Correlation between gene mutation status and molecular subtypes

Overview

Introduction

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

Summary

Testing the association between mutation status of 37 genes and 12 molecular subtypes across 289 patients, 62 significant findings detected with P value < 0.05 and Q value < 0.25.

IDH1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
TP53 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
ATRX mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
CIC mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
NOTCH1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
FUBP1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
NF1 mutation correlated to 'METHLYATION_CNMF'.
PTEN mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
PIK3CA mutation correlated to 'METHLYATION_CNMF'.
EGFR mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 37 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 62 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
CIC	54 (19%)	235	0.0426 (1.00)	0.00301 (0.921)	1e-05 (0.00381)	1e-05 (0.00381)	3e-05 (0.0099)	0.498 (1.00)	1e-05 (0.00381)	1e-05 (0.00381)	1e-05 (0.00381)	1e-05 (0.00381)	1e-05 (0.00381)	1e-05 (0.00381)
IDH1	220 (76%)	69	0.271 (1.00)	0.885 (1.00)	1e-05 (0.00381)	1e-05 (0.00381)	1e-05 (0.00381)	0.00223 (0.691)	1e-05 (0.00381)	1e-05 (0.00381)	0.00796 (1.00)	1e-05 (0.00381)	1e-05 (0.00381)	1e-05 (0.00381)
TP53	146 (51%)	143	0.064 (1.00)	0.00504 (1.00)	1e-05 (0.00381)	1e-05 (0.00381)	0.0298 (1.00)	0.498 (1.00)	1e-05 (0.00381)	1e-05 (0.00381)	3e-05 (0.0099)	1e-05 (0.00381)	1e-05 (0.00381)	1e-05 (0.00381)
PTEN	13 (4%)	276			1e-05 (0.00381)	1e-05 (0.00381)	0.00052 (0.166)	0.00536 (1.00)	1e-05 (0.00381)	1e-05 (0.00381)	0.0394 (1.00)	1e-05 (0.00381)	1e-05 (0.00381)	1e-05 (0.00381)
ATRX	118 (41%)	171	0.0178 (1.00)	0.126 (1.00)	1e-05 (0.00381)	1e-05 (0.00381)	0.172 (1.00)	0.779 (1.00)	1e-05 (0.00381)	1e-05 (0.00381)	0.00205 (0.638)	1e-05 (0.00381)	1e-05 (0.00381)	1e-05 (0.00381)
NOTCH1	29 (10%)	260	0.462 (1.00)	0.245 (1.00)	0.003 (0.921)	1e-05 (0.00381)	0.89 (1.00)	0.86 (1.00)	1e-05 (0.00381)	3e-05 (0.0099)	7e-05 (0.0227)	0.00016 (0.0517)	0.00017 (0.0547)	3e-05 (0.0099)
EGFR	17 (6%)	272			1e-05 (0.00381)	1e-05 (0.00381)	0.00758 (1.00)	0.0235 (1.00)	4e-05 (0.013)	1e-05 (0.00381)	0.362 (1.00)	1e-05 (0.00381)	0.00045 (0.144)	1e-05 (0.00381)
FUBP1	26 (9%)	263	0.0252 (1.00)	0.00701 (1.00)	1e-05 (0.00381)	1e-05 (0.00381)	0.0177 (1.00)	0.733 (1.00)	1e-05 (0.00381)	1e-05 (0.00381)	1e-05 (0.00381)	0.00542 (1.00)	0.00098 (0.311)	4e-05 (0.013)
NF1	19 (7%)	270			0.0185 (1.00)	1e-05 (0.00381)	0.0308 (1.00)	0.221 (1.00)	0.0185 (1.00)	0.00846 (1.00)	0.759 (1.00)	0.00784 (1.00)	0.21 (1.00)	0.00116 (0.367)
PIK3CA	25 (9%)	264			0.00135 (0.425)	1e-05 (0.00381)	0.567 (1.00)	0.735 (1.00)	0.00559 (1.00)	0.0008 (0.255)	0.298 (1.00)	0.206 (1.00)	0.00091 (0.289)	0.00204 (0.636)
IDH2	12 (4%)	277			0.0162 (1.00)	0.0259 (1.00)	0.516 (1.00)	0.181 (1.00)	0.00247 (0.763)	0.00168 (0.526)	0.0989 (1.00)	0.0459 (1.00)	0.0557 (1.00)	0.00856 (1.00)
PIK3R1	13 (4%)	276	0.603 (1.00)	0.584 (1.00)	0.0778 (1.00)	0.146 (1.00)	0.892 (1.00)	1 (1.00)	0.709 (1.00)	0.787 (1.00)	0.138 (1.00)	0.369 (1.00)	0.689 (1.00)	0.735 (1.00)
STK19	8 (3%)	281			0.173 (1.00)	0.148 (1.00)	0.0181 (1.00)	0.141 (1.00)	0.616 (1.00)	0.481 (1.00)	0.423 (1.00)	0.92 (1.00)	0.697 (1.00)	0.502 (1.00)
ARID1A	12 (4%)	277			1 (1.00)	0.243 (1.00)	0.46 (1.00)	0.794 (1.00)	0.173 (1.00)	0.157 (1.00)	0.627 (1.00)	0.587 (1.00)	0.15 (1.00)	0.696 (1.00)
GAGE2B	4 (1%)	285			0.683 (1.00)	0.801 (1.00)	0.379 (1.00)	1 (1.00)	0.722 (1.00)	0.524 (1.00)	1 (1.00)	0.691 (1.00)	0.331 (1.00)	0.912 (1.00)
CREBZF	5 (2%)	284			0.171 (1.00)	0.036 (1.00)	0.0866 (1.00)	0.00475 (1.00)	0.578 (1.00)	0.413 (1.00)	0.352 (1.00)	0.268 (1.00)	0.555 (1.00)	0.122 (1.00)
TCF12	8 (3%)	281			0.596 (1.00)	0.459 (1.00)	0.198 (1.00)	0.452 (1.00)	0.246 (1.00)	0.59 (1.00)	0.291 (1.00)	1 (1.00)	0.331 (1.00)	0.803 (1.00)
SMARCA4	13 (4%)	276			0.201 (1.00)	0.143 (1.00)	0.318 (1.00)	0.852 (1.00)	0.14 (1.00)	0.568 (1.00)	0.153 (1.00)	0.146 (1.00)	0.351 (1.00)	0.191 (1.00)
VAV3	8 (3%)	281			0.479 (1.00)	0.839 (1.00)	0.961 (1.00)	0.574 (1.00)	0.0405 (1.00)	0.479 (1.00)	0.77 (1.00)	0.317 (1.00)	0.967 (1.00)	0.675 (1.00)
TMEM216	3 (1%)	286			0.338 (1.00)	1 (1.00)	0.793 (1.00)	0.794 (1.00)	0.897 (1.00)	0.887 (1.00)	0.325 (1.00)	0.768 (1.00)	1 (1.00)	0.261 (1.00)
ROBO3	4 (1%)	285			0.685 (1.00)	0.899 (1.00)			0.64 (1.00)	0.72 (1.00)	0.65 (1.00)	0.76 (1.00)	0.776 (1.00)	0.656 (1.00)
IRS4	5 (2%)	284			0.538 (1.00)	0.721 (1.00)	1 (1.00)	0.197 (1.00)	0.859 (1.00)	0.931 (1.00)	0.919 (1.00)	1 (1.00)	0.207 (1.00)	1 (1.00)
HTRA2	4 (1%)	285			0.123 (1.00)	1 (1.00)	0.414 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.414 (1.00)	0.758 (1.00)	0.369 (1.00)	0.912 (1.00)
EIF1AX	4 (1%)	285			0.824 (1.00)	0.309 (1.00)	0.376 (1.00)	0.262 (1.00)	0.868 (1.00)	0.84 (1.00)	0.807 (1.00)	0.469 (1.00)	0.358 (1.00)	0.108 (1.00)
FAM47C	7 (2%)	282			0.381 (1.00)	0.357 (1.00)	0.247 (1.00)	0.317 (1.00)	0.0581 (1.00)	0.0279 (1.00)	0.157 (1.00)	0.0082 (1.00)	0.182 (1.00)	0.0016 (0.502)
PLCG1	4 (1%)	285			0.0028 (0.862)	0.0115 (1.00)			0.166 (1.00)	0.664 (1.00)	0.0242 (1.00)	0.293 (1.00)	0.312 (1.00)	0.208 (1.00)
DDX5	4 (1%)	285			0.682 (1.00)	0.8 (1.00)	1 (1.00)	0.442 (1.00)	0.206 (1.00)	0.14 (1.00)	0.472 (1.00)	0.425 (1.00)	0.129 (1.00)	0.656 (1.00)
ZNF709	3 (1%)	286			0.792 (1.00)		0.89 (1.00)	0.793 (1.00)	0.0682 (1.00)	0.192 (1.00)	1 (1.00)	0.671 (1.00)	0.317 (1.00)	0.41 (1.00)
TRERF1	3 (1%)	286			0.0507 (1.00)	0.527 (1.00)	0.443 (1.00)	0.0695 (1.00)	0.193 (1.00)	0.557 (1.00)	1 (1.00)	0.669 (1.00)	0.805 (1.00)	0.412 (1.00)
BCOR	9 (3%)	280	1 (1.00)	0.869 (1.00)	0.259 (1.00)	0.797 (1.00)	0.917 (1.00)	0.887 (1.00)	0.846 (1.00)	0.39 (1.00)	0.963 (1.00)	0.82 (1.00)	0.609 (1.00)	0.781 (1.00)
SRPX	3 (1%)	286			0.467 (1.00)	0.122 (1.00)	0.335 (1.00)	1 (1.00)	0.173 (1.00)	0.0925 (1.00)	0.175 (1.00)	0.504 (1.00)	0.0771 (1.00)	0.113 (1.00)
DOCK5	6 (2%)	283			0.0758 (1.00)	0.0544 (1.00)	0.371 (1.00)	0.227 (1.00)	0.134 (1.00)	0.0716 (1.00)	0.235 (1.00)	0.0613 (1.00)	0.0353 (1.00)	0.302 (1.00)
GIGYF2	4 (1%)	285			0.0336 (1.00)	0.619 (1.00)	0.0835 (1.00)	0.809 (1.00)	0.542 (1.00)	0.409 (1.00)	0.176 (1.00)	0.195 (1.00)	0.151 (1.00)	0.0598 (1.00)
NIPBL	6 (2%)	283			0.0979 (1.00)	0.0465 (1.00)	0.842 (1.00)	0.81 (1.00)	0.0709 (1.00)	0.0488 (1.00)	0.829 (1.00)	0.938 (1.00)	0.158 (1.00)	0.111 (1.00)
ZBTB20	13 (4%)	276			0.0414 (1.00)	0.0276 (1.00)	0.597 (1.00)	0.358 (1.00)	0.072 (1.00)	0.0797 (1.00)	0.514 (1.00)	0.353 (1.00)	0.0479 (1.00)	0.674 (1.00)
TRIP12	5 (2%)	284			0.308 (1.00)	0.545 (1.00)	0.497 (1.00)	0.283 (1.00)	0.597 (1.00)	0.578 (1.00)	0.844 (1.00)	0.51 (1.00)	0.458 (1.00)	0.505 (1.00)
KIAA0664	5 (2%)	284			0.255 (1.00)	0.144 (1.00)	0.674 (1.00)	0.261 (1.00)	0.644 (1.00)	0.52 (1.00)	0.297 (1.00)	0.144 (1.00)	0.632 (1.00)	0.193 (1.00)

