318 (1.00)
PCDHGA9	5 (3%)	149	0.373 (1.00)	0.417 (1.00)	0.543 (1.00)	0.649 (1.00)	0.385 (1.00)	0.394 (1.00)	0.257 (1.00)	1 (1.00)	1 (1.00)
PCDHGA7	5 (3%)	149	0.703 (1.00)	0.848 (1.00)	0.544 (1.00)			0.392 (1.00)	0.668 (1.00)	1 (1.00)	0.36 (1.00)
KLK2	3 (2%)	151	0.419 (1.00)	0.131 (1.00)	1 (1.00)			1 (1.00)	0.241 (1.00)	1 (1.00)

'APC MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
APC MUTATED	18	42	21	17
APC WILD-TYPE	16	15	7	5

'APC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0065 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
APC MUTATED	22	50	26
APC WILD-TYPE	20	19	4

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

'APC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
APC MUTATED	39	52	14
APC WILD-TYPE	28	13	6

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

'APC MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S4. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
APC MUTATED	20	29	12	10
APC WILD-TYPE	3	18	6	6

'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S5. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
APC MUTATED	9	20	3	26	8	5
APC WILD-TYPE	0	12	3	10	5	3

'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
APC MUTATED	13	6	86
APC WILD-TYPE	4	5	38

'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
APC MUTATED	2	1	0	84	18
APC WILD-TYPE	2	0	1	27	17

Figure S3. Get High-res Image Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S8. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
APC MUTATED	3	95
APC WILD-TYPE	1	42

'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S9. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
APC MUTATED	3	24	71
APC WILD-TYPE	1	12	30

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00509 (Fisher's exact test), Q value = 1

Table S10. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
TP53 MUTATED	12	38	9	10
TP53 WILD-TYPE	22	19	19	12

Figure S4. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00337 (Fisher's exact test), Q value = 0.73

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
TP53 MUTATED	12	37	20
TP53 WILD-TYPE	30	32	10

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

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S12. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
TP53 MUTATED	14	47	11
TP53 WILD-TYPE	53	18	9

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

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S13. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
TP53 MUTATED	7	24	8	4
TP53 WILD-TYPE	16	23	10	12

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.737 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
TP53 MUTATED	3	14	3	17	3	3
TP53 WILD-TYPE	6	18	3	19	10	5

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0886 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
TP53 MUTATED	10	2	60
TP53 WILD-TYPE	7	9	64

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.26

Table S16. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
TP53 MUTATED	3	0	0	61	8
TP53 WILD-TYPE	1	1	1	50	27

Figure S7. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S17. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
TP53 MUTATED	1	67
TP53 WILD-TYPE	3	70

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S18. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
TP53 MUTATED	3	16	49
TP53 WILD-TYPE	1	20	52

'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 1

Table S19. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
KRAS MUTATED	10	17	17	7
KRAS WILD-TYPE	24	40	11	15

Figure S8. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0075 (Fisher's exact test), Q value = 1

Table S20. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
KRAS MUTATED	16	31	4
KRAS WILD-TYPE	26	38	26

Figure S9. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
KRAS MUTATED	28	23	7
KRAS WILD-TYPE	39	42	13

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S22. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
KRAS MUTATED	9	22	6	8
KRAS WILD-TYPE	14	25	12	8

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.992 (Fisher's exact test), Q value = 1

Table S23. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
KRAS MUTATED	4	13	3	16	5	4
KRAS WILD-TYPE	5	19	3	20	8	4

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S24. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
KRAS MUTATED	3	3	51
KRAS WILD-TYPE	14	8	73

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.722 (Fisher's exact test), Q value = 1

Table S25. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
KRAS MUTATED	2	1	0	41	13
KRAS WILD-TYPE	2	0	1	70	22

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S26. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
KRAS MUTATED	2	51
KRAS WILD-TYPE	2	86

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S27. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
KRAS MUTATED	1	11	41
KRAS WILD-TYPE	3	25	60

'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0768 (Fisher's exact test), Q value = 1

Table S28. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
NRAS MUTATED	0	8	4	2
NRAS WILD-TYPE	34	49	24	20

'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0919 (Fisher's exact test), Q value = 1

Table S29. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
NRAS MUTATED	2	11	1
NRAS WILD-TYPE	40	58	29

'NRAS MUTATION STATUS' versus 'CN_CNMF'

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

Table S30. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
NRAS MUTATED	7	7	1
NRAS WILD-TYPE	60	58	19

'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
NRAS MUTATED	1	8	1	2
NRAS WILD-TYPE	22	39	17	14

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.954 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
NRAS MUTATED	1	4	0	5	2	0
NRAS WILD-TYPE	8	28	6	31	11	8

