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 63 genes and 10 molecular subtypes across 147 patients, 42 significant findings detected with P value < 0.05 and Q value < 0.25.

KIT mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
KRAS mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
CSGALNACT2 mutation correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
NRAS mutation correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
SP8 mutation correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
SPTAN1 mutation correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
AHDC1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', '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 63 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 42 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
KIT	26 (18%)	121	0.0017 (0.063)	0.00012 (0.0054)	1e-05 (0.000573)	1e-05 (0.000573)	1e-05 (0.000573)	1e-05 (0.000573)	1e-05 (0.000573)	1e-05 (0.000573)	1e-05 (0.000573)	1e-05 (0.000573)
KRAS	19 (13%)	128	0.00631 (0.166)	0.00032 (0.0126)	0.00308 (0.102)	0.00019 (0.00798)	1e-05 (0.000573)	0.00181 (0.0633)	2e-05 (0.000969)	1e-05 (0.000573)	1e-05 (0.000573)	2e-05 (0.000969)
SPTAN1	4 (3%)	143	0.0384 (0.397)	0.323 (1.00)			0.00444 (0.133)	0.0095 (0.194)	0.00486 (0.136)	0.00939 (0.194)	0.0106 (0.202)	0.0146 (0.236)
AHDC1	4 (3%)	143	0.56 (1.00)	0.00792 (0.192)	0.0619 (0.527)	0.108 (0.689)	0.00412 (0.13)	0.0268 (0.315)	0.00496 (0.136)	0.00955 (0.194)	0.0102 (0.202)	0.0143 (0.236)
CSGALNACT2	5 (3%)	142	0.013 (0.227)	0.194 (0.925)	0.00875 (0.194)	0.0229 (0.304)	0.00865 (0.194)	0.0115 (0.213)	0.0309 (0.341)	0.0162 (0.249)	0.0247 (0.305)	0.0779 (0.613)
NRAS	7 (5%)	140	0.0504 (0.475)	0.0798 (0.621)	0.0973 (0.652)	0.275 (1.00)	0.0166 (0.249)	0.145 (0.814)	0.013 (0.227)	0.0179 (0.258)	0.0691 (0.558)	0.0133 (0.227)
SP8	6 (4%)	141	0.0897 (0.643)	0.517 (1.00)	0.0308 (0.341)	0.0237 (0.304)	0.0157 (0.247)	0.00676 (0.17)	0.0481 (0.475)	0.0214 (0.293)	0.0241 (0.304)	0.0839 (0.633)
ANKLE1	12 (8%)	135	0.154 (0.828)	0.287 (1.00)	0.869 (1.00)	0.363 (1.00)	0.637 (1.00)	0.876 (1.00)	1 (1.00)	0.74 (1.00)	0.739 (1.00)	0.421 (1.00)
FAM104B	7 (5%)	140	0.377 (1.00)	0.502 (1.00)	0.382 (1.00)	0.617 (1.00)	0.353 (1.00)	0.264 (1.00)	0.0973 (0.652)	0.25 (1.00)	0.54 (1.00)	0.545 (1.00)
DDX11	8 (5%)	139	1 (1.00)	0.279 (1.00)	0.279 (1.00)	0.145 (0.814)	0.408 (1.00)	0.363 (1.00)	0.132 (0.791)	0.291 (1.00)	0.652 (1.00)	0.101 (0.67)
PNPLA4	5 (3%)	142	0.521 (1.00)	1 (1.00)	0.378 (1.00)	0.616 (1.00)	0.522 (1.00)	0.553 (1.00)	0.374 (1.00)	0.449 (1.00)	0.318 (1.00)	0.476 (1.00)
SERINC2	4 (3%)	143	0.462 (1.00)	0.834 (1.00)	0.139 (0.807)	0.103 (0.67)	0.811 (1.00)	0.738 (1.00)	1 (1.00)	0.585 (1.00)	0.812 (1.00)	0.843 (1.00)
RBM10	5 (3%)	142	0.621 (1.00)	0.277 (1.00)	0.92 (1.00)	0.724 (1.00)	0.45 (1.00)	0.709 (1.00)	0.634 (1.00)	0.598 (1.00)	0.604 (1.00)	0.555 (1.00)
DEK	5 (3%)	142	0.0359 (0.384)	0.865 (1.00)	0.622 (1.00)	0.275 (1.00)	0.381 (1.00)	0.0184 (0.258)	0.376 (1.00)	0.319 (1.00)	0.441 (1.00)	0.157 (0.84)
ERC1	7 (5%)	140	0.886 (1.00)	0.796 (1.00)	0.607 (1.00)	0.865 (1.00)	1 (1.00)	0.561 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.954 (1.00)
HSF4	6 (4%)	141	0.247 (1.00)	0.217 (0.978)	0.392 (1.00)	1 (1.00)	0.423 (1.00)	0.142 (0.814)	0.202 (0.934)	0.369 (1.00)	0.276 (1.00)	0.284 (1.00)
MUC6	15 (10%)	132	0.695 (1.00)	0.622 (1.00)	0.351 (1.00)	0.0894 (0.643)	0.834 (1.00)	0.966 (1.00)	1 (1.00)	0.735 (1.00)	0.775 (1.00)	0.917 (1.00)
FANK1	4 (3%)	143	0.386 (1.00)	0.835 (1.00)	0.176 (0.909)	0.601 (1.00)	0.378 (1.00)	0.709 (1.00)	0.455 (1.00)	0.278 (1.00)	0.271 (1.00)	0.191 (0.925)
MLLT3	4 (3%)	143	0.559 (1.00)	0.833 (1.00)			0.81 (1.00)	0.283 (1.00)	1 (1.00)	0.587 (1.00)	0.464 (1.00)	0.842 (1.00)
RHPN2	6 (4%)	141	0.878 (1.00)	0.247 (1.00)	1 (1.00)	1 (1.00)	0.88 (1.00)	0.921 (1.00)	0.577 (1.00)	1 (1.00)	1 (1.00)	0.853 (1.00)
KRTAP1-1	3 (2%)	144	1 (1.00)	0.774 (1.00)			0.794 (1.00)	0.475 (1.00)	0.779 (1.00)	0.614 (1.00)	0.61 (1.00)	0.704 (1.00)
ANKRD11	7 (5%)	140	0.887 (1.00)	0.0817 (0.628)	0.777 (1.00)	0.571 (1.00)	0.257 (1.00)	0.851 (1.00)	0.335 (1.00)	0.286 (1.00)	0.277 (1.00)	0.379 (1.00)
SPIN2A	3 (2%)	144	0.631 (1.00)	1 (1.00)			1 (1.00)	0.373 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.892 (1.00)
ATXN3	3 (2%)	144	0.779 (1.00)	0.3 (1.00)	0.217 (0.978)	0.0547 (0.5)	0.154 (0.828)	0.18 (0.916)	0.489 (1.00)	0.0932 (0.643)	0.0931 (0.643)	0.502 (1.00)
MEF2A	3 (2%)	144	1 (1.00)	1 (1.00)			1 (1.00)	0.33 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.892 (1.00)
SSBP3	3 (2%)	144	0.778 (1.00)	0.298 (1.00)			0.154 (0.828)	0.0582 (0.509)	0.489 (1.00)	0.0939 (0.643)	0.0927 (0.643)	0.503 (1.00)
KRTAP10-10	5 (3%)	142	1 (1.00)	0.626 (1.00)	0.731 (1.00)	0.535 (1.00)	0.451 (1.00)	0.87 (1.00)	0.185 (0.925)	0.598 (1.00)	0.602 (1.00)	0.617 (1.00)
BCL11B	5 (3%)	142	0.519 (1.00)	0.277 (1.00)	0.653 (1.00)	0.534 (1.00)	0.323 (1.00)	0.936 (1.00)	0.527 (1.00)	0.382 (1.00)	0.441 (1.00)	0.423 (1.00)
FAM101B	4 (3%)	143	1 (1.00)	0.69 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.501 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
PSMD11	4 (3%)	143	0.0678 (0.555)	0.0368 (0.386)	0.44 (1.00)	0.229 (1.00)	0.193 (0.925)	0.753 (1.00)	0.315 (1.00)	0.195 (0.925)	0.367 (1.00)	0.134 (0.798)
FAM8A1	3 (2%)	144	0.497 (1.00)	0.108 (0.689)			0.248 (1.00)	0.518 (1.00)	0.0597 (0.516)	0.342 (1.00)	0.332 (1.00)	0.0241 (0.304)
CRB2	6 (4%)	141	0.579 (1.00)	0.594 (1.00)	0.778 (1.00)	0.574 (1.00)	0.661 (1.00)	0.439 (1.00)	0.449 (1.00)	0.659 (1.00)	0.659 (1.00)	0.0648 (0.545)
OPLAH	4 (3%)	143	0.824 (1.00)	0.549 (1.00)	0.528 (1.00)	1 (1.00)	1 (1.00)	0.309 (1.00)	0.56 (1.00)	0.278 (1.00)	1 (1.00)	0.539 (1.00)
C22ORF43	3 (2%)	144	0.373 (1.00)	1 (1.00)	0.0563 (0.506)	1 (1.00)	1 (1.00)	0.735 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
GAS2L2	3 (2%)	144	1 (1.00)	0.201 (0.934)	0.855 (1.00)	0.601 (1.00)	1 (1.00)	0.421 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
CDC27	6 (4%)	141	0.0335 (0.364)	0.775 (1.00)	0.189 (0.925)	0.179 (0.916)	0.169 (0.89)	0.0574 (0.509)	0.33 (1.00)	0.138 (0.807)	0.169 (0.89)	0.0488 (0.475)
MUC2	16 (11%)	131	0.4 (1.00)	0.945 (1.00)	0.262 (1.00)	0.425 (1.00)	0.518 (1.00)	0.985 (1.00)	0.501 (1.00)	0.944 (1.00)	0.792 (1.00)	0.793 (1.00)
TPTE2	5 (3%)	142	0.622 (1.00)	0.232 (1.00)	1 (1.00)	1 (1.00)	0.318 (1.00)	0.636 (1.00)	0.0505 (0.475)	0.381 (1.00)	0.443 (1.00)	0.422 (1.00)
NAT10	4 (3%)	143	0.387 (1.00)	1 (1.00)	0.855 (1.00)	0.602 (1.00)	1 (1.00)	0.254 (1.00)	0.832 (1.00)	1 (1.00)	1 (1.00)	0.493 (1.00)
INTS4	3 (2%)	144	1 (1.00)	1 (1.00)			0.796 (1.00)	0.95 (1.00)	0.629 (1.00)	0.614 (1.00)	0.608 (1.00)	0.707 (1.00)
TTC38	4 (3%)	143	0.384 (1.00)	0.114 (0.709)	0.891 (1.00)	0.197 (0.926)	0.287 (1.00)	0.817 (1.00)	0.193 (0.925)	0.381 (1.00)	0.578 (1.00)	0.255 (1.00)
RBM3	3 (2%)	144	0.374 (1.00)	0.774 (1.00)			0.796 (1.00)	0.95 (1.00)	0.115 (0.709)	0.618 (1.00)	0.605 (1.00)	0.131 (0.791)
TCHH	5 (3%)	142	0.518 (1.00)	0.131 (0.791)	0.0734 (0.585)	0.533 (1.00)	0.379 (1.00)	0.909 (1.00)	0.372 (1.00)	0.322 (1.00)	0.209 (0.954)	0.331 (1.00)
ZC3H11A	3 (2%)	144	0.0526 (0.488)	0.774 (1.00)			0.618 (1.00)	0.471 (1.00)	0.373 (1.00)	0.796 (1.00)	0.794 (1.00)	0.397 (1.00)
RAC1	4 (3%)	143	0.384 (1.00)	0.388 (1.00)	0.62 (1.00)	1 (1.00)	0.59 (1.00)	0.634 (1.00)	0.316 (1.00)	0.481 (1.00)	0.366 (1.00)	0.0849 (0.633)
MTIF3	3 (2%)	144	1 (1.00)	0.402 (1.00)	1 (1.00)	1 (1.00)	0.621 (1.00)	1 (1.00)	0.373 (1.00)	0.797 (1.00)	0.793 (1.00)	0.797 (1.00)
MFF	3 (2%)	144	1 (1.00)	0.774 (1.00)	0.617 (1.00)	1 (1.00)	0.797 (1.00)	0.949 (1.00)	0.631 (1.00)	0.617 (1.00)	0.608 (1.00)	0.704 (1.00)
PABPC3	4 (3%)	143	1 (1.00)	0.464 (1.00)			0.284 (1.00)	0.609 (1.00)	0.192 (0.925)	0.38 (1.00)	0.576 (1.00)	0.305 (1.00)
CUX1	5 (3%)	142	0.731 (1.00)	0.863 (1.00)	0.856 (1.00)	0.602 (1.00)	0.722 (1.00)	0.962 (1.00)	0.635 (1.00)	0.855 (1.00)	0.858 (1.00)	0.72 (1.00)
PCMTD1	5 (3%)	142	0.0915 (0.643)	0.625 (1.00)	0.462 (1.00)	0.535 (1.00)	0.382 (1.00)	0.447 (1.00)	0.373 (1.00)	0.317 (1.00)	0.208 (0.954)	0.33 (1.00)
EZH2	4 (3%)	143	0.826 (1.00)	0.548 (1.00)			0.379 (1.00)	0.544 (1.00)	0.56 (1.00)	0.278 (1.00)	0.275 (1.00)	0.279 (1.00)
HTT	3 (2%)	144	1 (1.00)	0.774 (1.00)			0.795 (1.00)	0.682 (1.00)	0.628 (1.00)	0.618 (1.00)	0.606 (1.00)	0.705 (1.00)
GSX2	4 (3%)	143	0.31 (1.00)	0.324 (1.00)	0.324 (1.00)	0.0273 (0.315)	0.698 (1.00)	0.243 (1.00)	0.0666 (0.552)	0.151 (0.828)	0.813 (1.00)	0.788 (1.00)
RFC3	3 (2%)	144	1 (1.00)	0.52 (1.00)	0.528 (1.00)	0.599 (1.00)	0.451 (1.00)	0.329 (1.00)	0.779 (1.00)	0.244 (1.00)	1 (1.00)	0.252 (1.00)
CHD4	4 (3%)	143	1 (1.00)	0.69 (1.00)	1 (1.00)	0.831 (1.00)	1 (1.00)	0.409 (1.00)	1 (1.00)	1 (1.00)	0.576 (1.00)	1 (1.00)
RUNX2	4 (3%)	143	1 (1.00)	0.686 (1.00)	0.856 (1.00)	0.601 (1.00)	1 (1.00)	1 (1.00)	0.832 (1.00)	1 (1.00)	1 (1.00)	0.495 (1.00)
SP4	4 (3%)	143	0.306 (1.00)	0.0184 (0.258)			0.0503 (0.475)	0.112 (0.703)	0.252 (1.00)	0.0274 (0.315)	0.0275 (0.315)	0.173 (0.9)
DIAPH1	3 (2%)	144	1 (1.00)	0.644 (1.00)			0.62 (1.00)	0.813 (1.00)	1 (1.00)	0.794 (1.00)	0.796 (1.00)	0.797 (1.00)
PLEC	10 (7%)	137	0.0498 (0.475)	0.272 (1.00)	0.379 (1.00)	0.148 (0.826)	0.639 (1.00)	0.195 (0.925)	0.425 (1.00)	0.698 (1.00)	0.336 (1.00)	0.0854 (0.633)
NHS	3 (2%)	144	0.78 (1.00)	0.773 (1.00)	0.318 (1.00)	1 (1.00)	0.794 (1.00)	0.772 (1.00)	0.627 (1.00)	0.618 (1.00)	0.608 (1.00)	0.705 (1.00)
PIK3CD	4 (3%)	143	0.24 (1.00)	0.265 (1.00)			0.483 (1.00)	0.369 (1.00)	0.14 (0.807)	0.699 (1.00)	0.69 (1.00)	0.102 (0.67)
EPAS1	5 (3%)	142	0.446 (1.00)	0.866 (1.00)	0.808 (1.00)	0.83 (1.00)	0.724 (1.00)	0.788 (1.00)	0.633 (1.00)	0.853 (1.00)	0.858 (1.00)	0.719 (1.00)
DLC1	3 (2%)	144	0.276 (1.00)	1 (1.00)	0.623 (1.00)	1 (1.00)	0.796 (1.00)	0.95 (1.00)	0.629 (1.00)	0.616 (1.00)	0.608 (1.00)	0.702 (1.00)