'IDH1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S1. Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	7
IDH1 MUTATED	9	7	6
IDH1 WILD-TYPE	0	3	1

'IDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.885 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	5
IDH1 MUTATED	6	6	5	5
IDH1 WILD-TYPE	1	1	2	0

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S3. Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
IDH1 MUTATED	90	26	102
IDH1 WILD-TYPE	6	43	19

Figure S1. Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S4. Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
IDH1 MUTATED	125	0	21	71
IDH1 WILD-TYPE	3	36	22	7

Figure S2. Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S5. Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
IDH1 MUTATED	42	31	61	57
IDH1 WILD-TYPE	10	30	4	16

Figure S3. Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00223 (Fisher's exact test), Q value = 0.69

Table S6. Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
IDH1 MUTATED	60	90	41
IDH1 WILD-TYPE	6	38	16

Figure S4. Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S7. Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
IDH1 MUTATED	74	21	46	65	13
IDH1 WILD-TYPE	1	44	5	18	1

Figure S5. Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S8. Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
IDH1 MUTATED	77	22	53	67
IDH1 WILD-TYPE	1	43	5	20

Figure S6. Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00796 (Fisher's exact test), Q value = 1

Table S9. Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
IDH1 MUTATED	56	40	94	30
IDH1 WILD-TYPE	27	17	23	2

Figure S7. Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S10. Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
IDH1 MUTATED	90	42	71	17
IDH1 WILD-TYPE	8	3	18	40

Figure S8. Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S11. Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
IDH1 MUTATED	66	23	24	64	29	3	11
IDH1 WILD-TYPE	1	37	3	20	5	3	0

Figure S9. Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S12. Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
IDH1 MUTATED	91	62	54	13
IDH1 WILD-TYPE	7	5	15	42

Figure S10. Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.064 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	7
TP53 MUTATED	8	4	3
TP53 WILD-TYPE	1	6	4

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00504 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	5
TP53 MUTATED	5	7	1	2
TP53 WILD-TYPE	2	0	6	3

Figure S11. 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 = 0.0038

Table S15. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
TP53 MUTATED	91	26	29
TP53 WILD-TYPE	5	43	92

Figure S12. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S16. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
TP53 MUTATED	124	7	12	3
TP53 WILD-TYPE	4	29	31	75

Figure S13. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 1

Table S17. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
TP53 MUTATED	33	30	39	29
TP53 WILD-TYPE	19	31	26	44

Figure S14. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S18. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
TP53 MUTATED	37	68	26
TP53 WILD-TYPE	29	60	31

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S19. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
TP53 MUTATED	74	25	3	37	7
TP53 WILD-TYPE	1	40	48	46	7

Figure S15. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S20. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
TP53 MUTATED	75	27	3	41
TP53 WILD-TYPE	3	38	55	46

Figure S16. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0099

Table S21. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
TP53 MUTATED	50	41	46	9
TP53 WILD-TYPE	33	16	71	23

Figure S17. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S22. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
TP53 MUTATED	75	12	37	22
TP53 WILD-TYPE	23	33	52	35

Figure S18. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S23. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
TP53 MUTATED	65	22	3	32	16	5	3
TP53 WILD-TYPE	2	38	24	52	18	1	8

Figure S19. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S24. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
TP53 MUTATED	81	20	26	19
TP53 WILD-TYPE	17	47	43	36

Figure S20. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	7
ATRX MUTATED	8	3	2
ATRX WILD-TYPE	1	7	5

Figure S21. Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ATRX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	5
ATRX MUTATED	5	5	1	2
ATRX WILD-TYPE	2	2	6	3

'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
ATRX MUTATED	77	19	22
ATRX WILD-TYPE	19	50	99

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

'ATRX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
ATRX MUTATED	104	1	11	2
ATRX WILD-TYPE	24	35	32	76

Figure S23. Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ATRX MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
ATRX MUTATED	27	23	32	26
ATRX WILD-TYPE	25	38	33	47

'ATRX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
ATRX MUTATED	31	53	24
ATRX WILD-TYPE	35	75	33

'ATRX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
ATRX MUTATED	65	15	1	32	5
ATRX WILD-TYPE	10	50	50	51	9

Figure S24. Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
ATRX MUTATED	65	17	1	35
ATRX WILD-TYPE	13	48	57	52

Figure S25. Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.64

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
ATRX MUTATED	37	34	39	8
ATRX WILD-TYPE	46	23	78	24

Figure S26. Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
ATRX MUTATED	62	13	31	12
ATRX WILD-TYPE	36	32	58	45

Figure S27. Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
ATRX MUTATED	52	15	2	26	15	4	4
ATRX WILD-TYPE	15	45	25	58	19	2	7

Figure S28. Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'ATRX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
ATRX MUTATED	68	17	24	9
ATRX WILD-TYPE	30	50	45	46

Figure S29. Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	7
CIC MUTATED	0	5	2
CIC WILD-TYPE	9	5	5

Figure S30. Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CIC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00301 (Fisher's exact test), Q value = 0.92

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	5
CIC MUTATED	0	0	5	2
CIC WILD-TYPE	7	7	2	3

Figure S31. Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
CIC MUTATED	0	4	50
CIC WILD-TYPE	96	65	71

Figure S32. Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CIC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
CIC MUTATED	0	0	2	51
CIC WILD-TYPE	128	36	41	27

Figure S33. Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CIC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0099

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
CIC MUTATED	1	6	20	15
CIC WILD-TYPE	51	55	45	58

Figure S34. Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CIC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
CIC MUTATED	8	24	10
CIC WILD-TYPE	58	104	47

'CIC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
CIC MUTATED	0	1	32	19	2
CIC WILD-TYPE	75	64	19	64	12