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S33. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
NRAS MUTATED	2	0	12
NRAS WILD-TYPE	15	11	112

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S34. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
NRAS MUTATED	0	0	0	12	2
NRAS WILD-TYPE	4	1	1	99	33

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S35. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
NRAS MUTATED	0	13
NRAS WILD-TYPE	4	124

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S36. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
NRAS MUTATED	0	3	10
NRAS WILD-TYPE	4	33	91

'SMAD4 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S37. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
SMAD4 MUTATED	6	4	5	2
SMAD4 WILD-TYPE	28	53	23	20

'SMAD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S38. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
SMAD4 MUTATED	7	9	1
SMAD4 WILD-TYPE	35	60	29

'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.008 (Fisher's exact test), Q value = 1

Table S39. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
SMAD4 MUTATED	12	2	4
SMAD4 WILD-TYPE	55	63	16

Figure S10. Get High-res Image Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S40. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
SMAD4 MUTATED	3	8	2	1
SMAD4 WILD-TYPE	20	39	16	15

'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S41. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
SMAD4 MUTATED	2	5	1	3	1	2
SMAD4 WILD-TYPE	7	27	5	33	12	6

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 1

Table S42. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
SMAD4 MUTATED	1	0	16
SMAD4 WILD-TYPE	16	11	108

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S43. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
SMAD4 MUTATED	0	0	0	11	6
SMAD4 WILD-TYPE	4	1	1	100	29

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S44. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
SMAD4 MUTATED	0	17
SMAD4 WILD-TYPE	4	120

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S45. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
SMAD4 MUTATED	0	5	12
SMAD4 WILD-TYPE	4	31	89

'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 1

Table S46. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
FBXW7 MUTATED	10	7	5	3
FBXW7 WILD-TYPE	24	50	23	19

'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.056 (Fisher's exact test), Q value = 1

Table S47. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
FBXW7 MUTATED	12	11	2
FBXW7 WILD-TYPE	30	58	28

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00194 (Fisher's exact test), Q value = 0.42

Table S48. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
FBXW7 MUTATED	21	5	3
FBXW7 WILD-TYPE	46	60	17

Figure S11. Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00349 (Fisher's exact test), Q value = 0.75

Table S49. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
FBXW7 MUTATED	4	8	1	9
FBXW7 WILD-TYPE	19	39	17	7

Figure S12. Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S50. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
FBXW7 MUTATED	1	6	2	5	6	2
FBXW7 WILD-TYPE	8	26	4	31	7	6

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.851 (Fisher's exact test), Q value = 1

Table S51. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
FBXW7 MUTATED	2	2	25
FBXW7 WILD-TYPE	15	9	99

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00442 (Fisher's exact test), Q value = 0.94

Table S52. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
FBXW7 MUTATED	1	0	0	14	14
FBXW7 WILD-TYPE	3	1	1	97	21

Figure S13. Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S53. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
FBXW7 MUTATED	0	27
FBXW7 WILD-TYPE	4	110

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S54. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
FBXW7 MUTATED	2	5	20
FBXW7 WILD-TYPE	2	31	81

'SMAD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0991 (Fisher's exact test), Q value = 1

Table S55. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
SMAD2 MUTATED	3	1	4	1
SMAD2 WILD-TYPE	31	56	24	21

'SMAD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S56. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
SMAD2 MUTATED	5	4	0
SMAD2 WILD-TYPE	37	65	30

'SMAD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0502 (Fisher's exact test), Q value = 1

Table S57. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
SMAD2 MUTATED	8	1	1
SMAD2 WILD-TYPE	59	64	19

'SMAD2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S58. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
SMAD2 MUTATED	2	3	1	1
SMAD2 WILD-TYPE	21	44	17	15

'SMAD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.941 (Fisher's exact test), Q value = 1

Table S59. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
SMAD2 MUTATED	0	2	0	3	1	1
SMAD2 WILD-TYPE	9	30	6	33	12	7

'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S60. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
SMAD2 MUTATED	0	0	10
SMAD2 WILD-TYPE	17	11	114

'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S61. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
SMAD2 MUTATED	0	0	0	7	3
SMAD2 WILD-TYPE	4	1	1	104	32

'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S62. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
SMAD2 MUTATED	0	9
SMAD2 WILD-TYPE	4	128

'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S63. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
SMAD2 MUTATED	0	2	7
SMAD2 WILD-TYPE	4	34	94

'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S64. Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
BRAF MUTATED	14	1	3	0
BRAF WILD-TYPE	20	56	25	22

Figure S14. Get High-res Image Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S65. Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
BRAF MUTATED	15	2	1
BRAF WILD-TYPE	27	67	29