'KIT MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.063

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
KIT MUTATED	14	9	3
KIT WILD-TYPE	33	33	55

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

'KIT MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0054

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
KIT MUTATED	19	2	5
KIT WILD-TYPE	35	46	40

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

'KIT MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S3. Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
KIT MUTATED	19	2	1	0
KIT WILD-TYPE	28	12	33	21

Figure S3. Get High-res Image Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'KIT MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S4. Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
KIT MUTATED	20	1	1
KIT WILD-TYPE	29	23	42

Figure S4. Get High-res Image Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
KIT MUTATED	25	0	1
KIT WILD-TYPE	43	40	38

Figure S5. Get High-res Image Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KIT MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
KIT MUTATED	25	0	0	1	0	0	0
KIT WILD-TYPE	17	26	12	23	8	23	12

Figure S6. Get High-res Image Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S7. Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
KIT MUTATED	23	2	1
KIT WILD-TYPE	28	54	39

Figure S7. Get High-res Image Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KIT MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S8. Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
KIT MUTATED	25	0	1
KIT WILD-TYPE	43	38	40

Figure S8. Get High-res Image Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S9. Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
KIT MUTATED	25	0	1
KIT WILD-TYPE	42	36	43

Figure S9. Get High-res Image Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'KIT MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S10. Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
KIT MUTATED	21	4	0	1
KIT WILD-TYPE	15	28	38	40

Figure S10. Get High-res Image Gene #1: 'KIT MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00631 (Fisher's exact test), Q value = 0.17

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
KRAS MUTATED	7	10	2
KRAS WILD-TYPE	40	32	56

Figure S11. Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.013

Table S12. Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
KRAS MUTATED	13	0	6
KRAS WILD-TYPE	41	48	39

Figure S12. Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00308 (Fisher's exact test), Q value = 0.1

Table S13. Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
KRAS MUTATED	12	1	1	0
KRAS WILD-TYPE	35	13	33	21

Figure S13. Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.008

Table S14. Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
KRAS MUTATED	13	0	1
KRAS WILD-TYPE	36	24	42

Figure S14. Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S15. Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
KRAS MUTATED	18	0	1
KRAS WILD-TYPE	50	40	38

Figure S15. Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00181 (Fisher's exact test), Q value = 0.063

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
KRAS MUTATED	12	6	0	1	0	0	0
KRAS WILD-TYPE	30	20	12	23	8	23	12

Figure S16. Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00097

Table S17. Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
KRAS MUTATED	16	2	1
KRAS WILD-TYPE	35	54	39

Figure S17. Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S18. Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
KRAS MUTATED	18	0	1
KRAS WILD-TYPE	50	38	40

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

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S19. Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
KRAS MUTATED	18	0	1
KRAS WILD-TYPE	49	36	43

Figure S19. Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00097

Table S20. Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
KRAS MUTATED	9	9	0	1
KRAS WILD-TYPE	27	23	38	40

Figure S20. Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ANKLE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.83

Table S21. Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
ANKLE1 MUTATED	1	5	6
ANKLE1 WILD-TYPE	46	37	52

'ANKLE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S22. Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
ANKLE1 MUTATED	4	2	6
ANKLE1 WILD-TYPE	50	46	39

'ANKLE1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S23. Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
ANKLE1 MUTATED	4	0	3	1
ANKLE1 WILD-TYPE	43	14	31	20

'ANKLE1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
ANKLE1 MUTATED	4	0	4
ANKLE1 WILD-TYPE	45	24	39

'ANKLE1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.637 (Fisher's exact test), Q value = 1

Table S25. Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
ANKLE1 MUTATED	7	2	3
ANKLE1 WILD-TYPE	61	38	36

'ANKLE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S26. Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
ANKLE1 MUTATED	3	4	1	2	0	1	1
ANKLE1 WILD-TYPE	39	22	11	22	8	22	11

'ANKLE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S27. Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
ANKLE1 MUTATED	4	5	3
ANKLE1 WILD-TYPE	47	51	37

'ANKLE1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S28. Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
ANKLE1 MUTATED	7	2	3
ANKLE1 WILD-TYPE	61	36	38

'ANKLE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.739 (Fisher's exact test), Q value = 1

Table S29. Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
ANKLE1 MUTATED	7	2	3
ANKLE1 WILD-TYPE	60	34	41

'ANKLE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 1

Table S30. Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
ANKLE1 MUTATED	2	5	2	3
ANKLE1 WILD-TYPE	34	27	36	38

'FAM104B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
FAM104B MUTATED	3	3	1
FAM104B WILD-TYPE	44	39	57

'FAM104B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S32. Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
FAM104B MUTATED	4	1	2
FAM104B WILD-TYPE	50	47	43

'FAM104B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
FAM104B MUTATED	3	1	0	1
FAM104B WILD-TYPE	44	13	34	20

'FAM104B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S34. Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
FAM104B MUTATED	2	0	3
FAM104B WILD-TYPE	47	24	40

'FAM104B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 1

Table S35. Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
FAM104B MUTATED	5	2	0
FAM104B WILD-TYPE	63	38	39

'FAM104B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S36. Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
FAM104B MUTATED	5	0	1	0	0	1	0
FAM104B WILD-TYPE	37	26	11	24	8	22	12

'FAM104B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0973 (Fisher's exact test), Q value = 0.65

Table S37. Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
FAM104B MUTATED	5	2	0
FAM104B WILD-TYPE	46	54	40

'FAM104B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S38. Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
FAM104B MUTATED	5	2	0
FAM104B WILD-TYPE	63	36	41