Figure S35. Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CIC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
CIC MUTATED	0	1	38	15
CIC WILD-TYPE	78	64	20	72

Figure S36. Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
CIC MUTATED	9	2	27	16
CIC WILD-TYPE	74	55	90	16

Figure S37. Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CIC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
CIC MUTATED	14	22	17	1
CIC WILD-TYPE	84	23	72	56

Figure S38. Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
CIC MUTATED	1	6	18	19	6	0	4
CIC WILD-TYPE	66	54	9	65	28	6	7

Figure S39. Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CIC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
CIC MUTATED	7	33	14	0
CIC WILD-TYPE	91	34	55	55

Figure S40. Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S49. Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	7
NOTCH1 MUTATED	0	2	1
NOTCH1 WILD-TYPE	9	8	6

'NOTCH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.245 (Fisher's exact test), Q value = 1

Table S50. Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	5
NOTCH1 MUTATED	0	0	2	1
NOTCH1 WILD-TYPE	7	7	5	4

'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.92

Table S51. Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
NOTCH1 MUTATED	4	4	21
NOTCH1 WILD-TYPE	92	65	100

Figure S41. Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S52. Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
NOTCH1 MUTATED	6	0	0	22
NOTCH1 WILD-TYPE	122	36	43	56

Figure S42. Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.89 (Fisher's exact test), Q value = 1

Table S53. Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
NOTCH1 MUTATED	4	6	7	9
NOTCH1 WILD-TYPE	48	55	58	64

'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S54. Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
NOTCH1 MUTATED	6	13	7
NOTCH1 WILD-TYPE	60	115	50

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S55. Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
NOTCH1 MUTATED	1	2	15	11	0
NOTCH1 WILD-TYPE	74	63	36	72	14

Figure S43. Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0099

Table S56. Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
NOTCH1 MUTATED	1	2	14	12
NOTCH1 WILD-TYPE	77	63	44	75

Figure S44. Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.023

Table S57. Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
NOTCH1 MUTATED	1	2	20	6
NOTCH1 WILD-TYPE	82	55	97	26

Figure S45. Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.052

Table S58. Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
NOTCH1 MUTATED	3	11	13	2
NOTCH1 WILD-TYPE	95	34	76	55

Figure S46. Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.055

Table S59. Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
NOTCH1 MUTATED	1	2	8	15	3	0	0
NOTCH1 WILD-TYPE	66	58	19	69	31	6	11

Figure S47. Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0099

Table S60. Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
NOTCH1 MUTATED	4	14	11	0
NOTCH1 WILD-TYPE	94	53	58	55

Figure S48. Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S61. Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
IDH2 MUTATED	1	1	10
IDH2 WILD-TYPE	95	68	111

Figure S49. Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'IDH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 1

Table S62. Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
IDH2 MUTATED	2	0	3	7
IDH2 WILD-TYPE	126	36	40	71

Figure S50. Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'IDH2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S63. Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
IDH2 MUTATED	1	4	2	5
IDH2 WILD-TYPE	51	57	63	68

'IDH2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.181 (Fisher's exact test), Q value = 1

Table S64. Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
IDH2 MUTATED	1	6	5
IDH2 WILD-TYPE	65	122	52

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.76

Table S65. Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
IDH2 MUTATED	0	0	5	7	0
IDH2 WILD-TYPE	75	65	46	76	14

Figure S51. Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00168 (Fisher's exact test), Q value = 0.53

Table S66. Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
IDH2 MUTATED	0	0	5	7
IDH2 WILD-TYPE	78	65	53	80

Figure S52. Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0989 (Fisher's exact test), Q value = 1

Table S67. Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
IDH2 MUTATED	2	0	8	2
IDH2 WILD-TYPE	81	57	109	30

'IDH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0459 (Fisher's exact test), Q value = 1

Table S68. Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
IDH2 MUTATED	2	3	7	0
IDH2 WILD-TYPE	96	42	82	57

Figure S53. Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0557 (Fisher's exact test), Q value = 1

Table S69. Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
IDH2 MUTATED	0	2	3	7	0	0	0
IDH2 WILD-TYPE	67	58	24	77	34	6	11

'IDH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00856 (Fisher's exact test), Q value = 1

Table S70. Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
IDH2 MUTATED	1	5	6	0
IDH2 WILD-TYPE	97	62	63	55

Figure S54. Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FUBP1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S71. Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	7
FUBP1 MUTATED	0	4	0
FUBP1 WILD-TYPE	9	6	7

Figure S55. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'FUBP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00701 (Fisher's exact test), Q value = 1

Table S72. Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	5
FUBP1 MUTATED	0	0	4	0
FUBP1 WILD-TYPE	7	7	3	5

Figure S56. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FUBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S73. Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
FUBP1 MUTATED	0	0	26
FUBP1 WILD-TYPE	96	69	95

Figure S57. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FUBP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S74. Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
FUBP1 MUTATED	0	0	1	22
FUBP1 WILD-TYPE	128	36	42	56

Figure S58. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FUBP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 1

Table S75. Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
FUBP1 MUTATED	1	2	9	10
FUBP1 WILD-TYPE	51	59	56	63

Figure S59. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'FUBP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.733 (Fisher's exact test), Q value = 1

Table S76. Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
FUBP1 MUTATED	7	10	5
FUBP1 WILD-TYPE	59	118	52

'FUBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S77. Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
FUBP1 MUTATED	0	1	16	7	2
FUBP1 WILD-TYPE	75	64	35	76	12

Figure S60. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FUBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S78. Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
FUBP1 MUTATED	0	1	18	7
FUBP1 WILD-TYPE	78	64	40	80

Figure S61. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FUBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S79. Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
FUBP1 MUTATED	4	0	12	10
FUBP1 WILD-TYPE	79	57	105	22

Figure S62. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'FUBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00542 (Fisher's exact test), Q value = 1

Table S80. Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
FUBP1 MUTATED	8	8	10	0
FUBP1 WILD-TYPE	90	37	79	57

Figure S63. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FUBP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.31

Table S81. Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
FUBP1 MUTATED	1	2	8	10	3	0	2
FUBP1 WILD-TYPE	66	58	19	74	31	6	9

Figure S64. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'FUBP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.013

Table S82. Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
FUBP1 MUTATED	3	14	9	0
FUBP1 WILD-TYPE	95	53	60	55

Figure S65. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S83. Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
NF1 MUTATED	3	10	6
NF1 WILD-TYPE	93	59	115

Figure S66. Get High-res Image Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S84. Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
NF1 MUTATED	1	7	6	1
NF1 WILD-TYPE	127	29	37	77

Figure S67. Get High-res Image Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S85. Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
NF1 MUTATED	1	9	2	4
NF1 WILD-TYPE	51	52	63	69

Figure S68. Get High-res Image Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S86. Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
NF1 MUTATED	4	11	1
NF1 WILD-TYPE	62	117	56

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S87. Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
NF1 MUTATED	1	10	3	4	1
NF1 WILD-TYPE	74	55	48	79	13

Figure S69. Get High-res Image Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00846 (Fisher's exact test), Q value = 1

Table S88. Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
NF1 MUTATED	1	10	4	4
NF1 WILD-TYPE	77	55	54	83

Figure S70. Get High-res Image Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S89. Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
NF1 MUTATED	6	5	6	2
NF1 WILD-TYPE	77	52	111	30

'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00784 (Fisher's exact test), Q value = 1

Table S90. Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
NF1 MUTATED	4	2	3	10
NF1 WILD-TYPE	94	43	86	47

Figure S71. Get High-res Image Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S91. Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
NF1 MUTATED	2	8	2	4	2	1	0
NF1 WILD-TYPE	65	52	25	80	32	5	11

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.37

Table S92. Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
NF1 MUTATED	4	2	2	11
NF1 WILD-TYPE	94	65	67	44

Figure S72. Get High-res Image Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 1

Table S93. Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	7
PIK3R1 MUTATED	2	1	0
PIK3R1 WILD-TYPE	7	9	7

'PIK3R1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S94. Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	5
PIK3R1 MUTATED	2	0	1	0
PIK3R1 WILD-TYPE	5	7	6	5

'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S95. Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
PIK3R1 MUTATED	1	3	9
PIK3R1 WILD-TYPE	95	66	112

'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S96. Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
PIK3R1 MUTATED	3	1	1	7
PIK3R1 WILD-TYPE	125	35	42	71

'PIK3R1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S97. Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
PIK3R1 MUTATED	3	2	4	4
PIK3R1 WILD-TYPE	49	59	61	69

'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S98. Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
PIK3R1 MUTATED	3	7	3
PIK3R1 WILD-TYPE	63	121	54

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.709 (Fisher's exact test), Q value = 1

Table S99. Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
PIK3R1 MUTATED	2	3	4	4	0
PIK3R1 WILD-TYPE	73	62	47	79	14