Figure S15. Get High-res Image Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.02

Table S66. Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
BRAF MUTATED	17	1	2
BRAF WILD-TYPE	50	64	18

Figure S16. Get High-res Image Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S67. Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
BRAF MUTATED	3	4	3	1
BRAF WILD-TYPE	20	43	15	15

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S68. Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
BRAF MUTATED	1	3	2	3	1	1
BRAF WILD-TYPE	8	29	4	33	12	7

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.12

Table S69. Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
BRAF MUTATED	0	6	14
BRAF WILD-TYPE	17	5	110

Figure S17. Get High-res Image Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S70. Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
BRAF MUTATED	0	0	1	4	15
BRAF WILD-TYPE	4	1	0	107	20

Figure S18. Get High-res Image Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 1

Table S71. Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
BRAF MUTATED	1	19
BRAF WILD-TYPE	3	118

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 1

Table S72. Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
BRAF MUTATED	0	1	19
BRAF WILD-TYPE	4	35	82

Figure S19. Get High-res Image Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

'FAM123B MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S73. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
FAM123B MUTATED	8	6	4	1
FAM123B WILD-TYPE	26	51	24	21

'FAM123B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S74. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
FAM123B MUTATED	9	8	2
FAM123B WILD-TYPE	33	61	28

'FAM123B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00946 (Fisher's exact test), Q value = 1

Table S75. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
FAM123B MUTATED	14	4	0
FAM123B WILD-TYPE	53	61	20

Figure S20. Get High-res Image Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FAM123B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S76. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
FAM123B MUTATED	2	4	1	4
FAM123B WILD-TYPE	21	43	17	12

'FAM123B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 1

Table S77. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
FAM123B MUTATED	1	4	0	2	4	0
FAM123B WILD-TYPE	8	28	6	34	9	8

'FAM123B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 1

Table S78. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
FAM123B MUTATED	0	2	17
FAM123B WILD-TYPE	17	9	107

'FAM123B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S79. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
FAM123B MUTATED	0	0	0	11	8
FAM123B WILD-TYPE	4	1	1	100	27

'FAM123B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S80. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
FAM123B MUTATED	1	17
FAM123B WILD-TYPE	3	120

'FAM123B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S81. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
FAM123B MUTATED	1	3	14
FAM123B WILD-TYPE	3	33	87

'MGC42105 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00393 (Fisher's exact test), Q value = 0.84

Table S82. Gene #10: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
MGC42105 MUTATED	7	1	2	0
MGC42105 WILD-TYPE	27	56	26	22

Figure S21. Get High-res Image Gene #10: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MGC42105 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S83. Gene #10: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
MGC42105 MUTATED	6	3	1
MGC42105 WILD-TYPE	36	66	29

'MGC42105 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 1

Table S84. Gene #10: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
MGC42105 MUTATED	7	2	1
MGC42105 WILD-TYPE	60	63	19

'MGC42105 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.413 (Fisher's exact test), Q value = 1

Table S85. Gene #10: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
MGC42105 MUTATED	0	3	1	2
MGC42105 WILD-TYPE	23	44	17	14

'MGC42105 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S86. Gene #10: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
MGC42105 MUTATED	1	0	0	2	2	1
MGC42105 WILD-TYPE	8	32	6	34	11	7

'MGC42105 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S87. Gene #10: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
MGC42105 MUTATED	0	2	7
MGC42105 WILD-TYPE	17	9	117

'MGC42105 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 1

Table S88. Gene #10: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
MGC42105 MUTATED	0	0	0	4	5
MGC42105 WILD-TYPE	4	1	1	107	30

'MGC42105 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S89. Gene #10: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
MGC42105 MUTATED	0	10
MGC42105 WILD-TYPE	4	127

'MGC42105 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 1

Table S90. Gene #10: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
MGC42105 MUTATED	0	1	9
MGC42105 WILD-TYPE	4	35	92

'ACVR1B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 1

Table S91. Gene #11: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
ACVR1B MUTATED	4	2	3	1
ACVR1B WILD-TYPE	30	55	25	21

'ACVR1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 1

Table S92. Gene #11: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
ACVR1B MUTATED	5	5	0
ACVR1B WILD-TYPE	37	64	30

'ACVR1B MUTATION STATUS' versus 'CN_CNMF'

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

Table S93. Gene #11: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
ACVR1B MUTATED	11	1	1
ACVR1B WILD-TYPE	56	64	19

Figure S22. Get High-res Image Gene #11: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ACVR1B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S94. Gene #11: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
ACVR1B MUTATED	2	5	1	3
ACVR1B WILD-TYPE	21	42	17	13