'FAM104B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S39. Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
FAM104B MUTATED	5	1	1
FAM104B WILD-TYPE	62	35	43

'FAM104B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S40. Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
FAM104B MUTATED	2	3	1	1
FAM104B WILD-TYPE	34	29	37	40

'CSGALNACT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.23

Table S41. Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
CSGALNACT2 MUTATED	0	0	5
CSGALNACT2 WILD-TYPE	47	42	53

Figure S21. Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 0.92

Table S42. Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
CSGALNACT2 MUTATED	0	3	2
CSGALNACT2 WILD-TYPE	54	45	43

'CSGALNACT2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00875 (Fisher's exact test), Q value = 0.19

Table S43. Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
CSGALNACT2 MUTATED	0	0	5	0
CSGALNACT2 WILD-TYPE	47	14	29	21

Figure S22. Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.3

Table S44. Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
CSGALNACT2 MUTATED	0	3	2
CSGALNACT2 WILD-TYPE	49	21	41

Figure S23. Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00865 (Fisher's exact test), Q value = 0.19

Table S45. Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
CSGALNACT2 MUTATED	0	1	4
CSGALNACT2 WILD-TYPE	68	39	35

Figure S24. Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.21

Table S46. Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
CSGALNACT2 MUTATED	0	0	2	3	0	0	0
CSGALNACT2 WILD-TYPE	42	26	10	21	8	23	12

Figure S25. Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.34

Table S47. Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
CSGALNACT2 MUTATED	0	1	4
CSGALNACT2 WILD-TYPE	51	55	36

Figure S26. Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.25

Table S48. Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
CSGALNACT2 MUTATED	0	1	4
CSGALNACT2 WILD-TYPE	68	37	37

Figure S27. Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.3

Table S49. Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
CSGALNACT2 MUTATED	0	1	4
CSGALNACT2 WILD-TYPE	67	35	40

Figure S28. Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0779 (Fisher's exact test), Q value = 0.61

Table S50. Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
CSGALNACT2 MUTATED	0	0	1	4
CSGALNACT2 WILD-TYPE	36	32	37	37

'DDX11 MUTATION STATUS' versus 'CN_CNMF'

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

Table S51. Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
DDX11 MUTATED	3	2	3
DDX11 WILD-TYPE	44	40	55

'DDX11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 1

Table S52. Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
DDX11 MUTATED	1	4	3
DDX11 WILD-TYPE	53	44	42

'DDX11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 1

Table S53. Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
DDX11 MUTATED	2	1	1	3
DDX11 WILD-TYPE	45	13	33	18

'DDX11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.81

Table S54. Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
DDX11 MUTATED	2	0	5
DDX11 WILD-TYPE	47	24	38

'DDX11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 1

Table S55. Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
DDX11 MUTATED	3	4	1
DDX11 WILD-TYPE	65	36	38

'DDX11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 1

Table S56. Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
DDX11 MUTATED	1	2	1	0	1	2	1
DDX11 WILD-TYPE	41	24	11	24	7	21	11

'DDX11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.79

Table S57. Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
DDX11 MUTATED	1	6	1
DDX11 WILD-TYPE	50	50	39

'DDX11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S58. Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
DDX11 MUTATED	3	4	1
DDX11 WILD-TYPE	65	34	40

'DDX11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 1

Table S59. Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
DDX11 MUTATED	3	3	2
DDX11 WILD-TYPE	64	33	42

'DDX11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 0.67

Table S60. Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
DDX11 MUTATED	0	3	4	1
DDX11 WILD-TYPE	36	29	34	40

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0504 (Fisher's exact test), Q value = 0.48

Table S61. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
NRAS MUTATED	4	3	0
NRAS WILD-TYPE	43	39	58

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0798 (Fisher's exact test), Q value = 0.62

Table S62. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
NRAS MUTATED	5	0	2
NRAS WILD-TYPE	49	48	43

'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0973 (Fisher's exact test), Q value = 0.65

Table S63. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
NRAS MUTATED	5	0	0	0
NRAS WILD-TYPE	42	14	34	21

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 1

Table S64. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
NRAS MUTATED	4	0	1
NRAS WILD-TYPE	45	24	42

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.25

Table S65. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
NRAS MUTATED	7	0	0
NRAS WILD-TYPE	61	40	39

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

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.81

Table S66. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
NRAS MUTATED	6	1	0	0	0	0	0
NRAS WILD-TYPE	36	25	12	24	8	23	12

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.23

Table S67. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
NRAS MUTATED	6	1	0
NRAS WILD-TYPE	45	55	40

Figure S30. Get High-res Image Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.26

Table S68. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
NRAS MUTATED	7	0	0
NRAS WILD-TYPE	61	38	41

Figure S31. Get High-res Image Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0691 (Fisher's exact test), Q value = 0.56

Table S69. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
NRAS MUTATED	6	1	0
NRAS WILD-TYPE	61	35	44

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.23

Table S70. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
NRAS MUTATED	4	3	0	0
NRAS WILD-TYPE	32	29	38	41

Figure S32. Get High-res Image Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PNPLA4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.521 (Fisher's exact test), Q value = 1

Table S71. Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
PNPLA4 MUTATED	3	1	1
PNPLA4 WILD-TYPE	44	41	57

'PNPLA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S72. Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
PNPLA4 MUTATED	2	2	1
PNPLA4 WILD-TYPE	52	46	44

'PNPLA4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S73. Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
PNPLA4 MUTATED	3	1	0	1
PNPLA4 WILD-TYPE	44	13	34	20

'PNPLA4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S74. Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
PNPLA4 MUTATED	2	0	3
PNPLA4 WILD-TYPE	47	24	40

'PNPLA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 1

Table S75. Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
PNPLA4 MUTATED	3	2	0
PNPLA4 WILD-TYPE	65	38	39

'PNPLA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S76. Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
PNPLA4 MUTATED	3	0	1	0	0	1	0
PNPLA4 WILD-TYPE	39	26	11	24	8	22	12

'PNPLA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S77. Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
PNPLA4 MUTATED	3	2	0
PNPLA4 WILD-TYPE	48	54	40

'PNPLA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S78. Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
PNPLA4 MUTATED	3	2	0
PNPLA4 WILD-TYPE	65	36	41

'PNPLA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S79. Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
PNPLA4 MUTATED	3	2	0
PNPLA4 WILD-TYPE	64	34	44

'PNPLA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S80. Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
PNPLA4 MUTATED	2	1	2	0
PNPLA4 WILD-TYPE	34	31	36	41

'SERINC2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S81. Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
SERINC2 MUTATED	1	0	3
SERINC2 WILD-TYPE	46	42	55

'SERINC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S82. Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
SERINC2 MUTATED	1	2	1
SERINC2 WILD-TYPE	53	46	44

'SERINC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.81

Table S83. Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
SERINC2 MUTATED	0	1	2	0
SERINC2 WILD-TYPE	47	13	32	21

'SERINC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.67

Table S84. Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
SERINC2 MUTATED	0	0	3
SERINC2 WILD-TYPE	49	24	40

'SERINC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.811 (Fisher's exact test), Q value = 1

Table S85. Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
SERINC2 MUTATED	1	2	1
SERINC2 WILD-TYPE	67	38	38

'SERINC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.738 (Fisher's exact test), Q value = 1

Table S86. Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
SERINC2 MUTATED	1	0	1	1	0	1	0
SERINC2 WILD-TYPE	41	26	11	23	8	22	12

'SERINC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S87. Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
SERINC2 MUTATED	1	2	1
SERINC2 WILD-TYPE	50	54	39

'SERINC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 1

Table S88. Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
SERINC2 MUTATED	1	2	1
SERINC2 WILD-TYPE	67	36	40

'SERINC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.812 (Fisher's exact test), Q value = 1

Table S89. Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
SERINC2 MUTATED	1	1	2
SERINC2 WILD-TYPE	66	35	42

'SERINC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S90. Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
SERINC2 MUTATED	1	0	2	1
SERINC2 WILD-TYPE	35	32	36	40

'RBM10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S91. Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
RBM10 MUTATED	2	2	1
RBM10 WILD-TYPE	45	40	57

'RBM10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S92. Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
RBM10 MUTATED	3	0	2
RBM10 WILD-TYPE	51	48	43

'RBM10 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S93. Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
RBM10 MUTATED	3	0	1	1
RBM10 WILD-TYPE	44	14	33	20

'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S94. Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
RBM10 MUTATED	3	0	2
RBM10 WILD-TYPE	46	24	41

'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 1

Table S95. Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
RBM10 MUTATED	3	0	2
RBM10 WILD-TYPE	65	40	37

'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S96. Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
RBM10 MUTATED	1	2	0	1	0	0	1
RBM10 WILD-TYPE	41	24	12	23	8	23	11

'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S97. Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
RBM10 MUTATED	2	1	2
RBM10 WILD-TYPE	49	55	38

'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S98. Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
RBM10 MUTATED	3	0	2
RBM10 WILD-TYPE	65	38	39

'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S99. Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
RBM10 MUTATED	3	0	2
RBM10 WILD-TYPE	64	36	42

'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S100. Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
RBM10 MUTATED	1	2	0	2
RBM10 WILD-TYPE	35	30	38	39

'DEK MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.38

Table S101. Gene #11: 'DEK MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
DEK MUTATED	0	4	1
DEK WILD-TYPE	47	38	57

Figure S33. Get High-res Image Gene #11: 'DEK MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'DEK MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.865 (Fisher's exact test), Q value = 1

Table S102. Gene #11: 'DEK MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
DEK MUTATED	2	1	2
DEK WILD-TYPE	52	47	43

'DEK MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S103. Gene #11: 'DEK MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
DEK MUTATED	3	1	1	0
DEK WILD-TYPE	44	13	33	21

'DEK MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 1

Table S104. Gene #11: 'DEK MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
DEK MUTATED	4	0	1
DEK WILD-TYPE	45	24	42

'DEK MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S105. Gene #11: 'DEK MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
DEK MUTATED	4	1	0
DEK WILD-TYPE	64	39	39

'DEK MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.26

Table S106. Gene #11: 'DEK MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
DEK MUTATED	0	4	1	0	0	0	0
DEK WILD-TYPE	42	22	11	24	8	23	12

Figure S34. Get High-res Image Gene #11: 'DEK MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'DEK MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S107. Gene #11: 'DEK MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
DEK MUTATED	3	2	0
DEK WILD-TYPE	48	54	40

'DEK MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 1

Table S108. Gene #11: 'DEK MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
DEK MUTATED	4	1	0
DEK WILD-TYPE	64	37	41

'DEK MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S109. Gene #11: 'DEK MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
DEK MUTATED	4	0	1
DEK WILD-TYPE	63	36	43

'DEK MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 0.84

Table S110. Gene #11: 'DEK MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
DEK MUTATED	1	3	1	0
DEK WILD-TYPE	35	29	37	41

'ERC1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S111. Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
ERC1 MUTATED	3	2	2
ERC1 WILD-TYPE	44	40	56

'ERC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S112. Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
ERC1 MUTATED	2	2	3
ERC1 WILD-TYPE	52	46	42