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.787 (Fisher's exact test), Q value = 1

Table S100. Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
PIK3R1 MUTATED	3	2	4	4
PIK3R1 WILD-TYPE	75	63	54	83

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S101. Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
PIK3R1 MUTATED	4	1	4	4
PIK3R1 WILD-TYPE	79	56	113	28

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 1

Table S102. Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
PIK3R1 MUTATED	5	4	3	1
PIK3R1 WILD-TYPE	93	41	86	56

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S103. Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
PIK3R1 MUTATED	2	2	3	4	2	0	0
PIK3R1 WILD-TYPE	65	58	24	80	32	6	11

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.735 (Fisher's exact test), Q value = 1

Table S104. Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
PIK3R1 MUTATED	6	3	3	1
PIK3R1 WILD-TYPE	92	64	66	54

'STK19 MUTATION STATUS' versus 'CN_CNMF'

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

Table S105. Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
STK19 MUTATED	4	3	1
STK19 WILD-TYPE	92	66	120

'STK19 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 1

Table S106. Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
STK19 MUTATED	4	2	2	0
STK19 WILD-TYPE	124	34	41	78

'STK19 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S107. Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
STK19 MUTATED	4	0	0	2
STK19 WILD-TYPE	48	61	65	71

Figure S73. Get High-res Image Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'STK19 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S108. Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
STK19 MUTATED	3	1	2
STK19 WILD-TYPE	63	127	55

'STK19 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S109. Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
STK19 MUTATED	2	2	0	4	0
STK19 WILD-TYPE	73	63	51	79	14

'STK19 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S110. Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
STK19 MUTATED	2	2	0	4
STK19 WILD-TYPE	76	63	58	83

'STK19 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S111. Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
STK19 MUTATED	1	3	4	0
STK19 WILD-TYPE	82	54	113	32

'STK19 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S112. Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
STK19 MUTATED	2	1	3	2
STK19 WILD-TYPE	96	44	86	55

'STK19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S113. Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
STK19 MUTATED	1	3	0	4	0	0	0
STK19 WILD-TYPE	66	57	27	80	34	6	11

'STK19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.502 (Fisher's exact test), Q value = 1

Table S114. Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
STK19 MUTATED	1	3	2	2
STK19 WILD-TYPE	97	64	67	53

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S115. Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
PTEN MUTATED	0	13	0
PTEN WILD-TYPE	96	56	121

Figure S74. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S116. Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
PTEN MUTATED	0	12	0	0
PTEN WILD-TYPE	128	24	43	78

Figure S75. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.17

Table S117. Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
PTEN MUTATED	1	8	1	0
PTEN WILD-TYPE	51	53	64	73

Figure S76. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00536 (Fisher's exact test), Q value = 1

Table S118. Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
PTEN MUTATED	0	10	0
PTEN WILD-TYPE	66	118	57

Figure S77. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S119. Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
PTEN MUTATED	0	13	0	0	0
PTEN WILD-TYPE	75	52	51	83	14

Figure S78. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S120. Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
PTEN MUTATED	0	12	0	1
PTEN WILD-TYPE	78	53	58	86

Figure S79. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 1

Table S121. Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
PTEN MUTATED	8	3	2	0
PTEN WILD-TYPE	75	54	115	32

Figure S80. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S122. Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
PTEN MUTATED	0	0	0	13
PTEN WILD-TYPE	98	45	89	44

Figure S81. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S123. Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
PTEN MUTATED	0	12	0	1	0	0	0
PTEN WILD-TYPE	67	48	27	83	34	6	11

Figure S82. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S124. Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
PTEN MUTATED	0	0	0	13
PTEN WILD-TYPE	98	67	69	42

Figure S83. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.43

Table S125. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
PIK3CA MUTATED	1	9	15
PIK3CA WILD-TYPE	95	60	106

Figure S84. Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S126. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
PIK3CA MUTATED	1	5	3	16
PIK3CA WILD-TYPE	127	31	40	62

Figure S85. Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S127. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
PIK3CA MUTATED	3	7	4	8
PIK3CA WILD-TYPE	49	54	61	65

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.735 (Fisher's exact test), Q value = 1

Table S128. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
PIK3CA MUTATED	7	10	5
PIK3CA WILD-TYPE	59	118	52

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00559 (Fisher's exact test), Q value = 1

Table S129. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
PIK3CA MUTATED	1	5	9	7	3
PIK3CA WILD-TYPE	74	60	42	76	11

Figure S86. Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.26

Table S130. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
PIK3CA MUTATED	0	6	10	9
PIK3CA WILD-TYPE	78	59	48	78

Figure S87. Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.298 (Fisher's exact test), Q value = 1

Table S131. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
PIK3CA MUTATED	4	5	11	5
PIK3CA WILD-TYPE	79	52	106	27

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S132. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
PIK3CA MUTATED	4	5	10	6
PIK3CA WILD-TYPE	94	40	79	51

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.29

Table S133. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
PIK3CA MUTATED	0	6	6	9	1	0	3
PIK3CA WILD-TYPE	67	54	21	75	33	6	8

Figure S88. Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00204 (Fisher's exact test), Q value = 0.64

Table S134. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
PIK3CA MUTATED	1	8	10	6
PIK3CA WILD-TYPE	97	59	59	49

Figure S89. Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S135. Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
ARID1A MUTATED	4	2	5
ARID1A WILD-TYPE	92	67	116

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S136. Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
ARID1A MUTATED	5	1	0	6
ARID1A WILD-TYPE	123	35	43	72

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 1

Table S137. Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
ARID1A MUTATED	2	1	5	4
ARID1A WILD-TYPE	50	60	60	69

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S138. Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
ARID1A MUTATED	2	7	3
ARID1A WILD-TYPE	64	121	54

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S139. Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
ARID1A MUTATED	3	0	4	5	0
ARID1A WILD-TYPE	72	65	47	78	14

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S140. Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
ARID1A MUTATED	3	0	4	5
ARID1A WILD-TYPE	75	65	54	82

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S141. Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
ARID1A MUTATED	3	1	6	2
ARID1A WILD-TYPE	80	56	111	30

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 1

Table S142. Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
ARID1A MUTATED	5	3	3	1
ARID1A WILD-TYPE	93	42	86	56

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S143. Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
ARID1A MUTATED	1	1	4	5	1	0	0
ARID1A WILD-TYPE	66	59	23	79	33	6	11

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S144. Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
ARID1A MUTATED	5	4	2	1
ARID1A WILD-TYPE	93	63	67	54

'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S145. Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
EGFR MUTATED	0	16	1
EGFR WILD-TYPE	96	53	120

Figure S90. Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S146. Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
EGFR MUTATED	0	14	2	1
EGFR WILD-TYPE	128	22	41	77

Figure S91. Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00758 (Fisher's exact test), Q value = 1

Table S147. Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
EGFR MUTATED	1	9	1	3
EGFR WILD-TYPE	51	52	64	70

Figure S92. Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 1

Table S148. Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
EGFR MUTATED	0	11	3
EGFR WILD-TYPE	66	117	54

Figure S93. Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.013

Table S149. Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
EGFR MUTATED	0	13	1	3	0
EGFR WILD-TYPE	75	52	50	80	14

Figure S94. Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S150. Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
EGFR MUTATED	0	13	1	3
EGFR WILD-TYPE	78	52	57	84

Figure S95. Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.362 (Fisher's exact test), Q value = 1

Table S151. Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
EGFR MUTATED	7	4	6	0
EGFR WILD-TYPE	76	53	111	32

'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S152. Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
EGFR MUTATED	0	1	2	14
EGFR WILD-TYPE	98	44	87	43

Figure S96. Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.14

Table S153. Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
EGFR MUTATED	0	12	0	4	1	0	0
EGFR WILD-TYPE	67	48	27	80	33	6	11

Figure S97. Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'EGFR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S154. Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
EGFR MUTATED	0	1	2	14
EGFR WILD-TYPE	98	66	67	41

Figure S98. Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GAGE2B MUTATION STATUS' versus 'CN_CNMF'

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

Table S155. Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
GAGE2B MUTATED	2	0	2
GAGE2B WILD-TYPE	94	69	119

'GAGE2B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.801 (Fisher's exact test), Q value = 1

Table S156. Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
GAGE2B MUTATED	2	0	0	2
GAGE2B WILD-TYPE	126	36	43	76

'GAGE2B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S157. Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
GAGE2B MUTATED	0	0	2	2
GAGE2B WILD-TYPE	52	61	63	71

'GAGE2B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S158. Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
GAGE2B MUTATED	1	2	1
GAGE2B WILD-TYPE	65	126	56

'GAGE2B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S159. Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
GAGE2B MUTATED	2	0	1	1	0
GAGE2B WILD-TYPE	73	65	50	82	14