'ACVR1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S95. Gene #11: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
ACVR1B MUTATED	1	1	1	5	2	1
ACVR1B WILD-TYPE	8	31	5	31	11	7

'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0468 (Fisher's exact test), Q value = 1

Table S96. Gene #11: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
ACVR1B MUTATED	0	3	10
ACVR1B WILD-TYPE	17	8	114

Figure S23. Get High-res Image Gene #11: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S97. Gene #11: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
ACVR1B MUTATED	0	0	0	6	7
ACVR1B WILD-TYPE	4	1	1	105	28

'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S98. Gene #11: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
ACVR1B MUTATED	0	13
ACVR1B WILD-TYPE	4	124

'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 1

Table S99. Gene #11: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
ACVR1B MUTATED	1	2	10
ACVR1B WILD-TYPE	3	34	91

'DNMT1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 1

Table S100. Gene #12: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
DNMT1 MUTATED	6	1	3	1
DNMT1 WILD-TYPE	28	56	25	21

Figure S24. Get High-res Image Gene #12: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'DNMT1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00816 (Fisher's exact test), Q value = 1

Table S101. Gene #12: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
DNMT1 MUTATED	8	2	1
DNMT1 WILD-TYPE	34	67	29

Figure S25. Get High-res Image Gene #12: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'DNMT1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S102. Gene #12: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
DNMT1 MUTATED	9	2	1
DNMT1 WILD-TYPE	58	63	19

'DNMT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0509 (Fisher's exact test), Q value = 1

Table S103. Gene #12: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
DNMT1 MUTATED	1	3	0	4
DNMT1 WILD-TYPE	22	44	18	12

'DNMT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.347 (Fisher's exact test), Q value = 1

Table S104. Gene #12: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
DNMT1 MUTATED	1	2	0	2	3	0
DNMT1 WILD-TYPE	8	30	6	34	10	8

'DNMT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S105. Gene #12: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
DNMT1 MUTATED	1	2	9
DNMT1 WILD-TYPE	16	9	115

'DNMT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S106. Gene #12: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
DNMT1 MUTATED	1	0	0	4	7
DNMT1 WILD-TYPE	3	1	1	107	28

Figure S26. Get High-res Image Gene #12: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'DNMT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S107. Gene #12: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
DNMT1 MUTATED	0	10
DNMT1 WILD-TYPE	4	127

'DNMT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.97

Table S108. Gene #12: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
DNMT1 MUTATED	2	0	8
DNMT1 WILD-TYPE	2	36	93

Figure S27. Get High-res Image Gene #12: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

'PCBP1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S109. Gene #13: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
PCBP1 MUTATED	0	2	2	0
PCBP1 WILD-TYPE	34	55	26	22

'PCBP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S110. Gene #13: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
PCBP1 MUTATED	0	3	1
PCBP1 WILD-TYPE	42	66	29

'PCBP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S111. Gene #13: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
PCBP1 MUTATED	1	3	0
PCBP1 WILD-TYPE	66	62	20

'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S112. Gene #13: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
PCBP1 MUTATED	0	0	4
PCBP1 WILD-TYPE	17	11	120

'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S113. Gene #13: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
PCBP1 MUTATED	0	0	0	4	0
PCBP1 WILD-TYPE	4	1	1	107	35

'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S114. Gene #13: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
PCBP1 MUTATED	0	3
PCBP1 WILD-TYPE	4	134

'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S115. Gene #13: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
PCBP1 MUTATED	0	0	3
PCBP1 WILD-TYPE	4	36	98

'CDC27 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.47

Table S116. Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
CDC27 MUTATED	5	0	4	0
CDC27 WILD-TYPE	29	57	24	22

Figure S28. Get High-res Image Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDC27 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0734 (Fisher's exact test), Q value = 1

Table S117. Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
CDC27 MUTATED	6	2	1
CDC27 WILD-TYPE	36	67	29

'CDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.93

Table S118. Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
CDC27 MUTATED	9	0	1
CDC27 WILD-TYPE	58	65	19

Figure S29. Get High-res Image Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CDC27 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S119. Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
CDC27 MUTATED	2	4	1	1
CDC27 WILD-TYPE	21	43	17	15

'CDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.954 (Fisher's exact test), Q value = 1

Table S120. Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
CDC27 MUTATED	1	2	0	4	1	0
CDC27 WILD-TYPE	8	30	6	32	12	8

'CDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S121. Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
CDC27 MUTATED	1	1	8
CDC27 WILD-TYPE	16	10	116

'CDC27 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 1

Table S122. Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
CDC27 MUTATED	0	0	1	4	5
CDC27 WILD-TYPE	4	1	0	107	30

Figure S30. Get High-res Image Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'CDC27 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 1