'ERC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.607 (Fisher's exact test), Q value = 1

Table S113. Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
ERC1 MUTATED	2	1	1	2
ERC1 WILD-TYPE	45	13	33	19

'ERC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.865 (Fisher's exact test), Q value = 1

Table S114. Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
ERC1 MUTATED	2	1	3
ERC1 WILD-TYPE	47	23	40

'ERC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S115. Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
ERC1 MUTATED	3	2	2
ERC1 WILD-TYPE	65	38	37

'ERC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.561 (Fisher's exact test), Q value = 1

Table S116. Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
ERC1 MUTATED	3	0	0	1	1	1	1
ERC1 WILD-TYPE	39	26	12	23	7	22	11

'ERC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S117. Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
ERC1 MUTATED	2	3	2
ERC1 WILD-TYPE	49	53	38

'ERC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S118. Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
ERC1 MUTATED	3	2	2
ERC1 WILD-TYPE	65	36	39

'ERC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S119. Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
ERC1 MUTATED	3	2	2
ERC1 WILD-TYPE	64	34	42

'ERC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S120. Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
ERC1 MUTATED	1	2	2	2
ERC1 WILD-TYPE	35	30	36	39

'HSF4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S121. Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
HSF4 MUTATED	4	1	1
HSF4 WILD-TYPE	43	41	57

'HSF4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 0.98

Table S122. Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
HSF4 MUTATED	4	2	0
HSF4 WILD-TYPE	50	46	45

'HSF4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S123. Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
HSF4 MUTATED	2	2	1	1
HSF4 WILD-TYPE	45	12	33	20

'HSF4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S124. Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
HSF4 MUTATED	3	1	2
HSF4 WILD-TYPE	46	23	41

'HSF4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S125. Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
HSF4 MUTATED	4	2	0
HSF4 WILD-TYPE	64	38	39

'HSF4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.142 (Fisher's exact test), Q value = 0.81

Table S126. Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
HSF4 MUTATED	4	0	1	0	1	0	0
HSF4 WILD-TYPE	38	26	11	24	7	23	12

'HSF4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.93

Table S127. Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
HSF4 MUTATED	4	2	0
HSF4 WILD-TYPE	47	54	40

'HSF4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S128. Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
HSF4 MUTATED	4	2	0
HSF4 WILD-TYPE	64	36	41

'HSF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 1

Table S129. Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
HSF4 MUTATED	4	2	0
HSF4 WILD-TYPE	63	34	44

'HSF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.284 (Fisher's exact test), Q value = 1

Table S130. Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
HSF4 MUTATED	3	1	2	0
HSF4 WILD-TYPE	33	31	36	41

'MUC6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.695 (Fisher's exact test), Q value = 1

Table S131. Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
MUC6 MUTATED	6	3	6
MUC6 WILD-TYPE	41	39	52

'MUC6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S132. Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
MUC6 MUTATED	4	5	6
MUC6 WILD-TYPE	50	43	39

'MUC6 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S133. Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
MUC6 MUTATED	4	0	3	4
MUC6 WILD-TYPE	43	14	31	17

'MUC6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0894 (Fisher's exact test), Q value = 0.64

Table S134. Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
MUC6 MUTATED	4	0	7
MUC6 WILD-TYPE	45	24	36

'MUC6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S135. Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
MUC6 MUTATED	6	5	4
MUC6 WILD-TYPE	62	35	35

'MUC6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S136. Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
MUC6 MUTATED	4	2	1	2	1	3	2
MUC6 WILD-TYPE	38	24	11	22	7	20	10

'MUC6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S137. Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
MUC6 MUTATED	5	6	4
MUC6 WILD-TYPE	46	50	36

'MUC6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S138. Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
MUC6 MUTATED	6	5	4
MUC6 WILD-TYPE	62	33	37

'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S139. Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
MUC6 MUTATED	6	5	4
MUC6 WILD-TYPE	61	31	40

'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.917 (Fisher's exact test), Q value = 1

Table S140. Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
MUC6 MUTATED	3	3	5	4
MUC6 WILD-TYPE	33	29	33	37

'FANK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 1

Table S141. Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
FANK1 MUTATED	0	2	2
FANK1 WILD-TYPE	47	40	56

'FANK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S142. Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
FANK1 MUTATED	1	2	1
FANK1 WILD-TYPE	53	46	44

'FANK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 0.91

Table S143. Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
FANK1 MUTATED	1	0	0	2
FANK1 WILD-TYPE	46	14	34	19

'FANK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S144. Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
FANK1 MUTATED	1	0	2
FANK1 WILD-TYPE	48	24	41

'FANK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S145. Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
FANK1 MUTATED	2	2	0
FANK1 WILD-TYPE	66	38	39

'FANK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S146. Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
FANK1 MUTATED	1	1	0	0	0	2	0
FANK1 WILD-TYPE	41	25	12	24	8	21	12

'FANK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S147. Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
FANK1 MUTATED	1	3	0
FANK1 WILD-TYPE	50	53	40

'FANK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 1

Table S148. Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
FANK1 MUTATED	2	2	0
FANK1 WILD-TYPE	66	36	41

'FANK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S149. Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
FANK1 MUTATED	2	2	0
FANK1 WILD-TYPE	65	34	44

'FANK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.92

Table S150. Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
FANK1 MUTATED	0	2	2	0
FANK1 WILD-TYPE	36	30	36	41

'MLLT3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S151. Gene #16: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
MLLT3 MUTATED	2	0	2
MLLT3 WILD-TYPE	45	42	56

'MLLT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S152. Gene #16: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
MLLT3 MUTATED	1	2	1
MLLT3 WILD-TYPE	53	46	44

'MLLT3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.81 (Fisher's exact test), Q value = 1

Table S153. Gene #16: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
MLLT3 MUTATED	1	2	1
MLLT3 WILD-TYPE	67	38	38

'MLLT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S154. Gene #16: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
MLLT3 MUTATED	1	0	0	0	1	1	1
MLLT3 WILD-TYPE	41	26	12	24	7	22	11

'MLLT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S155. Gene #16: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
MLLT3 MUTATED	1	2	1
MLLT3 WILD-TYPE	50	54	39

'MLLT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S156. Gene #16: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
MLLT3 MUTATED	1	2	1
MLLT3 WILD-TYPE	67	36	40

'MLLT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S157. Gene #16: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
MLLT3 MUTATED	1	2	1
MLLT3 WILD-TYPE	66	34	43

'MLLT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.842 (Fisher's exact test), Q value = 1

Table S158. Gene #16: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
MLLT3 MUTATED	1	0	2	1
MLLT3 WILD-TYPE	35	32	36	40

'RHPN2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S159. Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
RHPN2 MUTATED	2	1	3
RHPN2 WILD-TYPE	45	41	55

'RHPN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S160. Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
RHPN2 MUTATED	1	1	4
RHPN2 WILD-TYPE	53	47	41

'RHPN2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S161. Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
RHPN2 MUTATED	3	0	2	1
RHPN2 WILD-TYPE	44	14	32	20

'RHPN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S162. Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
RHPN2 MUTATED	3	1	2
RHPN2 WILD-TYPE	46	23	41

'RHPN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S163. Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
RHPN2 MUTATED	3	1	2
RHPN2 WILD-TYPE	65	39	37

'RHPN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.921 (Fisher's exact test), Q value = 1

Table S164. Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
RHPN2 MUTATED	1	2	0	1	0	1	1
RHPN2 WILD-TYPE	41	24	12	23	8	22	11

'RHPN2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.577 (Fisher's exact test), Q value = 1

Table S165. Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
RHPN2 MUTATED	3	1	2
RHPN2 WILD-TYPE	48	55	38

'RHPN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S166. Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
RHPN2 MUTATED	3	1	2
RHPN2 WILD-TYPE	65	37	39

'RHPN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S167. Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
RHPN2 MUTATED	3	1	2
RHPN2 WILD-TYPE	64	35	42

'RHPN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.853 (Fisher's exact test), Q value = 1

Table S168. Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
RHPN2 MUTATED	1	2	1	2
RHPN2 WILD-TYPE	35	30	37	39

'SP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0897 (Fisher's exact test), Q value = 0.64

Table S169. Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
SP8 MUTATED	0	1	5
SP8 WILD-TYPE	47	41	53

'SP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 1

Table S170. Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
SP8 MUTATED	1	3	2
SP8 WILD-TYPE	53	45	43

'SP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.34

Table S171. Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
SP8 MUTATED	0	1	4	0
SP8 WILD-TYPE	47	13	30	21

Figure S35. Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'SP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.3

Table S172. Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
SP8 MUTATED	0	3	2
SP8 WILD-TYPE	49	21	41

Figure S36. Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'SP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.25

Table S173. Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
SP8 MUTATED	0	2	4
SP8 WILD-TYPE	68	38	35

Figure S37. Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00676 (Fisher's exact test), Q value = 0.17

Table S174. Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
SP8 MUTATED	0	0	1	4	1	0	0
SP8 WILD-TYPE	42	26	11	20	7	23	12

Figure S38. Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.48

Table S175. Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
SP8 MUTATED	0	2	4
SP8 WILD-TYPE	51	54	36

Figure S39. Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.29

Table S176. Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
SP8 MUTATED	0	2	4
SP8 WILD-TYPE	68	36	37

Figure S40. Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.3

Table S177. Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
SP8 MUTATED	0	2	4
SP8 WILD-TYPE	67	34	40

Figure S41. Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0839 (Fisher's exact test), Q value = 0.63

Table S178. Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
SP8 MUTATED	0	0	2	4
SP8 WILD-TYPE	36	32	36	37

'KRTAP1-1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S179. Gene #19: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
KRTAP1-1 MUTATED	1	1	1
KRTAP1-1 WILD-TYPE	46	41	57

'KRTAP1-1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S180. Gene #19: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
KRTAP1-1 MUTATED	2	1	0
KRTAP1-1 WILD-TYPE	52	47	45

'KRTAP1-1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S181. Gene #19: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
KRTAP1-1 MUTATED	2	1	0
KRTAP1-1 WILD-TYPE	66	39	39

'KRTAP1-1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S182. Gene #19: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
KRTAP1-1 MUTATED	2	0	1	0	0	0	0
KRTAP1-1 WILD-TYPE	40	26	11	24	8	23	12

'KRTAP1-1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S183. Gene #19: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
KRTAP1-1 MUTATED	1	2	0
KRTAP1-1 WILD-TYPE	50	54	40

'KRTAP1-1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.614 (Fisher's exact test), Q value = 1

Table S184. Gene #19: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
KRTAP1-1 MUTATED	2	1	0
KRTAP1-1 WILD-TYPE	66	37	41

'KRTAP1-1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.61 (Fisher's exact test), Q value = 1

Table S185. Gene #19: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
KRTAP1-1 MUTATED	2	1	0
KRTAP1-1 WILD-TYPE	65	35	44

'KRTAP1-1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.704 (Fisher's exact test), Q value = 1

Table S186. Gene #19: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
KRTAP1-1 MUTATED	1	1	1	0
KRTAP1-1 WILD-TYPE	35	31	37	41

'ANKRD11 MUTATION STATUS' versus 'CN_CNMF'