'GAGE2B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S160. Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
GAGE2B MUTATED	2	0	0	2
GAGE2B WILD-TYPE	76	65	58	85

'GAGE2B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S161. Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
GAGE2B MUTATED	1	1	2	0
GAGE2B WILD-TYPE	82	56	115	32

'GAGE2B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S162. Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
GAGE2B MUTATED	2	0	2	0
GAGE2B WILD-TYPE	96	45	87	57

'GAGE2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S163. Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
GAGE2B MUTATED	1	0	0	2	0	0	1
GAGE2B WILD-TYPE	66	60	27	82	34	6	10

'GAGE2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S164. Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
GAGE2B MUTATED	2	1	1	0
GAGE2B WILD-TYPE	96	66	68	55

'CREBZF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 1

Table S165. Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
CREBZF MUTATED	0	1	4
CREBZF WILD-TYPE	96	68	117

'CREBZF MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S166. Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
CREBZF MUTATED	0	0	1	4
CREBZF WILD-TYPE	128	36	42	74

Figure S99. Get High-res Image Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CREBZF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0866 (Fisher's exact test), Q value = 1

Table S167. Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
CREBZF MUTATED	0	1	0	4
CREBZF WILD-TYPE	52	60	65	69

'CREBZF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00475 (Fisher's exact test), Q value = 1

Table S168. Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
CREBZF MUTATED	1	0	4
CREBZF WILD-TYPE	65	128	53

Figure S100. Get High-res Image Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'CREBZF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.578 (Fisher's exact test), Q value = 1

Table S169. Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
CREBZF MUTATED	0	1	1	3	0
CREBZF WILD-TYPE	75	64	50	80	14

'CREBZF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S170. Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
CREBZF MUTATED	0	1	1	3
CREBZF WILD-TYPE	78	64	57	84

'CREBZF MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S171. Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
CREBZF MUTATED	0	1	3	1
CREBZF WILD-TYPE	83	56	114	31

'CREBZF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S172. Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
CREBZF MUTATED	0	1	3	1
CREBZF WILD-TYPE	98	44	86	56

'CREBZF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S173. Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
CREBZF MUTATED	0	1	1	3	0	0	0
CREBZF WILD-TYPE	67	59	26	81	34	6	11

'CREBZF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S174. Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
CREBZF MUTATED	0	1	3	1
CREBZF WILD-TYPE	98	66	66	54

'TCF12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.596 (Fisher's exact test), Q value = 1

Table S175. Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
TCF12 MUTATED	2	1	5
TCF12 WILD-TYPE	94	68	116

'TCF12 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S176. Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
TCF12 MUTATED	2	1	1	4
TCF12 WILD-TYPE	126	35	42	74

'TCF12 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S177. Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
TCF12 MUTATED	1	1	5	1
TCF12 WILD-TYPE	51	60	60	72

'TCF12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S178. Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
TCF12 MUTATED	1	6	1
TCF12 WILD-TYPE	65	122	56

'TCF12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.246 (Fisher's exact test), Q value = 1

Table S179. Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
TCF12 MUTATED	1	2	4	1	0
TCF12 WILD-TYPE	74	63	47	82	14

'TCF12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S180. Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
TCF12 MUTATED	1	2	3	2
TCF12 WILD-TYPE	77	63	55	85

'TCF12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S181. Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
TCF12 MUTATED	3	0	3	2
TCF12 WILD-TYPE	80	57	114	30

'TCF12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S182. Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
TCF12 MUTATED	3	1	3	1
TCF12 WILD-TYPE	95	44	86	56

'TCF12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S183. Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
TCF12 MUTATED	2	1	3	2	0	0	0
TCF12 WILD-TYPE	65	59	24	82	34	6	11

'TCF12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.803 (Fisher's exact test), Q value = 1

Table S184. Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
TCF12 MUTATED	2	2	3	1
TCF12 WILD-TYPE	96	65	66	54

'SMARCA4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S185. Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
SMARCA4 MUTATED	7	1	5
SMARCA4 WILD-TYPE	89	68	116

'SMARCA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S186. Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
SMARCA4 MUTATED	9	0	0	4
SMARCA4 WILD-TYPE	119	36	43	74

'SMARCA4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S187. Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
SMARCA4 MUTATED	0	3	4	4
SMARCA4 WILD-TYPE	52	58	61	69

'SMARCA4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S188. Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
SMARCA4 MUTATED	2	6	3
SMARCA4 WILD-TYPE	64	122	54

'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S189. Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
SMARCA4 MUTATED	3	0	4	5	1
SMARCA4 WILD-TYPE	72	65	47	78	13

'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 1

Table S190. Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
SMARCA4 MUTATED	5	1	3	4
SMARCA4 WILD-TYPE	73	64	55	83

'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S191. Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
SMARCA4 MUTATED	3	0	8	2
SMARCA4 WILD-TYPE	80	57	109	30

'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S192. Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
SMARCA4 MUTATED	5	4	4	0
SMARCA4 WILD-TYPE	93	41	85	57

'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S193. Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
SMARCA4 MUTATED	4	0	1	5	2	0	1
SMARCA4 WILD-TYPE	63	60	26	79	32	6	10

'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S194. Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
SMARCA4 MUTATED	4	5	4	0
SMARCA4 WILD-TYPE	94	62	65	55

'VAV3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S195. Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
VAV3 MUTATED	3	3	2
VAV3 WILD-TYPE	93	66	119

'VAV3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S196. Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
VAV3 MUTATED	3	1	2	2
VAV3 WILD-TYPE	125	35	41	76

'VAV3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.961 (Fisher's exact test), Q value = 1

Table S197. Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
VAV3 MUTATED	1	2	2	3
VAV3 WILD-TYPE	51	59	63	70

'VAV3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S198. Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
VAV3 MUTATED	2	3	3
VAV3 WILD-TYPE	64	125	54

'VAV3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S199. Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
VAV3 MUTATED	0	3	1	2	2
VAV3 WILD-TYPE	75	62	50	81	12

Figure S101. Get High-res Image Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VAV3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S200. Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
VAV3 MUTATED	2	2	0	4
VAV3 WILD-TYPE	76	63	58	83

'VAV3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.77 (Fisher's exact test), Q value = 1

Table S201. Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
VAV3 MUTATED	2	1	5	0
VAV3 WILD-TYPE	81	56	112	32

'VAV3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 1

Table S202. Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
VAV3 MUTATED	2	0	5	1
VAV3 WILD-TYPE	96	45	84	56

'VAV3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.967 (Fisher's exact test), Q value = 1

Table S203. Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
VAV3 MUTATED	1	2	1	3	1	0	0
VAV3 WILD-TYPE	66	58	26	81	33	6	11

'VAV3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S204. Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
VAV3 MUTATED	2	1	3	2
VAV3 WILD-TYPE	96	66	66	53

'TMEM216 MUTATION STATUS' versus 'CN_CNMF'

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

Table S205. Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
TMEM216 MUTATED	2	1	0
TMEM216 WILD-TYPE	94	68	121

'TMEM216 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S206. Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
TMEM216 MUTATED	2	0	0	1
TMEM216 WILD-TYPE	126	36	43	77

'TMEM216 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S207. Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
TMEM216 MUTATED	1	1	0	1
TMEM216 WILD-TYPE	51	60	65	72

'TMEM216 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S208. Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
TMEM216 MUTATED	1	1	1
TMEM216 WILD-TYPE	65	127	56

'TMEM216 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.897 (Fisher's exact test), Q value = 1

Table S209. Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
TMEM216 MUTATED	1	0	1	1	0
TMEM216 WILD-TYPE	74	65	50	82	14

'TMEM216 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.887 (Fisher's exact test), Q value = 1

Table S210. Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
TMEM216 MUTATED	1	0	1	1
TMEM216 WILD-TYPE	77	65	57	86

'TMEM216 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 1

Table S211. Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
TMEM216 MUTATED	0	1	1	1
TMEM216 WILD-TYPE	83	56	116	31

'TMEM216 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S212. Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
TMEM216 MUTATED	1	1	1	0
TMEM216 WILD-TYPE	97	44	88	57

'TMEM216 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S213. Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
TMEM216 MUTATED	1	1	0	1	0	0	0
TMEM216 WILD-TYPE	66	59	27	83	34	6	11

'TMEM216 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S214. Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
TMEM216 MUTATED	0	2	1	0
TMEM216 WILD-TYPE	98	65	68	55

'ROBO3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S215. Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
ROBO3 MUTATED	2	0	2
ROBO3 WILD-TYPE	94	69	119

'ROBO3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.899 (Fisher's exact test), Q value = 1

Table S216. Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
ROBO3 MUTATED	3	0	0	1
ROBO3 WILD-TYPE	125	36	43	77