Table S123. Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
CDC27 MUTATED	1	6
CDC27 WILD-TYPE	3	131

'CDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 1

Table S124. Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
CDC27 MUTATED	2	1	4
CDC27 WILD-TYPE	2	35	97

Figure S31. Get High-res Image Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 1

Table S125. Gene #15: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
PIK3CA MUTATED	6	5	6	4
PIK3CA WILD-TYPE	28	52	22	18

'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.58 (Fisher's exact test), Q value = 1

Table S126. Gene #15: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
PIK3CA MUTATED	8	10	3
PIK3CA WILD-TYPE	34	59	27

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00881 (Fisher's exact test), Q value = 1

Table S127. Gene #15: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
PIK3CA MUTATED	18	5	2
PIK3CA WILD-TYPE	49	60	18

Figure S32. Get High-res Image Gene #15: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S128. Gene #15: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
PIK3CA MUTATED	8	8	1	4
PIK3CA WILD-TYPE	15	39	17	12

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S129. Gene #15: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
PIK3CA MUTATED	3	5	1	7	3	2
PIK3CA WILD-TYPE	6	27	5	29	10	6

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.316 (Fisher's exact test), Q value = 1

Table S130. Gene #15: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
PIK3CA MUTATED	1	3	22
PIK3CA WILD-TYPE	16	8	102

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S131. Gene #15: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
PIK3CA MUTATED	1	0	0	17	8
PIK3CA WILD-TYPE	3	1	1	94	27

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.514 (Fisher's exact test), Q value = 1

Table S132. Gene #15: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
PIK3CA MUTATED	1	22
PIK3CA WILD-TYPE	3	115

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.231 (Fisher's exact test), Q value = 1

Table S133. Gene #15: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
PIK3CA MUTATED	1	3	19
PIK3CA WILD-TYPE	3	33	82

'BCOR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 1

Table S134. Gene #16: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
BCOR MUTATED	3	0	2	0
BCOR WILD-TYPE	31	57	26	22

Figure S33. Get High-res Image Gene #16: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BCOR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0548 (Fisher's exact test), Q value = 1

Table S135. Gene #16: 'BCOR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
BCOR MUTATED	4	1	0
BCOR WILD-TYPE	38	68	30

'BCOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 1

Table S136. Gene #16: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
BCOR MUTATED	6	0	0
BCOR WILD-TYPE	61	65	20

Figure S34. Get High-res Image Gene #16: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BCOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 1

Table S137. Gene #16: 'BCOR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
BCOR MUTATED	0	4	0	2
BCOR WILD-TYPE	23	43	18	14

'BCOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S138. Gene #16: 'BCOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
BCOR MUTATED	0	1	1	3	1	0
BCOR WILD-TYPE	9	31	5	33	12	8

'BCOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S139. Gene #16: 'BCOR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
BCOR MUTATED	0	0	6
BCOR WILD-TYPE	17	11	118

'BCOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S140. Gene #16: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
BCOR MUTATED	0	0	0	2	4
BCOR WILD-TYPE	4	1	1	109	31

'BCOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S141. Gene #16: 'BCOR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
BCOR MUTATED	0	5
BCOR WILD-TYPE	4	132

'BCOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0946 (Fisher's exact test), Q value = 1

Table S142. Gene #16: 'BCOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
BCOR MUTATED	1	0	4
BCOR WILD-TYPE	3	36	97

'ZHX2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S143. Gene #17: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
ZHX2 MUTATED	4	2	1	0
ZHX2 WILD-TYPE	30	55	27	22

'ZHX2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S144. Gene #17: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
ZHX2 MUTATED	4	3	0
ZHX2 WILD-TYPE	38	66	30

'ZHX2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S145. Gene #17: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
ZHX2 MUTATED	6	2	0
ZHX2 WILD-TYPE	61	63	20

'ZHX2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 1

Table S146. Gene #17: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
ZHX2 MUTATED	0	3	0	2
ZHX2 WILD-TYPE	23	44	18	14

'ZHX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S147. Gene #17: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
ZHX2 MUTATED	0	1	0	2	2	0
ZHX2 WILD-TYPE	9	31	6	34	11	8

'ZHX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S148. Gene #17: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
ZHX2 MUTATED	0	0	8
ZHX2 WILD-TYPE	17	11	116

'ZHX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0846 (Fisher's exact test), Q value = 1

Table S149. Gene #17: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
ZHX2 MUTATED	0	0	0	3	5
ZHX2 WILD-TYPE	4	1	1	108	30

'ZHX2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S150. Gene #17: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
ZHX2 MUTATED	0	6
ZHX2 WILD-TYPE	4	131