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

Table S187. Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
ANKRD11 MUTATED	3	2	2
ANKRD11 WILD-TYPE	44	40	56

'ANKRD11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0817 (Fisher's exact test), Q value = 0.63

Table S188. Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
ANKRD11 MUTATED	5	0	2
ANKRD11 WILD-TYPE	49	48	43

'ANKRD11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S189. Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
ANKRD11 MUTATED	3	1	2	0
ANKRD11 WILD-TYPE	44	13	32	21

'ANKRD11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S190. Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
ANKRD11 MUTATED	4	1	1
ANKRD11 WILD-TYPE	45	23	42

'ANKRD11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S191. Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
ANKRD11 MUTATED	5	0	2
ANKRD11 WILD-TYPE	63	40	37

'ANKRD11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S192. Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
ANKRD11 MUTATED	3	2	0	1	0	0	1
ANKRD11 WILD-TYPE	39	24	12	23	8	23	11

'ANKRD11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S193. Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
ANKRD11 MUTATED	4	1	2
ANKRD11 WILD-TYPE	47	55	38

'ANKRD11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 1

Table S194. Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
ANKRD11 MUTATED	5	0	2
ANKRD11 WILD-TYPE	63	38	39

'ANKRD11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S195. Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
ANKRD11 MUTATED	5	0	2
ANKRD11 WILD-TYPE	62	36	42

'ANKRD11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S196. Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
ANKRD11 MUTATED	3	2	0	2
ANKRD11 WILD-TYPE	33	30	38	39

'SPIN2A MUTATION STATUS' versus 'CN_CNMF'

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

Table S197. Gene #21: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
SPIN2A MUTATED	0	1	2
SPIN2A WILD-TYPE	47	41	56

'SPIN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S198. Gene #21: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
SPIN2A MUTATED	1	1	1
SPIN2A WILD-TYPE	53	47	44

'SPIN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S199. Gene #21: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
SPIN2A MUTATED	1	1	1
SPIN2A WILD-TYPE	67	39	38

'SPIN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S200. Gene #21: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
SPIN2A MUTATED	0	1	1	1	0	0	0
SPIN2A WILD-TYPE	42	25	11	23	8	23	12

'SPIN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S201. Gene #21: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
SPIN2A MUTATED	1	1	1
SPIN2A WILD-TYPE	50	55	39

'SPIN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S202. Gene #21: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
SPIN2A MUTATED	1	1	1
SPIN2A WILD-TYPE	67	37	40

'SPIN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S203. Gene #21: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
SPIN2A MUTATED	1	1	1
SPIN2A WILD-TYPE	66	35	43

'SPIN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S204. Gene #21: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
SPIN2A MUTATED	0	1	1	1
SPIN2A WILD-TYPE	36	31	37	40

'ATXN3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S205. Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
ATXN3 MUTATED	1	0	2
ATXN3 WILD-TYPE	46	42	56

'ATXN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S206. Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
ATXN3 MUTATED	0	2	1
ATXN3 WILD-TYPE	54	46	44

'ATXN3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 0.98

Table S207. Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
ATXN3 MUTATED	0	1	1	1
ATXN3 WILD-TYPE	47	13	33	20

'ATXN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0547 (Fisher's exact test), Q value = 0.5

Table S208. Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
ATXN3 MUTATED	0	2	1
ATXN3 WILD-TYPE	49	22	42

'ATXN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.83

Table S209. Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
ATXN3 MUTATED	0	2	1
ATXN3 WILD-TYPE	68	38	38

'ATXN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 0.92

Table S210. Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
ATXN3 MUTATED	0	0	0	1	1	1	0
ATXN3 WILD-TYPE	42	26	12	23	7	22	12

'ATXN3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S211. Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
ATXN3 MUTATED	0	2	1
ATXN3 WILD-TYPE	51	54	39

'ATXN3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0932 (Fisher's exact test), Q value = 0.64

Table S212. Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
ATXN3 MUTATED	0	2	1
ATXN3 WILD-TYPE	68	36	40

'ATXN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0931 (Fisher's exact test), Q value = 0.64

Table S213. Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
ATXN3 MUTATED	0	2	1
ATXN3 WILD-TYPE	67	34	43

'ATXN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S214. Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
ATXN3 MUTATED	0	0	2	1
ATXN3 WILD-TYPE	36	32	36	40

'MEF2A MUTATION STATUS' versus 'CN_CNMF'

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

Table S215. Gene #23: 'MEF2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
MEF2A MUTATED	1	1	1
MEF2A WILD-TYPE	46	41	57

'MEF2A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S216. Gene #23: 'MEF2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
MEF2A MUTATED	1	1	1
MEF2A WILD-TYPE	53	47	44

'MEF2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S217. Gene #23: 'MEF2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
MEF2A MUTATED	1	1	1
MEF2A WILD-TYPE	67	39	38

'MEF2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S218. Gene #23: 'MEF2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
MEF2A MUTATED	0	1	1	0	0	1	0
MEF2A WILD-TYPE	42	25	11	24	8	22	12

'MEF2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S219. Gene #23: 'MEF2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
MEF2A MUTATED	1	1	1
MEF2A WILD-TYPE	50	55	39

'MEF2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S220. Gene #23: 'MEF2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
MEF2A MUTATED	1	1	1
MEF2A WILD-TYPE	67	37	40

'MEF2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S221. Gene #23: 'MEF2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
MEF2A MUTATED	1	1	1
MEF2A WILD-TYPE	66	35	43

'MEF2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S222. Gene #23: 'MEF2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
MEF2A MUTATED	0	1	1	1
MEF2A WILD-TYPE	36	31	37	40

'SSBP3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S223. Gene #24: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
SSBP3 MUTATED	1	0	2
SSBP3 WILD-TYPE	46	42	56

'SSBP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S224. Gene #24: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
SSBP3 MUTATED	0	2	1
SSBP3 WILD-TYPE	54	46	44

'SSBP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.83

Table S225. Gene #24: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
SSBP3 MUTATED	0	2	1
SSBP3 WILD-TYPE	68	38	38

'SSBP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0582 (Fisher's exact test), Q value = 0.51

Table S226. Gene #24: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
SSBP3 MUTATED	0	0	0	0	1	1	1
SSBP3 WILD-TYPE	42	26	12	24	7	22	11

'SSBP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S227. Gene #24: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
SSBP3 MUTATED	0	2	1
SSBP3 WILD-TYPE	51	54	39

'SSBP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0939 (Fisher's exact test), Q value = 0.64

Table S228. Gene #24: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
SSBP3 MUTATED	0	2	1
SSBP3 WILD-TYPE	68	36	40

'SSBP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0927 (Fisher's exact test), Q value = 0.64

Table S229. Gene #24: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
SSBP3 MUTATED	0	2	1
SSBP3 WILD-TYPE	67	34	43

'SSBP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.503 (Fisher's exact test), Q value = 1

Table S230. Gene #24: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
SSBP3 MUTATED	0	0	2	1
SSBP3 WILD-TYPE	36	32	36	40

'KRTAP10-10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S231. Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
KRTAP10-10 MUTATED	2	1	2
KRTAP10-10 WILD-TYPE	45	41	56

'KRTAP10-10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S232. Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
KRTAP10-10 MUTATED	3	1	1
KRTAP10-10 WILD-TYPE	51	47	44

'KRTAP10-10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.731 (Fisher's exact test), Q value = 1

Table S233. Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
KRTAP10-10 MUTATED	3	0	1	0
KRTAP10-10 WILD-TYPE	44	14	33	21

'KRTAP10-10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S234. Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
KRTAP10-10 MUTATED	3	0	1
KRTAP10-10 WILD-TYPE	46	24	42

'KRTAP10-10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S235. Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
KRTAP10-10 MUTATED	3	0	2
KRTAP10-10 WILD-TYPE	65	40	37

'KRTAP10-10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S236. Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
KRTAP10-10 MUTATED	2	1	0	1	0	0	1
KRTAP10-10 WILD-TYPE	40	25	12	23	8	23	11

'KRTAP10-10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.92

Table S237. Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
KRTAP10-10 MUTATED	3	0	2
KRTAP10-10 WILD-TYPE	48	56	38

'KRTAP10-10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S238. Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
KRTAP10-10 MUTATED	3	0	2
KRTAP10-10 WILD-TYPE	65	38	39

'KRTAP10-10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S239. Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
KRTAP10-10 MUTATED	3	0	2
KRTAP10-10 WILD-TYPE	64	36	42

'KRTAP10-10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S240. Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
KRTAP10-10 MUTATED	2	1	0	2
KRTAP10-10 WILD-TYPE	34	31	38	39

'BCL11B MUTATION STATUS' versus 'CN_CNMF'

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

Table S241. Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
BCL11B MUTATED	3	1	1
BCL11B WILD-TYPE	44	41	57

'BCL11B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S242. Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
BCL11B MUTATED	3	0	2
BCL11B WILD-TYPE	51	48	43

'BCL11B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S243. Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
BCL11B MUTATED	2	1	1	0
BCL11B WILD-TYPE	45	13	33	21

'BCL11B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.534 (Fisher's exact test), Q value = 1

Table S244. Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
BCL11B MUTATED	3	0	1
BCL11B WILD-TYPE	46	24	42

'BCL11B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S245. Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
BCL11B MUTATED	4	0	1
BCL11B WILD-TYPE	64	40	38

'BCL11B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.936 (Fisher's exact test), Q value = 1

Table S246. Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
BCL11B MUTATED	3	1	0	1	0	0	0
BCL11B WILD-TYPE	39	25	12	23	8	23	12

'BCL11B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S247. Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
BCL11B MUTATED	3	1	1
BCL11B WILD-TYPE	48	55	39

'BCL11B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S248. Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
BCL11B MUTATED	4	0	1
BCL11B WILD-TYPE	64	38	40

'BCL11B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S249. Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
BCL11B MUTATED	4	0	1
BCL11B WILD-TYPE	63	36	43

'BCL11B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S250. Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
BCL11B MUTATED	2	2	0	1
BCL11B WILD-TYPE	34	30	38	40

'FAM101B MUTATION STATUS' versus 'CN_CNMF'

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

Table S251. Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
FAM101B MUTATED	1	1	2
FAM101B WILD-TYPE	46	41	56

'FAM101B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S252. Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
FAM101B MUTATED	1	1	2
FAM101B WILD-TYPE	53	47	43

'FAM101B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S253. Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
FAM101B MUTATED	2	0	1	0
FAM101B WILD-TYPE	45	14	33	21

'FAM101B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S254. Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
FAM101B MUTATED	2	0	1
FAM101B WILD-TYPE	47	24	42

'FAM101B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S255. Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
FAM101B MUTATED	2	1	1
FAM101B WILD-TYPE	66	39	38

'FAM101B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.501 (Fisher's exact test), Q value = 1

Table S256. Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
FAM101B MUTATED	0	2	0	1	0	1	0
FAM101B WILD-TYPE	42	24	12	23	8	22	12

'FAM101B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S257. Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
FAM101B MUTATED	1	2	1
FAM101B WILD-TYPE	50	54	39