'ROBO3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S217. Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
ROBO3 MUTATED	2	0	0	2	0
ROBO3 WILD-TYPE	73	65	51	81	14

'ROBO3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.72 (Fisher's exact test), Q value = 1

Table S218. Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
ROBO3 MUTATED	2	0	1	1
ROBO3 WILD-TYPE	76	65	57	86

'ROBO3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.65 (Fisher's exact test), Q value = 1

Table S219. Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
ROBO3 MUTATED	1	0	2	1
ROBO3 WILD-TYPE	82	57	115	31

'ROBO3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.76 (Fisher's exact test), Q value = 1

Table S220. Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
ROBO3 MUTATED	2	1	1	0
ROBO3 WILD-TYPE	96	44	88	57

'ROBO3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.776 (Fisher's exact test), Q value = 1

Table S221. Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
ROBO3 MUTATED	2	0	0	2	0	0	0
ROBO3 WILD-TYPE	65	60	27	82	34	6	11

'ROBO3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S222. Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
ROBO3 MUTATED	1	2	1	0
ROBO3 WILD-TYPE	97	65	68	55

'IRS4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 1

Table S223. Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
IRS4 MUTATED	2	2	1
IRS4 WILD-TYPE	94	67	120

'IRS4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S224. Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
IRS4 MUTATED	3	1	0	1
IRS4 WILD-TYPE	125	35	43	77

'IRS4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S225. Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
IRS4 MUTATED	0	1	1	1
IRS4 WILD-TYPE	52	60	64	72

'IRS4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S226. Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
IRS4 MUTATED	0	1	2
IRS4 WILD-TYPE	66	127	55

'IRS4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.859 (Fisher's exact test), Q value = 1

Table S227. Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
IRS4 MUTATED	2	1	0	2	0
IRS4 WILD-TYPE	73	64	51	81	14

'IRS4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S228. Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
IRS4 MUTATED	2	1	1	1
IRS4 WILD-TYPE	76	64	57	86

'IRS4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.919 (Fisher's exact test), Q value = 1

Table S229. Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
IRS4 MUTATED	1	1	3	0
IRS4 WILD-TYPE	82	56	114	32

'IRS4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S230. Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
IRS4 MUTATED	2	1	1	1
IRS4 WILD-TYPE	96	44	88	56

'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S231. Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
IRS4 MUTATED	1	0	0	2	1	1	0
IRS4 WILD-TYPE	66	60	27	82	33	5	11

'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S232. Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
IRS4 MUTATED	2	1	1	1
IRS4 WILD-TYPE	96	66	68	54

'HTRA2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S233. Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
HTRA2 MUTATED	3	1	0
HTRA2 WILD-TYPE	93	68	121

'HTRA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S234. Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
HTRA2 MUTATED	2	0	1	1
HTRA2 WILD-TYPE	126	36	42	77

'HTRA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 1

Table S235. Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
HTRA2 MUTATED	2	1	0	1
HTRA2 WILD-TYPE	50	60	65	72

'HTRA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S236. Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
HTRA2 MUTATED	1	2	1
HTRA2 WILD-TYPE	65	126	56

'HTRA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S237. Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
HTRA2 MUTATED	1	1	1	1	0
HTRA2 WILD-TYPE	74	64	50	82	14

'HTRA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S238. Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
HTRA2 MUTATED	1	1	1	1
HTRA2 WILD-TYPE	77	64	57	86

'HTRA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 1

Table S239. Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
HTRA2 MUTATED	2	0	1	1
HTRA2 WILD-TYPE	81	57	116	31

'HTRA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.758 (Fisher's exact test), Q value = 1

Table S240. Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
HTRA2 MUTATED	2	1	1	0
HTRA2 WILD-TYPE	96	44	88	57

'HTRA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.369 (Fisher's exact test), Q value = 1

Table S241. Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
HTRA2 MUTATED	0	3	0	1	0	0	0
HTRA2 WILD-TYPE	67	57	27	83	34	6	11

'HTRA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S242. Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
HTRA2 MUTATED	2	1	1	0
HTRA2 WILD-TYPE	96	66	68	55

'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S243. Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
EIF1AX MUTATED	2	1	1
EIF1AX WILD-TYPE	94	68	120

'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S244. Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
EIF1AX MUTATED	4	0	0	0
EIF1AX WILD-TYPE	124	36	43	78

'EIF1AX MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S245. Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
EIF1AX MUTATED	0	0	2	2
EIF1AX WILD-TYPE	52	61	63	71

'EIF1AX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 1

Table S246. Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
EIF1AX MUTATED	0	2	2
EIF1AX WILD-TYPE	66	126	55

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S247. Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
EIF1AX MUTATED	2	1	0	1	0
EIF1AX WILD-TYPE	73	64	51	82	14

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S248. Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
EIF1AX MUTATED	2	1	0	1
EIF1AX WILD-TYPE	76	64	58	86

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S249. Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
EIF1AX MUTATED	2	1	1	0
EIF1AX WILD-TYPE	81	56	116	32

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 1

Table S250. Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
EIF1AX MUTATED	2	1	0	1
EIF1AX WILD-TYPE	96	44	89	56

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S251. Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
EIF1AX MUTATED	3	1	0	0	0	0	0
EIF1AX WILD-TYPE	64	59	27	84	34	6	11

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S252. Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
EIF1AX MUTATED	4	0	0	0
EIF1AX WILD-TYPE	94	67	69	55

'FAM47C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S253. Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
FAM47C MUTATED	1	1	5
FAM47C WILD-TYPE	95	68	116

'FAM47C MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S254. Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
FAM47C MUTATED	2	0	1	4
FAM47C WILD-TYPE	126	36	42	74

'FAM47C MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S255. Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
FAM47C MUTATED	1	0	1	4
FAM47C WILD-TYPE	51	61	64	69

'FAM47C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 1

Table S256. Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
FAM47C MUTATED	1	2	3
FAM47C WILD-TYPE	65	126	54

'FAM47C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0581 (Fisher's exact test), Q value = 1

Table S257. Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
FAM47C MUTATED	0	0	2	5	0
FAM47C WILD-TYPE	75	65	49	78	14

'FAM47C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 1

Table S258. Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
FAM47C MUTATED	0	0	2	5
FAM47C WILD-TYPE	78	65	56	82

Figure S102. Get High-res Image Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FAM47C MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S259. Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
FAM47C MUTATED	1	0	6	0
FAM47C WILD-TYPE	82	57	111	32

'FAM47C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0082 (Fisher's exact test), Q value = 1

Table S260. Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
FAM47C MUTATED	0	1	6	0
FAM47C WILD-TYPE	98	44	83	57

Figure S103. Get High-res Image Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S261. Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
FAM47C MUTATED	0	0	1	5	1	0	0
FAM47C WILD-TYPE	67	60	26	79	33	6	11

'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0016 (Fisher's exact test), Q value = 0.5

Table S262. Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
FAM47C MUTATED	0	1	6	0
FAM47C WILD-TYPE	98	66	63	55

Figure S104. Get High-res Image Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PLCG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0028 (Fisher's exact test), Q value = 0.86

Table S263. Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
PLCG1 MUTATED	0	4	0
PLCG1 WILD-TYPE	96	65	121

Figure S105. Get High-res Image Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PLCG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 1

Table S264. Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
PLCG1 MUTATED	1	3	0	0
PLCG1 WILD-TYPE	127	33	43	78

Figure S106. Get High-res Image Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PLCG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S265. Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
PLCG1 MUTATED	1	3	0	0	0
PLCG1 WILD-TYPE	74	62	51	83	14

'PLCG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S266. Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
PLCG1 MUTATED	1	2	0	1
PLCG1 WILD-TYPE	77	63	58	86

'PLCG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S267. Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
PLCG1 MUTATED	4	0	0	0
PLCG1 WILD-TYPE	79	57	117	32

Figure S107. Get High-res Image Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PLCG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S268. Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
PLCG1 MUTATED	2	0	0	2
PLCG1 WILD-TYPE	96	45	89	55

'PLCG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 1

Table S269. Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
PLCG1 MUTATED	1	3	0	0	0	0	0
PLCG1 WILD-TYPE	66	57	27	84	34	6	11

'PLCG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.208 (Fisher's exact test), Q value = 1

Table S270. Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
PLCG1 MUTATED	2	0	0	2
PLCG1 WILD-TYPE	96	67	69	53

'DDX5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S271. Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
DDX5 MUTATED	2	0	2
DDX5 WILD-TYPE	94	69	119

'DDX5 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S272. Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
DDX5 MUTATED	2	0	0	2
DDX5 WILD-TYPE	126	36	43	76

'DDX5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S273. Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
DDX5 MUTATED	1	1	1	1
DDX5 WILD-TYPE	51	60	64	72

'DDX5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S274. Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
DDX5 MUTATED	2	1	1
DDX5 WILD-TYPE	64	127	56