'ZHX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S151. Gene #17: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
ZHX2 MUTATED	1	1	4
ZHX2 WILD-TYPE	3	35	97

'KLHL5 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S152. Gene #18: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
KLHL5 MUTATED	2	1	2	0
KLHL5 WILD-TYPE	32	56	26	22

'KLHL5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S153. Gene #18: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
KLHL5 MUTATED	2	1	2
KLHL5 WILD-TYPE	40	68	28

'KLHL5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S154. Gene #18: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
KLHL5 MUTATED	4	1	0
KLHL5 WILD-TYPE	63	64	20

'KLHL5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S155. Gene #18: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
KLHL5 MUTATED	0	2	0	2
KLHL5 WILD-TYPE	23	45	18	14

'KLHL5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S156. Gene #18: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
KLHL5 MUTATED	0	2	0	1	1	0
KLHL5 WILD-TYPE	9	30	6	35	12	8

'KLHL5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S157. Gene #18: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
KLHL5 MUTATED	0	0	5
KLHL5 WILD-TYPE	17	11	119

'KLHL5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S158. Gene #18: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
KLHL5 MUTATED	0	0	0	4	1
KLHL5 WILD-TYPE	4	1	1	107	34

'KLHL5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S159. Gene #18: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
KLHL5 MUTATED	0	4
KLHL5 WILD-TYPE	4	133

'KLHL5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S160. Gene #18: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
KLHL5 MUTATED	1	1	2
KLHL5 WILD-TYPE	3	35	99

'CASP8 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.1

Table S161. Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
CASP8 MUTATED	7	0	2	0
CASP8 WILD-TYPE	27	57	26	22

Figure S35. Get High-res Image Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.009

Table S162. Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
CASP8 MUTATED	9	0	0
CASP8 WILD-TYPE	33	69	30

Figure S36. Get High-res Image Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.16

Table S163. Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
CASP8 MUTATED	10	0	0
CASP8 WILD-TYPE	57	65	20

Figure S37. Get High-res Image Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 1

Table S164. Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
CASP8 MUTATED	4	1	0	3
CASP8 WILD-TYPE	19	46	18	13

Figure S38. Get High-res Image Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.147 (Fisher's exact test), Q value = 1

Table S165. Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
CASP8 MUTATED	1	2	1	1	3	0
CASP8 WILD-TYPE	8	30	5	35	10	8

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S166. Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
CASP8 MUTATED	0	1	9
CASP8 WILD-TYPE	17	10	115

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S167. Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
CASP8 MUTATED	0	0	0	0	10
CASP8 WILD-TYPE	4	1	1	111	25

Figure S39. Get High-res Image Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S168. Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
CASP8 MUTATED	0	8
CASP8 WILD-TYPE	4	129

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0771 (Fisher's exact test), Q value = 1

Table S169. Gene #19: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
CASP8 MUTATED	1	0	7
CASP8 WILD-TYPE	3	36	94

'PCDHGB1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S170. Gene #20: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
PCDHGB1 MUTATED	3	1	3	0
PCDHGB1 WILD-TYPE	31	56	25	22

'PCDHGB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S171. Gene #20: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
PCDHGB1 MUTATED	4	2	1
PCDHGB1 WILD-TYPE	38	67	29

'PCDHGB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S172. Gene #20: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
PCDHGB1 MUTATED	6	1	0
PCDHGB1 WILD-TYPE	61	64	20

'PCDHGB1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S173. Gene #20: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
PCDHGB1 MUTATED	1	2	0	2
PCDHGB1 WILD-TYPE	22	45	18	14

'PCDHGB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S174. Gene #20: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
PCDHGB1 MUTATED	0	2	0	2	1	0
PCDHGB1 WILD-TYPE	9	30	6	34	12	8

'PCDHGB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.531 (Fisher's exact test), Q value = 1

Table S175. Gene #20: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
PCDHGB1 MUTATED	0	1	6
PCDHGB1 WILD-TYPE	17	10	118

'PCDHGB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S176. Gene #20: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
PCDHGB1 MUTATED	0	0	0	4	3
PCDHGB1 WILD-TYPE	4	1	1	107	32

'PCDHGB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S177. Gene #20: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
PCDHGB1 MUTATED	0	6
PCDHGB1 WILD-TYPE	4	131

'PCDHGB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S178. Gene #20: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
PCDHGB1 MUTATED	1	1	4
PCDHGB1 WILD-TYPE	3	35	97

'UBXN11 MUTATION STATUS' versus 'CN_CNMF'

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

Table S179. Gene #21: 'UBXN11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
UBXN11 MUTATED	3	0	0
UBXN11 WILD-TYPE	64	65	20