'FAM101B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S258. Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
FAM101B MUTATED	2	1	1
FAM101B WILD-TYPE	66	37	40

'FAM101B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S259. Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
FAM101B MUTATED	2	1	1
FAM101B WILD-TYPE	65	35	43

'FAM101B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S260. Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
FAM101B MUTATED	1	1	1	1
FAM101B WILD-TYPE	35	31	37	40

'PSMD11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0678 (Fisher's exact test), Q value = 0.55

Table S261. Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
PSMD11 MUTATED	1	3	0
PSMD11 WILD-TYPE	46	39	58

'PSMD11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.39

Table S262. Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
PSMD11 MUTATED	4	0	0
PSMD11 WILD-TYPE	50	48	45

Figure S42. Get High-res Image Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PSMD11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 1

Table S263. Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
PSMD11 MUTATED	3	0	0	0
PSMD11 WILD-TYPE	44	14	34	21

'PSMD11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S264. Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
PSMD11 MUTATED	3	0	0
PSMD11 WILD-TYPE	46	24	43

'PSMD11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.193 (Fisher's exact test), Q value = 0.92

Table S265. Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
PSMD11 MUTATED	4	0	0
PSMD11 WILD-TYPE	64	40	39

'PSMD11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.753 (Fisher's exact test), Q value = 1

Table S266. Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
PSMD11 MUTATED	2	2	0	0	0	0	0
PSMD11 WILD-TYPE	40	24	12	24	8	23	12

'PSMD11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 1

Table S267. Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
PSMD11 MUTATED	3	1	0
PSMD11 WILD-TYPE	48	55	40

'PSMD11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.92

Table S268. Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
PSMD11 MUTATED	4	0	0
PSMD11 WILD-TYPE	64	38	41

'PSMD11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 1

Table S269. Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
PSMD11 MUTATED	3	1	0
PSMD11 WILD-TYPE	64	35	44

'PSMD11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.8

Table S270. Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
PSMD11 MUTATED	2	2	0	0
PSMD11 WILD-TYPE	34	30	38	41

'FAM8A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 1

Table S271. Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
FAM8A1 MUTATED	2	0	1
FAM8A1 WILD-TYPE	45	42	57

'FAM8A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 0.69

Table S272. Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
FAM8A1 MUTATED	3	0	0
FAM8A1 WILD-TYPE	51	48	45

'FAM8A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 1

Table S273. Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
FAM8A1 MUTATED	3	0	0
FAM8A1 WILD-TYPE	65	40	39

'FAM8A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S274. Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
FAM8A1 MUTATED	3	0	0	0	0	0	0
FAM8A1 WILD-TYPE	39	26	12	24	8	23	12

'FAM8A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0597 (Fisher's exact test), Q value = 0.52

Table S275. Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
FAM8A1 MUTATED	3	0	0
FAM8A1 WILD-TYPE	48	56	40

'FAM8A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.342 (Fisher's exact test), Q value = 1

Table S276. Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
FAM8A1 MUTATED	3	0	0
FAM8A1 WILD-TYPE	65	38	41

'FAM8A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 1

Table S277. Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
FAM8A1 MUTATED	3	0	0
FAM8A1 WILD-TYPE	64	36	44

'FAM8A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 0.3

Table S278. Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
FAM8A1 MUTATED	3	0	0	0
FAM8A1 WILD-TYPE	33	32	38	41

Figure S43. Get High-res Image Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SPTAN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.4

Table S279. Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
SPTAN1 MUTATED	0	0	4
SPTAN1 WILD-TYPE	47	42	54

Figure S44. Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SPTAN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S280. Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
SPTAN1 MUTATED	0	2	2
SPTAN1 WILD-TYPE	54	46	43

'SPTAN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.13

Table S281. Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
SPTAN1 MUTATED	0	0	4
SPTAN1 WILD-TYPE	68	40	35

Figure S45. Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SPTAN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0095 (Fisher's exact test), Q value = 0.19

Table S282. Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
SPTAN1 MUTATED	0	0	0	4	0	0	0
SPTAN1 WILD-TYPE	42	26	12	20	8	23	12

Figure S46. Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00486 (Fisher's exact test), Q value = 0.14

Table S283. Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
SPTAN1 MUTATED	0	0	4
SPTAN1 WILD-TYPE	51	56	36

Figure S47. Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00939 (Fisher's exact test), Q value = 0.19

Table S284. Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
SPTAN1 MUTATED	0	0	4
SPTAN1 WILD-TYPE	68	38	37

Figure S48. Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.2

Table S285. Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
SPTAN1 MUTATED	0	0	4
SPTAN1 WILD-TYPE	67	36	40

Figure S49. Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.24

Table S286. Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
SPTAN1 MUTATED	0	0	0	4
SPTAN1 WILD-TYPE	36	32	38	37

Figure S50. Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CRB2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S287. Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
CRB2 MUTATED	1	3	2
CRB2 WILD-TYPE	46	39	56

'CRB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S288. Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
CRB2 MUTATED	2	1	3
CRB2 WILD-TYPE	52	47	42

'CRB2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S289. Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
CRB2 MUTATED	4	0	1	1
CRB2 WILD-TYPE	43	14	33	20

'CRB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S290. Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
CRB2 MUTATED	4	1	1
CRB2 WILD-TYPE	45	23	42

'CRB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.661 (Fisher's exact test), Q value = 1

Table S291. Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
CRB2 MUTATED	4	1	1
CRB2 WILD-TYPE	64	39	38

'CRB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S292. Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
CRB2 MUTATED	1	3	1	1	0	0	0
CRB2 WILD-TYPE	41	23	11	23	8	23	12

'CRB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S293. Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
CRB2 MUTATED	1	4	1
CRB2 WILD-TYPE	50	52	39

'CRB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.659 (Fisher's exact test), Q value = 1

Table S294. Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
CRB2 MUTATED	4	1	1
CRB2 WILD-TYPE	64	37	40

'CRB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.659 (Fisher's exact test), Q value = 1

Table S295. Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
CRB2 MUTATED	4	1	1
CRB2 WILD-TYPE	63	35	43

'CRB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0648 (Fisher's exact test), Q value = 0.54

Table S296. Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
CRB2 MUTATED	0	4	1	1
CRB2 WILD-TYPE	36	28	37	40

'OPLAH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S297. Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
OPLAH MUTATED	2	1	1
OPLAH WILD-TYPE	45	41	57

'OPLAH MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S298. Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
OPLAH MUTATED	2	2	0
OPLAH WILD-TYPE	52	46	45

'OPLAH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.528 (Fisher's exact test), Q value = 1

Table S299. Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
OPLAH MUTATED	1	1	1	0
OPLAH WILD-TYPE	46	13	33	21

'OPLAH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S300. Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
OPLAH MUTATED	1	1	1
OPLAH WILD-TYPE	48	23	42

'OPLAH MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S301. Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
OPLAH MUTATED	2	1	1
OPLAH WILD-TYPE	66	39	38

'OPLAH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S302. Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
OPLAH MUTATED	1	1	1	0	1	0	0
OPLAH WILD-TYPE	41	25	11	24	7	23	12

'OPLAH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S303. Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
OPLAH MUTATED	2	2	0
OPLAH WILD-TYPE	49	54	40

'OPLAH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 1

Table S304. Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
OPLAH MUTATED	2	2	0
OPLAH WILD-TYPE	66	36	41

'OPLAH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S305. Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
OPLAH MUTATED	2	1	1
OPLAH WILD-TYPE	65	35	43

'OPLAH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.539 (Fisher's exact test), Q value = 1

Table S306. Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
OPLAH MUTATED	1	1	2	0
OPLAH WILD-TYPE	35	31	36	41

'C22ORF43 MUTATION STATUS' versus 'CN_CNMF'

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

Table S307. Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
C22ORF43 MUTATED	0	2	1
C22ORF43 WILD-TYPE	47	40	57

'C22ORF43 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S308. Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
C22ORF43 MUTATED	1	1	1
C22ORF43 WILD-TYPE	53	47	44

'C22ORF43 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0563 (Fisher's exact test), Q value = 0.51

Table S309. Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
C22ORF43 MUTATED	1	2	0	0
C22ORF43 WILD-TYPE	46	12	34	21

'C22ORF43 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S310. Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
C22ORF43 MUTATED	1	1	1
C22ORF43 WILD-TYPE	48	23	42

'C22ORF43 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S311. Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
C22ORF43 MUTATED	1	1	1
C22ORF43 WILD-TYPE	67	39	38

'C22ORF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S312. Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
C22ORF43 MUTATED	0	1	0	1	0	1	0
C22ORF43 WILD-TYPE	42	25	12	23	8	22	12

'C22ORF43 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S313. Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
C22ORF43 MUTATED	1	1	1
C22ORF43 WILD-TYPE	50	55	39

'C22ORF43 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S314. Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
C22ORF43 MUTATED	1	1	1
C22ORF43 WILD-TYPE	67	37	40

'C22ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S315. Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
C22ORF43 MUTATED	1	1	1
C22ORF43 WILD-TYPE	66	35	43

'C22ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S316. Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
C22ORF43 MUTATED	1	0	1	1
C22ORF43 WILD-TYPE	35	32	37	40

'GAS2L2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S317. Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
GAS2L2 MUTATED	1	1	1
GAS2L2 WILD-TYPE	46	41	57

'GAS2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 0.93

Table S318. Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
GAS2L2 MUTATED	0	1	2
GAS2L2 WILD-TYPE	54	47	43

'GAS2L2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S319. Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
GAS2L2 MUTATED	1	0	1	1
GAS2L2 WILD-TYPE	46	14	33	20

'GAS2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S320. Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
GAS2L2 MUTATED	1	0	2
GAS2L2 WILD-TYPE	48	24	41

'GAS2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S321. Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
GAS2L2 MUTATED	1	1	1
GAS2L2 WILD-TYPE	67	39	38

'GAS2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 1

Table S322. Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
GAS2L2 MUTATED	1	0	0	1	1	0	0
GAS2L2 WILD-TYPE	41	26	12	23	7	23	12

'GAS2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S323. Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
GAS2L2 MUTATED	1	1	1
GAS2L2 WILD-TYPE	50	55	39

'GAS2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S324. Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
GAS2L2 MUTATED	1	1	1
GAS2L2 WILD-TYPE	67	37	40

'GAS2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S325. Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
GAS2L2 MUTATED	1	1	1
GAS2L2 WILD-TYPE	66	35	43

'GAS2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S326. Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
GAS2L2 MUTATED	1	0	1	1
GAS2L2 WILD-TYPE	35	32	37	40

'CDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.36

Table S327. Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
CDC27 MUTATED	2	4	0
CDC27 WILD-TYPE	45	38	58

Figure S51. Get High-res Image Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CDC27 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S328. Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
CDC27 MUTATED	3	1	2
CDC27 WILD-TYPE	51	47	43

'CDC27 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.92

Table S329. Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
CDC27 MUTATED	4	1	0	0
CDC27 WILD-TYPE	43	13	34	21

'CDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.179 (Fisher's exact test), Q value = 0.92

Table S330. Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
CDC27 MUTATED	4	1	0
CDC27 WILD-TYPE	45	23	43

'CDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.89

Table S331. Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
CDC27 MUTATED	5	1	0
CDC27 WILD-TYPE	63	39	39

'CDC27 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0574 (Fisher's exact test), Q value = 0.51

Table S332. Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
CDC27 MUTATED	1	4	0	0	1	0	0
CDC27 WILD-TYPE	41	22	12	24	7	23	12

'CDC27 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S333. Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
CDC27 MUTATED	3	3	0
CDC27 WILD-TYPE	48	53	40

'CDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.81

Table S334. Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
CDC27 MUTATED	5	1	0
CDC27 WILD-TYPE	63	37	41

'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.89

Table S335. Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
CDC27 MUTATED	5	1	0
CDC27 WILD-TYPE	62	35	44

'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0488 (Fisher's exact test), Q value = 0.48

Table S336. Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
CDC27 MUTATED	1	4	1	0
CDC27 WILD-TYPE	35	28	37	41

Figure S52. Get High-res Image Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MUC2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S337. Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
MUC2 MUTATED	4	7	5
MUC2 WILD-TYPE	43	35	53

'MUC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.945 (Fisher's exact test), Q value = 1

Table S338. Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
MUC2 MUTATED	5	6	5
MUC2 WILD-TYPE	49	42	40

'MUC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 1

Table S339. Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
MUC2 MUTATED	4	0	6	1
MUC2 WILD-TYPE	43	14	28	20

'MUC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S340. Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
MUC2 MUTATED	4	4	3
MUC2 WILD-TYPE	45	20	40

'MUC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S341. Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
MUC2 MUTATED	7	3	6
MUC2 WILD-TYPE	61	37	33

'MUC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.985 (Fisher's exact test), Q value = 1

Table S342. Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
MUC2 MUTATED	4	3	1	3	1	2	2
MUC2 WILD-TYPE	38	23	11	21	7	21	10

'MUC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.501 (Fisher's exact test), Q value = 1

Table S343. Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
MUC2 MUTATED	7	4	5
MUC2 WILD-TYPE	44	52	35

'MUC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.944 (Fisher's exact test), Q value = 1

Table S344. Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
MUC2 MUTATED	7	4	5
MUC2 WILD-TYPE	61	34	36

'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S345. Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
MUC2 MUTATED	7	3	6
MUC2 WILD-TYPE	60	33	38

'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S346. Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
MUC2 MUTATED	5	2	4	5
MUC2 WILD-TYPE	31	30	34	36

'TPTE2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S347. Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
TPTE2 MUTATED	2	2	1
TPTE2 WILD-TYPE	45	40	57

'TPTE2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 1

Table S348. Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
TPTE2 MUTATED	2	0	3
TPTE2 WILD-TYPE	52	48	42

'TPTE2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S349. Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
TPTE2 MUTATED	2	0	1	0
TPTE2 WILD-TYPE	45	14	33	21

'TPTE2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S350. Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
TPTE2 MUTATED	2	0	1
TPTE2 WILD-TYPE	47	24	42

'TPTE2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S351. Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
TPTE2 MUTATED	4	0	1
TPTE2 WILD-TYPE	64	40	38

'TPTE2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.636 (Fisher's exact test), Q value = 1

Table S352. Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
TPTE2 MUTATED	3	1	0	0	0	0	1
TPTE2 WILD-TYPE	39	25	12	24	8	23	11

'TPTE2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0505 (Fisher's exact test), Q value = 0.48

Table S353. Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
TPTE2 MUTATED	4	0	1
TPTE2 WILD-TYPE	47	56	39

'TPTE2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S354. Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
TPTE2 MUTATED	4	0	1
TPTE2 WILD-TYPE	64	38	40

'TPTE2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S355. Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
TPTE2 MUTATED	4	0	1
TPTE2 WILD-TYPE	63	36	43

'TPTE2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.422 (Fisher's exact test), Q value = 1

Table S356. Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
TPTE2 MUTATED	2	2	0	1
TPTE2 WILD-TYPE	34	30	38	40

'NAT10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S357. Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
NAT10 MUTATED	0	2	2
NAT10 WILD-TYPE	47	40	56

'NAT10 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S358. Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
NAT10 MUTATED	2	1	1
NAT10 WILD-TYPE	52	47	44

'NAT10 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S359. Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
NAT10 MUTATED	1	0	1	1
NAT10 WILD-TYPE	46	14	33	20

'NAT10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S360. Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
NAT10 MUTATED	1	0	2
NAT10 WILD-TYPE	48	24	41

'NAT10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S361. Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
NAT10 MUTATED	2	1	1
NAT10 WILD-TYPE	66	39	38

'NAT10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.254 (Fisher's exact test), Q value = 1

Table S362. Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
NAT10 MUTATED	0	2	0	0	0	1	1
NAT10 WILD-TYPE	42	24	12	24	8	22	11

'NAT10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S363. Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
NAT10 MUTATED	2	1	1
NAT10 WILD-TYPE	49	55	39

'NAT10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S364. Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
NAT10 MUTATED	2	1	1
NAT10 WILD-TYPE	66	37	40

'NAT10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S365. Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
NAT10 MUTATED	2	1	1
NAT10 WILD-TYPE	65	35	43

'NAT10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S366. Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
NAT10 MUTATED	0	2	1	1
NAT10 WILD-TYPE	36	30	37	40

'INTS4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S367. Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
INTS4 MUTATED	1	1	1
INTS4 WILD-TYPE	46	41	57

'INTS4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S368. Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
INTS4 MUTATED	1	1	1
INTS4 WILD-TYPE	53	47	44

'INTS4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S369. Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
INTS4 MUTATED	2	1	0
INTS4 WILD-TYPE	66	39	39

'INTS4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S370. Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
INTS4 MUTATED	1	1	0	0	0	1	0
INTS4 WILD-TYPE	41	25	12	24	8	22	12

'INTS4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 1

Table S371. Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
INTS4 MUTATED	2	1	0
INTS4 WILD-TYPE	49	55	40

'INTS4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.614 (Fisher's exact test), Q value = 1

Table S372. Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
INTS4 MUTATED	2	1	0
INTS4 WILD-TYPE	66	37	41

'INTS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S373. Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
INTS4 MUTATED	2	1	0
INTS4 WILD-TYPE	65	35	44

'INTS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S374. Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
INTS4 MUTATED	1	1	1	0
INTS4 WILD-TYPE	35	31	37	41

'TTC38 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 1

Table S375. Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
TTC38 MUTATED	0	2	2
TTC38 WILD-TYPE	47	40	56

'TTC38 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 0.71

Table S376. Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
TTC38 MUTATED	1	0	3
TTC38 WILD-TYPE	53	48	42

'TTC38 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S377. Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
TTC38 MUTATED	2	0	2	0
TTC38 WILD-TYPE	45	14	32	21

'TTC38 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.93

Table S378. Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
TTC38 MUTATED	2	2	0
TTC38 WILD-TYPE	47	22	43

'TTC38 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S379. Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
TTC38 MUTATED	2	0	2
TTC38 WILD-TYPE	66	40	37

'TTC38 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S380. Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
TTC38 MUTATED	1	1	0	2	0	0	0
TTC38 WILD-TYPE	41	25	12	22	8	23	12

'TTC38 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.193 (Fisher's exact test), Q value = 0.92

Table S381. Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
TTC38 MUTATED	2	0	2
TTC38 WILD-TYPE	49	56	38

'TTC38 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S382. Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
TTC38 MUTATED	2	0	2
TTC38 WILD-TYPE	66	38	39

'TTC38 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S383. Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
TTC38 MUTATED	2	0	2
TTC38 WILD-TYPE	65	36	42

'TTC38 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S384. Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
TTC38 MUTATED	0	2	0	2
TTC38 WILD-TYPE	36	30	38	39

'RBM3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S385. Gene #41: 'RBM3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
RBM3 MUTATED	0	2	1
RBM3 WILD-TYPE	47	40	57

'RBM3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S386. Gene #41: 'RBM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
RBM3 MUTATED	2	1	0
RBM3 WILD-TYPE	52	47	45

'RBM3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S387. Gene #41: 'RBM3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
RBM3 MUTATED	2	1	0
RBM3 WILD-TYPE	66	39	39

'RBM3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S388. Gene #41: 'RBM3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
RBM3 MUTATED	1	1	0	0	0	1	0
RBM3 WILD-TYPE	41	25	12	24	8	22	12

'RBM3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 0.71

Table S389. Gene #41: 'RBM3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
RBM3 MUTATED	0	3	0
RBM3 WILD-TYPE	51	53	40

'RBM3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S390. Gene #41: 'RBM3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
RBM3 MUTATED	2	1	0
RBM3 WILD-TYPE	66	37	41

'RBM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S391. Gene #41: 'RBM3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
RBM3 MUTATED	2	1	0
RBM3 WILD-TYPE	65	35	44

'RBM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 0.79

Table S392. Gene #41: 'RBM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
RBM3 MUTATED	0	2	1	0
RBM3 WILD-TYPE	36	30	37	41

'TCHH MUTATION STATUS' versus 'CN_CNMF'

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

Table S393. Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
TCHH MUTATED	3	1	1
TCHH WILD-TYPE	44	41	57

'TCHH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 0.79

Table S394. Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
TCHH MUTATED	4	1	0
TCHH WILD-TYPE	50	47	45

'TCHH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0734 (Fisher's exact test), Q value = 0.59

Table S395. Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
TCHH MUTATED	1	2	0	1
TCHH WILD-TYPE	46	12	34	20

'TCHH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S396. Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
TCHH MUTATED	3	0	1
TCHH WILD-TYPE	46	24	42

'TCHH MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S397. Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
TCHH MUTATED	4	1	0
TCHH WILD-TYPE	64	39	39

'TCHH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.909 (Fisher's exact test), Q value = 1

Table S398. Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
TCHH MUTATED	3	1	0	0	0	1	0
TCHH WILD-TYPE	39	25	12	24	8	22	12

'TCHH MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S399. Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
TCHH MUTATED	3	2	0
TCHH WILD-TYPE	48	54	40

'TCHH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.322 (Fisher's exact test), Q value = 1

Table S400. Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
TCHH MUTATED	4	1	0
TCHH WILD-TYPE	64	37	41

'TCHH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 0.95

Table S401. Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
TCHH MUTATED	4	1	0
TCHH WILD-TYPE	63	35	44

'TCHH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S402. Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
TCHH MUTATED	2	2	1	0
TCHH WILD-TYPE	34	30	37	41

'ZC3H11A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0526 (Fisher's exact test), Q value = 0.49

Table S403. Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
ZC3H11A MUTATED	3	0	0
ZC3H11A WILD-TYPE	44	42	58

'ZC3H11A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S404. Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
ZC3H11A MUTATED	2	1	0
ZC3H11A WILD-TYPE	52	47	45

'ZC3H11A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S405. Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
ZC3H11A MUTATED	2	0	1
ZC3H11A WILD-TYPE	66	40	38

'ZC3H11A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S406. Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
ZC3H11A MUTATED	2	0	0	0	0	0	1
ZC3H11A WILD-TYPE	40	26	12	24	8	23	11

'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S407. Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
ZC3H11A MUTATED	2	0	1
ZC3H11A WILD-TYPE	49	56	39