'DDX5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S275. Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
DDX5 MUTATED	2	0	2	0	0
DDX5 WILD-TYPE	73	65	49	83	14

'DDX5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S276. Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
DDX5 MUTATED	2	0	2	0
DDX5 WILD-TYPE	76	65	56	87

'DDX5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S277. Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
DDX5 MUTATED	0	1	3	0
DDX5 WILD-TYPE	83	56	114	32

'DDX5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S278. Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
DDX5 MUTATED	1	0	3	0
DDX5 WILD-TYPE	97	45	86	57

'DDX5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S279. Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
DDX5 MUTATED	1	0	1	0	2	0	0
DDX5 WILD-TYPE	66	60	26	84	32	6	11

'DDX5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S280. Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
DDX5 MUTATED	1	2	1	0
DDX5 WILD-TYPE	97	65	68	55

'ZNF709 MUTATION STATUS' versus 'CN_CNMF'

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

Table S281. Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
ZNF709 MUTATED	1	0	2
ZNF709 WILD-TYPE	95	69	119

'ZNF709 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.89 (Fisher's exact test), Q value = 1

Table S282. Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
ZNF709 MUTATED	1	0	1	1
ZNF709 WILD-TYPE	51	61	64	72

'ZNF709 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S283. Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
ZNF709 MUTATED	1	1	1
ZNF709 WILD-TYPE	65	127	56

'ZNF709 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0682 (Fisher's exact test), Q value = 1

Table S284. Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
ZNF709 MUTATED	0	0	0	2	1
ZNF709 WILD-TYPE	75	65	51	81	13

'ZNF709 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S285. Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
ZNF709 MUTATED	0	0	2	1
ZNF709 WILD-TYPE	78	65	56	86

'ZNF709 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S286. Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
ZNF709 MUTATED	1	0	2	0
ZNF709 WILD-TYPE	82	57	115	32

'ZNF709 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.671 (Fisher's exact test), Q value = 1

Table S287. Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
ZNF709 MUTATED	1	0	2	0
ZNF709 WILD-TYPE	97	45	87	57

'ZNF709 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 1

Table S288. Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
ZNF709 MUTATED	1	0	0	1	0	0	1
ZNF709 WILD-TYPE	66	60	27	83	34	6	10

'ZNF709 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S289. Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
ZNF709 MUTATED	1	0	2	0
ZNF709 WILD-TYPE	97	67	67	55

'TRERF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0507 (Fisher's exact test), Q value = 1

Table S290. Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
TRERF1 MUTATED	3	0	0
TRERF1 WILD-TYPE	93	69	121

'TRERF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S291. Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
TRERF1 MUTATED	2	0	1	0
TRERF1 WILD-TYPE	126	36	42	78

'TRERF1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S292. Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
TRERF1 MUTATED	1	0	0	2
TRERF1 WILD-TYPE	51	61	65	71

'TRERF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0695 (Fisher's exact test), Q value = 1

Table S293. Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
TRERF1 MUTATED	1	0	2
TRERF1 WILD-TYPE	65	128	55

'TRERF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S294. Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
TRERF1 MUTATED	1	0	0	1	1
TRERF1 WILD-TYPE	74	65	51	82	13

'TRERF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S295. Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
TRERF1 MUTATED	2	0	0	1
TRERF1 WILD-TYPE	76	65	58	86

'TRERF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S296. Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
TRERF1 MUTATED	1	0	2	0
TRERF1 WILD-TYPE	82	57	115	32

'TRERF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.669 (Fisher's exact test), Q value = 1

Table S297. Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
TRERF1 MUTATED	1	0	2	0
TRERF1 WILD-TYPE	97	45	87	57

'TRERF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.805 (Fisher's exact test), Q value = 1

Table S298. Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
TRERF1 MUTATED	1	0	0	1	1	0	0
TRERF1 WILD-TYPE	66	60	27	83	33	6	11

'TRERF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S299. Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
TRERF1 MUTATED	1	0	2	0
TRERF1 WILD-TYPE	97	67	67	55

'BCOR MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S300. Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	7
BCOR MUTATED	1	1	1
BCOR WILD-TYPE	8	9	6

'BCOR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S301. Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	5
BCOR MUTATED	1	0	1	1
BCOR WILD-TYPE	6	7	6	4

'BCOR MUTATION STATUS' versus 'CN_CNMF'

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

Table S302. Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
BCOR MUTATED	1	2	6
BCOR WILD-TYPE	95	67	115

'BCOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S303. Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
BCOR MUTATED	3	1	1	4
BCOR WILD-TYPE	125	35	42	74

'BCOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.917 (Fisher's exact test), Q value = 1

Table S304. Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
BCOR MUTATED	2	2	1	2
BCOR WILD-TYPE	50	59	64	71

'BCOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.887 (Fisher's exact test), Q value = 1

Table S305. Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
BCOR MUTATED	2	3	2
BCOR WILD-TYPE	64	125	55

'BCOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.846 (Fisher's exact test), Q value = 1

Table S306. Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
BCOR MUTATED	2	1	2	4	0
BCOR WILD-TYPE	73	64	49	79	14

'BCOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S307. Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
BCOR MUTATED	1	1	2	5
BCOR WILD-TYPE	77	64	56	82

'BCOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.963 (Fisher's exact test), Q value = 1

Table S308. Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
BCOR MUTATED	3	1	4	1
BCOR WILD-TYPE	80	56	113	31

'BCOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S309. Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
BCOR MUTATED	2	2	3	2
BCOR WILD-TYPE	96	43	86	55

'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S310. Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
BCOR MUTATED	1	1	1	4	1	0	1
BCOR WILD-TYPE	66	59	26	80	33	6	10

'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S311. Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
BCOR MUTATED	3	1	3	2
BCOR WILD-TYPE	95	66	66	53

'SRPX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 1

Table S312. Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
SRPX MUTATED	0	1	2
SRPX WILD-TYPE	96	68	119

'SRPX MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S313. Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
SRPX MUTATED	0	1	0	2
SRPX WILD-TYPE	128	35	43	76

'SRPX MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S314. Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
SRPX MUTATED	0	1	2	0
SRPX WILD-TYPE	52	60	63	73

'SRPX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S315. Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
SRPX MUTATED	1	2	0
SRPX WILD-TYPE	65	126	57

'SRPX MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S316. Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
SRPX MUTATED	0	1	2	0	0
SRPX WILD-TYPE	75	64	49	83	14

'SRPX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0925 (Fisher's exact test), Q value = 1

Table S317. Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
SRPX MUTATED	0	1	2	0
SRPX WILD-TYPE	78	64	56	87

'SRPX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 1

Table S318. Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
SRPX MUTATED	1	1	0	1
SRPX WILD-TYPE	82	56	117	31

'SRPX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S319. Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
SRPX MUTATED	1	1	0	1
SRPX WILD-TYPE	97	44	89	56

'SRPX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S320. Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
SRPX MUTATED	0	1	2	0	0	0	0
SRPX WILD-TYPE	67	59	25	84	34	6	11

'SRPX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S321. Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
SRPX MUTATED	0	2	0	1
SRPX WILD-TYPE	98	65	69	54

'DOCK5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0758 (Fisher's exact test), Q value = 1

Table S322. Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
DOCK5 MUTATED	1	4	1
DOCK5 WILD-TYPE	95	65	120

'DOCK5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0544 (Fisher's exact test), Q value = 1

Table S323. Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
DOCK5 MUTATED	1	3	1	1
DOCK5 WILD-TYPE	127	33	42	77

'DOCK5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 1

Table S324. Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
DOCK5 MUTATED	2	2	0	1
DOCK5 WILD-TYPE	50	59	65	72

'DOCK5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S325. Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
DOCK5 MUTATED	3	2	0
DOCK5 WILD-TYPE	63	126	57

'DOCK5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S326. Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
DOCK5 MUTATED	0	4	1	1	0
DOCK5 WILD-TYPE	75	61	50	82	14

'DOCK5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S327. Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
DOCK5 MUTATED	0	4	1	1
DOCK5 WILD-TYPE	78	61	57	86

'DOCK5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 1

Table S328. Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
DOCK5 MUTATED	2	3	1	0
DOCK5 WILD-TYPE	81	54	116	32

'DOCK5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0613 (Fisher's exact test), Q value = 1

Table S329. Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
DOCK5 MUTATED	1	0	1	4
DOCK5 WILD-TYPE	97	45	88	53

'DOCK5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 1

Table S330. Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
DOCK5 MUTATED	0	4	0	1	0	1	0
DOCK5 WILD-TYPE	67	56	27	83	34	5	11

Figure S108. Get High-res Image Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'DOCK5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.302 (Fisher's exact test), Q value = 1