'UBXN11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 1

Table S180. Gene #21: 'UBXN11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
UBXN11 MUTATED	0	1	2
UBXN11 WILD-TYPE	17	10	122

'UBXN11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0571 (Fisher's exact test), Q value = 1

Table S181. Gene #21: 'UBXN11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
UBXN11 MUTATED	0	0	0	0	3
UBXN11 WILD-TYPE	4	1	1	111	32

'UBXN11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S182. Gene #21: 'UBXN11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
UBXN11 MUTATED	0	3
UBXN11 WILD-TYPE	4	134

'UBXN11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S183. Gene #21: 'UBXN11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
UBXN11 MUTATED	0	0	3
UBXN11 WILD-TYPE	4	36	98

'MIER3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.3

Table S184. Gene #22: 'MIER3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
MIER3 MUTATED	6	0	3	0
MIER3 WILD-TYPE	28	57	25	22

Figure S40. Get High-res Image Gene #22: 'MIER3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MIER3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00516 (Fisher's exact test), Q value = 1

Table S185. Gene #22: 'MIER3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
MIER3 MUTATED	7	1	1
MIER3 WILD-TYPE	35	68	29

Figure S41. Get High-res Image Gene #22: 'MIER3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'MIER3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.97

Table S186. Gene #22: 'MIER3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
MIER3 MUTATED	9	0	1
MIER3 WILD-TYPE	58	65	19

Figure S42. Get High-res Image Gene #22: 'MIER3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MIER3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.771 (Fisher's exact test), Q value = 1

Table S187. Gene #22: 'MIER3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
MIER3 MUTATED	2	4	0	1
MIER3 WILD-TYPE	21	43	18	15

'MIER3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S188. Gene #22: 'MIER3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
MIER3 MUTATED	0	4	0	3	0	0
MIER3 WILD-TYPE	9	28	6	33	13	8

'MIER3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S189. Gene #22: 'MIER3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
MIER3 MUTATED	1	1	8
MIER3 WILD-TYPE	16	10	116

'MIER3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S190. Gene #22: 'MIER3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
MIER3 MUTATED	1	0	0	3	6
MIER3 WILD-TYPE	3	1	1	108	29

Figure S43. Get High-res Image Gene #22: 'MIER3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'MIER3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S191. Gene #22: 'MIER3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
MIER3 MUTATED	0	10
MIER3 WILD-TYPE	4	127

'MIER3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S192. Gene #22: 'MIER3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
MIER3 MUTATED	1	1	8
MIER3 WILD-TYPE	3	35	93

'TBC1D10C MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S193. Gene #23: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
TBC1D10C MUTATED	1	0	1	1
TBC1D10C WILD-TYPE	33	57	27	21

'TBC1D10C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.129 (Fisher's exact test), Q value = 1

Table S194. Gene #23: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
TBC1D10C MUTATED	2	0	1
TBC1D10C WILD-TYPE	40	69	29

'TBC1D10C MUTATION STATUS' versus 'CN_CNMF'

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

Table S195. Gene #23: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
TBC1D10C MUTATED	2	1	0
TBC1D10C WILD-TYPE	65	64	20

'TBC1D10C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 1

Table S196. Gene #23: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
TBC1D10C MUTATED	0	1	2
TBC1D10C WILD-TYPE	17	10	122

'TBC1D10C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S197. Gene #23: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
TBC1D10C MUTATED	0	0	0	1	2
TBC1D10C WILD-TYPE	4	1	1	110	33

'TBC1D10C MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S198. Gene #23: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
TBC1D10C MUTATED	0	3
TBC1D10C WILD-TYPE	4	134

'TBC1D10C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S199. Gene #23: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
TBC1D10C MUTATED	0	0	3
TBC1D10C WILD-TYPE	4	36	98

'TCF7L2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S200. Gene #24: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
TCF7L2 MUTATED	3	1	3	1
TCF7L2 WILD-TYPE	31	56	25	21

'TCF7L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S201. Gene #24: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
TCF7L2 MUTATED	2	4	2
TCF7L2 WILD-TYPE	40	65	28

'TCF7L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.907 (Fisher's exact test), Q value = 1

Table S202. Gene #24: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
TCF7L2 MUTATED	6	4	1
TCF7L2 WILD-TYPE	61	61	19

'TCF7L2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S203. Gene #24: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
TCF7L2 MUTATED	1	5	1	1
TCF7L2 WILD-TYPE	22	42	17	15

'TCF7L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S204. Gene #24: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
TCF7L2 MUTATED	1	3	0	4	0	0
TCF7L2 WILD-TYPE	8	29	6	32	13	8

'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S205. Gene #24: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
TCF7L2 MUTATED	0	0	10
TCF7L2 WILD-TYPE	17	11	114