Table S331. Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
DOCK5 MUTATED	1	1	1	3
DOCK5 WILD-TYPE	97	66	68	52

'GIGYF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 1

Table S332. Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
GIGYF2 MUTATED	1	3	0
GIGYF2 WILD-TYPE	95	66	121

Figure S109. Get High-res Image Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'GIGYF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S333. Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
GIGYF2 MUTATED	1	1	0	1
GIGYF2 WILD-TYPE	127	35	43	77

'GIGYF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0835 (Fisher's exact test), Q value = 1

Table S334. Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
GIGYF2 MUTATED	0	3	1	0
GIGYF2 WILD-TYPE	52	58	64	73

'GIGYF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.809 (Fisher's exact test), Q value = 1

Table S335. Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
GIGYF2 MUTATED	1	3	0
GIGYF2 WILD-TYPE	65	125	57

'GIGYF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 1

Table S336. Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
GIGYF2 MUTATED	1	2	1	0	0
GIGYF2 WILD-TYPE	74	63	50	83	14

'GIGYF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 1

Table S337. Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
GIGYF2 MUTATED	1	2	1	0
GIGYF2 WILD-TYPE	77	63	57	87

'GIGYF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 1

Table S338. Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
GIGYF2 MUTATED	0	2	1	1
GIGYF2 WILD-TYPE	83	55	116	31

'GIGYF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S339. Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
GIGYF2 MUTATED	0	1	1	2
GIGYF2 WILD-TYPE	98	44	88	55

'GIGYF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S340. Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
GIGYF2 MUTATED	0	3	0	0	1	0	0
GIGYF2 WILD-TYPE	67	57	27	84	33	6	11

'GIGYF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0598 (Fisher's exact test), Q value = 1

Table S341. Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
GIGYF2 MUTATED	0	2	0	2
GIGYF2 WILD-TYPE	98	65	69	53

'NIPBL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0979 (Fisher's exact test), Q value = 1

Table S342. Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
NIPBL MUTATED	0	1	5
NIPBL WILD-TYPE	96	68	116

'NIPBL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 1

Table S343. Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
NIPBL MUTATED	1	0	0	5
NIPBL WILD-TYPE	127	36	43	73

Figure S110. Get High-res Image Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NIPBL MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S344. Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
NIPBL MUTATED	0	1	2	1
NIPBL WILD-TYPE	52	60	63	72

'NIPBL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.81 (Fisher's exact test), Q value = 1

Table S345. Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
NIPBL MUTATED	1	3	0
NIPBL WILD-TYPE	65	125	57

'NIPBL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0709 (Fisher's exact test), Q value = 1

Table S346. Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
NIPBL MUTATED	1	0	4	1	0
NIPBL WILD-TYPE	74	65	47	82	14

'NIPBL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0488 (Fisher's exact test), Q value = 1

Table S347. Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
NIPBL MUTATED	1	0	4	1
NIPBL WILD-TYPE	77	65	54	86

Figure S111. Get High-res Image Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NIPBL MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S348. Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
NIPBL MUTATED	2	2	2	0
NIPBL WILD-TYPE	81	55	115	32

'NIPBL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.938 (Fisher's exact test), Q value = 1

Table S349. Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
NIPBL MUTATED	3	1	1	1
NIPBL WILD-TYPE	95	44	88	56

'NIPBL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S350. Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
NIPBL MUTATED	1	1	3	1	0	0	0
NIPBL WILD-TYPE	66	59	24	83	34	6	11

'NIPBL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S351. Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
NIPBL MUTATED	1	4	1	0
NIPBL WILD-TYPE	97	63	68	55

'ZBTB20 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 1

Table S352. Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
ZBTB20 MUTATED	2	1	10
ZBTB20 WILD-TYPE	94	68	111

Figure S112. Get High-res Image Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZBTB20 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 1

Table S353. Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
ZBTB20 MUTATED	2	1	1	8
ZBTB20 WILD-TYPE	126	35	42	70

Figure S113. Get High-res Image Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ZBTB20 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S354. Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
ZBTB20 MUTATED	3	1	2	4
ZBTB20 WILD-TYPE	49	60	63	69

'ZBTB20 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S355. Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
ZBTB20 MUTATED	4	3	3
ZBTB20 WILD-TYPE	62	125	54

'ZBTB20 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.072 (Fisher's exact test), Q value = 1

Table S356. Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
ZBTB20 MUTATED	1	1	3	6	2
ZBTB20 WILD-TYPE	74	64	48	77	12

'ZBTB20 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0797 (Fisher's exact test), Q value = 1

Table S357. Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
ZBTB20 MUTATED	1	1	5	6
ZBTB20 WILD-TYPE	77	64	53	81

'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S358. Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
ZBTB20 MUTATED	3	1	8	1
ZBTB20 WILD-TYPE	80	56	109	31

'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.353 (Fisher's exact test), Q value = 1

Table S359. Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
ZBTB20 MUTATED	4	1	7	1
ZBTB20 WILD-TYPE	94	44	82	56

'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 1

Table S360. Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
ZBTB20 MUTATED	1	1	0	8	1	0	2
ZBTB20 WILD-TYPE	66	59	27	76	33	6	9

Figure S114. Get High-res Image Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S361. Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
ZBTB20 MUTATED	4	4	4	1
ZBTB20 WILD-TYPE	94	63	65	54

'TRIP12 MUTATION STATUS' versus 'CN_CNMF'

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

Table S362. Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
TRIP12 MUTATED	1	0	4
TRIP12 WILD-TYPE	95	69	117

'TRIP12 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S363. Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
TRIP12 MUTATED	2	0	0	3
TRIP12 WILD-TYPE	126	36	43	75

'TRIP12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 1

Table S364. Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
TRIP12 MUTATED	1	0	1	3
TRIP12 WILD-TYPE	51	61	64	70

'TRIP12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S365. Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
TRIP12 MUTATED	2	1	2
TRIP12 WILD-TYPE	64	127	55

'TRIP12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S366. Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
TRIP12 MUTATED	1	0	2	2	0
TRIP12 WILD-TYPE	74	65	49	81	14

'TRIP12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.578 (Fisher's exact test), Q value = 1

Table S367. Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
TRIP12 MUTATED	1	0	2	2
TRIP12 WILD-TYPE	77	65	56	85

'TRIP12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S368. Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
TRIP12 MUTATED	1	1	2	1
TRIP12 WILD-TYPE	82	56	115	31

'TRIP12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S369. Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
TRIP12 MUTATED	3	0	2	0
TRIP12 WILD-TYPE	95	45	87	57

'TRIP12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S370. Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
TRIP12 MUTATED	0	1	0	2	2	0	0
TRIP12 WILD-TYPE	67	59	27	82	32	6	11

'TRIP12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S371. Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
TRIP12 MUTATED	1	2	2	0
TRIP12 WILD-TYPE	97	65	67	55

'KIAA0664 MUTATION STATUS' versus 'CN_CNMF'

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

Table S372. Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	69	121
KIAA0664 MUTATED	0	2	3
KIAA0664 WILD-TYPE	96	67	118

'KIAA0664 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S373. Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	128	36	43	78
KIAA0664 MUTATED	1	2	0	2
KIAA0664 WILD-TYPE	127	34	43	76

'KIAA0664 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S374. Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	61	65	73
KIAA0664 MUTATED	1	1	0	2
KIAA0664 WILD-TYPE	51	60	65	71

'KIAA0664 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S375. Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	128	57
KIAA0664 MUTATED	0	2	2
KIAA0664 WILD-TYPE	66	126	55

'KIAA0664 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S376. Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	65	51	83	14
KIAA0664 MUTATED	0	2	1	2	0
KIAA0664 WILD-TYPE	75	63	50	81	14

'KIAA0664 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.52 (Fisher's exact test), Q value = 1

Table S377. Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	65	58	87
KIAA0664 MUTATED	0	2	1	2
KIAA0664 WILD-TYPE	78	63	57	85

'KIAA0664 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S378. Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	83	57	117	32
KIAA0664 MUTATED	0	2	3	0
KIAA0664 WILD-TYPE	83	55	114	32

'KIAA0664 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S379. Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	45	89	57
KIAA0664 MUTATED	0	0	3	2
KIAA0664 WILD-TYPE	98	45	86	55

'KIAA0664 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 1

Table S380. Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	67	60	27	84	34	6	11
KIAA0664 MUTATED	0	1	1	2	1	0	0
KIAA0664 WILD-TYPE	67	59	26	82	33	6	11

'KIAA0664 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S381. Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	67	69	55
KIAA0664 MUTATED	0	1	2	2
KIAA0664 WILD-TYPE	98	66	67	53

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = LGG-TP.transferedmergedcluster.txt
Number of patients = 289
Number of significantly mutated genes = 37
Number of Molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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