'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S206. Gene #24: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
TCF7L2 MUTATED	0	0	0	8	2
TCF7L2 WILD-TYPE	4	1	1	103	33

'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S207. Gene #24: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
TCF7L2 MUTATED	0	9
TCF7L2 WILD-TYPE	4	128

'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S208. Gene #24: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
TCF7L2 MUTATED	1	2	6
TCF7L2 WILD-TYPE	3	34	95

'PCDHGA9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 1

Table S209. Gene #25: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
PCDHGA9 MUTATED	2	1	2	0
PCDHGA9 WILD-TYPE	32	56	26	22

'PCDHGA9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.417 (Fisher's exact test), Q value = 1

Table S210. Gene #25: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
PCDHGA9 MUTATED	3	2	0
PCDHGA9 WILD-TYPE	39	67	30

'PCDHGA9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.543 (Fisher's exact test), Q value = 1

Table S211. Gene #25: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
PCDHGA9 MUTATED	3	1	1
PCDHGA9 WILD-TYPE	64	64	19

'PCDHGA9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.649 (Fisher's exact test), Q value = 1

Table S212. Gene #25: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
PCDHGA9 MUTATED	1	1	0	1
PCDHGA9 WILD-TYPE	22	46	18	15

'PCDHGA9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S213. Gene #25: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	9	32	6	36	13	8
PCDHGA9 MUTATED	0	3	0	0	0	0
PCDHGA9 WILD-TYPE	9	29	6	36	13	8

'PCDHGA9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S214. Gene #25: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
PCDHGA9 MUTATED	0	1	4
PCDHGA9 WILD-TYPE	17	10	120

'PCDHGA9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S215. Gene #25: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
PCDHGA9 MUTATED	0	0	0	2	3
PCDHGA9 WILD-TYPE	4	1	1	109	32

'PCDHGA9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S216. Gene #25: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
PCDHGA9 MUTATED	0	5
PCDHGA9 WILD-TYPE	4	132

'PCDHGA9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S217. Gene #25: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
PCDHGA9 MUTATED	0	1	4
PCDHGA9 WILD-TYPE	4	35	97

'PCDHGA7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.703 (Fisher's exact test), Q value = 1

Table S218. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
PCDHGA7 MUTATED	2	1	1	1
PCDHGA7 WILD-TYPE	32	56	27	21

'PCDHGA7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S219. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
PCDHGA7 MUTATED	2	2	1
PCDHGA7 WILD-TYPE	40	67	29

'PCDHGA7 MUTATION STATUS' versus 'CN_CNMF'

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

Table S220. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
PCDHGA7 MUTATED	3	1	1
PCDHGA7 WILD-TYPE	64	64	19

'PCDHGA7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S221. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
PCDHGA7 MUTATED	0	1	4
PCDHGA7 WILD-TYPE	17	10	120

'PCDHGA7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S222. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
PCDHGA7 MUTATED	0	0	0	3	2
PCDHGA7 WILD-TYPE	4	1	1	108	33

'PCDHGA7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S223. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
PCDHGA7 MUTATED	0	4
PCDHGA7 WILD-TYPE	4	133

'PCDHGA7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.36 (Fisher's exact test), Q value = 1

Table S224. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_3	CLUS_4
ALL	4	36	101
PCDHGA7 MUTATED	0	2	2
PCDHGA7 WILD-TYPE	4	34	99

'KLK2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.419 (Fisher's exact test), Q value = 1

Table S225. Gene #27: 'KLK2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
KLK2 MUTATED	2	1	0	0
KLK2 WILD-TYPE	32	56	28	22

'KLK2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S226. Gene #27: 'KLK2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	69	30
KLK2 MUTATED	2	0	1
KLK2 WILD-TYPE	40	69	29

'KLK2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S227. Gene #27: 'KLK2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	65	20
KLK2 MUTATED	2	1	0
KLK2 WILD-TYPE	65	64	20

'KLK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S228. Gene #27: 'KLK2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	11	124
KLK2 MUTATED	0	0	3
KLK2 WILD-TYPE	17	11	121

'KLK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.241 (Fisher's exact test), Q value = 1

Table S229. Gene #27: 'KLK2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	4	1	1	111	35
KLK2 MUTATED	0	0	0	1	2
KLK2 WILD-TYPE	4	1	1	110	33

'KLK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S230. Gene #27: 'KLK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
KLK2 MUTATED	0	2
KLK2 WILD-TYPE	4	135

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = COAD-TP.transferedmergedcluster.txt
Number of patients = 154
Number of significantly mutated genes = 27
Number of Molecular subtypes = 9
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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