'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S408. Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
ZC3H11A MUTATED	2	0	1
ZC3H11A WILD-TYPE	66	38	40

'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S409. Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
ZC3H11A MUTATED	2	0	1
ZC3H11A WILD-TYPE	65	36	43

'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S410. Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
ZC3H11A MUTATED	2	0	0	1
ZC3H11A WILD-TYPE	34	32	38	40

'RAC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 1

Table S411. Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
RAC1 MUTATED	0	2	2
RAC1 WILD-TYPE	47	40	56

'RAC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 1

Table S412. Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
RAC1 MUTATED	3	1	0
RAC1 WILD-TYPE	51	47	45

'RAC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.62 (Fisher's exact test), Q value = 1

Table S413. Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
RAC1 MUTATED	2	0	0	1
RAC1 WILD-TYPE	45	14	34	20

'RAC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S414. Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
RAC1 MUTATED	2	0	1
RAC1 WILD-TYPE	47	24	42

'RAC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S415. Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
RAC1 MUTATED	3	1	0
RAC1 WILD-TYPE	65	39	39

'RAC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S416. Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
RAC1 MUTATED	3	0	0	0	0	1	0
RAC1 WILD-TYPE	39	26	12	24	8	22	12

'RAC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S417. Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
RAC1 MUTATED	3	1	0
RAC1 WILD-TYPE	48	55	40

'RAC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S418. Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
RAC1 MUTATED	3	1	0
RAC1 WILD-TYPE	65	37	41

'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S419. Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
RAC1 MUTATED	3	1	0
RAC1 WILD-TYPE	64	35	44

'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0849 (Fisher's exact test), Q value = 0.63

Table S420. Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
RAC1 MUTATED	3	0	1	0
RAC1 WILD-TYPE	33	32	37	41

'MTIF3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S421. Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
MTIF3 MUTATED	1	1	1
MTIF3 WILD-TYPE	46	41	57

'MTIF3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.402 (Fisher's exact test), Q value = 1

Table S422. Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
MTIF3 MUTATED	1	0	2
MTIF3 WILD-TYPE	53	48	43

'MTIF3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S423. Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
MTIF3 MUTATED	2	0	1	0
MTIF3 WILD-TYPE	45	14	33	21

'MTIF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S424. Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
MTIF3 MUTATED	2	0	1
MTIF3 WILD-TYPE	47	24	42

'MTIF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S425. Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
MTIF3 MUTATED	2	0	1
MTIF3 WILD-TYPE	66	40	38

'MTIF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S426. Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
MTIF3 MUTATED	1	1	0	1	0	0	0
MTIF3 WILD-TYPE	41	25	12	23	8	23	12

'MTIF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S427. Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
MTIF3 MUTATED	2	0	1
MTIF3 WILD-TYPE	49	56	39

'MTIF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S428. Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
MTIF3 MUTATED	2	0	1
MTIF3 WILD-TYPE	66	38	40

'MTIF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S429. Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
MTIF3 MUTATED	2	0	1
MTIF3 WILD-TYPE	65	36	43

'MTIF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S430. Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
MTIF3 MUTATED	1	1	0	1
MTIF3 WILD-TYPE	35	31	38	40

'MFF MUTATION STATUS' versus 'CN_CNMF'

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

Table S431. Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
MFF MUTATED	1	1	1
MFF WILD-TYPE	46	41	57

'MFF MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S432. Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
MFF MUTATED	2	1	0
MFF WILD-TYPE	52	47	45

'MFF MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S433. Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
MFF MUTATED	2	0	0	1
MFF WILD-TYPE	45	14	34	20

'MFF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S434. Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
MFF MUTATED	2	0	1
MFF WILD-TYPE	47	24	42

'MFF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S435. Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
MFF MUTATED	2	1	0
MFF WILD-TYPE	66	39	39

'MFF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S436. Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
MFF MUTATED	1	1	0	0	0	1	0
MFF WILD-TYPE	41	25	12	24	8	22	12

'MFF MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S437. Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
MFF MUTATED	2	1	0
MFF WILD-TYPE	49	55	40

'MFF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S438. Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
MFF MUTATED	2	1	0
MFF WILD-TYPE	66	37	41

'MFF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S439. Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
MFF MUTATED	2	1	0
MFF WILD-TYPE	65	35	44

'MFF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.704 (Fisher's exact test), Q value = 1

Table S440. Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
MFF MUTATED	1	1	1	0
MFF WILD-TYPE	35	31	37	41

'PABPC3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S441. Gene #47: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
PABPC3 MUTATED	1	1	2
PABPC3 WILD-TYPE	46	41	56

'PABPC3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S442. Gene #47: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
PABPC3 MUTATED	2	0	2
PABPC3 WILD-TYPE	52	48	43

'PABPC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 1

Table S443. Gene #47: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
PABPC3 MUTATED	2	0	2
PABPC3 WILD-TYPE	66	40	37

'PABPC3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S444. Gene #47: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
PABPC3 MUTATED	2	0	0	1	0	0	1
PABPC3 WILD-TYPE	40	26	12	23	8	23	11

'PABPC3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.92

Table S445. Gene #47: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
PABPC3 MUTATED	2	0	2
PABPC3 WILD-TYPE	49	56	38

'PABPC3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 1

Table S446. Gene #47: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
PABPC3 MUTATED	2	0	2
PABPC3 WILD-TYPE	66	38	39

'PABPC3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.576 (Fisher's exact test), Q value = 1

Table S447. Gene #47: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
PABPC3 MUTATED	2	0	2
PABPC3 WILD-TYPE	65	36	42

'PABPC3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.305 (Fisher's exact test), Q value = 1

Table S448. Gene #47: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
PABPC3 MUTATED	2	0	0	2
PABPC3 WILD-TYPE	34	32	38	39

'CUX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.731 (Fisher's exact test), Q value = 1

Table S449. Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
CUX1 MUTATED	1	1	3
CUX1 WILD-TYPE	46	41	55

'CUX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S450. Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
CUX1 MUTATED	2	1	2
CUX1 WILD-TYPE	52	47	43

'CUX1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S451. Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
CUX1 MUTATED	1	0	1	1
CUX1 WILD-TYPE	46	14	33	20

'CUX1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S452. Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
CUX1 MUTATED	1	0	2
CUX1 WILD-TYPE	48	24	41

'CUX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S453. Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
CUX1 MUTATED	2	1	2
CUX1 WILD-TYPE	66	39	37

'CUX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.962 (Fisher's exact test), Q value = 1

Table S454. Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
CUX1 MUTATED	1	1	0	1	0	1	1
CUX1 WILD-TYPE	41	25	12	23	8	22	11

'CUX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S455. Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
CUX1 MUTATED	2	1	2
CUX1 WILD-TYPE	49	55	38

'CUX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S456. Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
CUX1 MUTATED	2	1	2
CUX1 WILD-TYPE	66	37	39

'CUX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S457. Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
CUX1 MUTATED	2	1	2
CUX1 WILD-TYPE	65	35	42

'CUX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S458. Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
CUX1 MUTATED	2	0	1	2
CUX1 WILD-TYPE	34	32	37	39

'PCMTD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0915 (Fisher's exact test), Q value = 0.64

Table S459. Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
PCMTD1 MUTATED	2	3	0
PCMTD1 WILD-TYPE	45	39	58

'PCMTD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S460. Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
PCMTD1 MUTATED	3	1	1
PCMTD1 WILD-TYPE	51	47	44

'PCMTD1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S461. Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
PCMTD1 MUTATED	3	0	0	1
PCMTD1 WILD-TYPE	44	14	34	20

'PCMTD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S462. Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
PCMTD1 MUTATED	3	0	1
PCMTD1 WILD-TYPE	46	24	42

'PCMTD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S463. Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
PCMTD1 MUTATED	4	1	0
PCMTD1 WILD-TYPE	64	39	39

'PCMTD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S464. Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
PCMTD1 MUTATED	1	3	0	0	0	1	0
PCMTD1 WILD-TYPE	41	23	12	24	8	22	12

'PCMTD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S465. Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
PCMTD1 MUTATED	3	2	0
PCMTD1 WILD-TYPE	48	54	40

'PCMTD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S466. Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
PCMTD1 MUTATED	4	1	0
PCMTD1 WILD-TYPE	64	37	41

'PCMTD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 0.95

Table S467. Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
PCMTD1 MUTATED	4	1	0
PCMTD1 WILD-TYPE	63	35	44

'PCMTD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S468. Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
PCMTD1 MUTATED	2	2	1	0
PCMTD1 WILD-TYPE	34	30	37	41

'EZH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S469. Gene #50: 'EZH2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
EZH2 MUTATED	2	1	1
EZH2 WILD-TYPE	45	41	57

'EZH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 1

Table S470. Gene #50: 'EZH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
EZH2 MUTATED	2	2	0
EZH2 WILD-TYPE	52	46	45

'EZH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S471. Gene #50: 'EZH2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
EZH2 MUTATED	2	2	0
EZH2 WILD-TYPE	66	38	39

'EZH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S472. Gene #50: 'EZH2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
EZH2 MUTATED	2	0	0	0	0	2	0
EZH2 WILD-TYPE	40	26	12	24	8	21	12

'EZH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S473. Gene #50: 'EZH2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
EZH2 MUTATED	2	2	0
EZH2 WILD-TYPE	49	54	40

'EZH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 1

Table S474. Gene #50: 'EZH2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
EZH2 MUTATED	2	2	0
EZH2 WILD-TYPE	66	36	41

'EZH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 1

Table S475. Gene #50: 'EZH2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
EZH2 MUTATED	2	2	0
EZH2 WILD-TYPE	65	34	44

'EZH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.279 (Fisher's exact test), Q value = 1

Table S476. Gene #50: 'EZH2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
EZH2 MUTATED	2	0	2	0
EZH2 WILD-TYPE	34	32	36	41

'HTT MUTATION STATUS' versus 'CN_CNMF'

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

Table S477. Gene #51: 'HTT MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
HTT MUTATED	1	1	1
HTT WILD-TYPE	46	41	57

'HTT MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S478. Gene #51: 'HTT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
HTT MUTATED	2	1	0
HTT WILD-TYPE	52	47	45

'HTT MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S479. Gene #51: 'HTT MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
HTT MUTATED	2	1	0
HTT WILD-TYPE	66	39	39

'HTT MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S480. Gene #51: 'HTT MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
HTT MUTATED	1	1	1	0	0	0	0
HTT WILD-TYPE	41	25	11	24	8	23	12

'HTT MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S481. Gene #51: 'HTT MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
HTT MUTATED	2	1	0
HTT WILD-TYPE	49	55	40

'HTT MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S482. Gene #51: 'HTT MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
HTT MUTATED	2	1	0
HTT WILD-TYPE	66	37	41

'HTT MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S483. Gene #51: 'HTT MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
HTT MUTATED	2	1	0
HTT WILD-TYPE	65	35	44

'HTT MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S484. Gene #51: 'HTT MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
HTT MUTATED	1	1	1	0
HTT WILD-TYPE	35	31	37	41

'GSX2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 1

Table S485. Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
GSX2 MUTATED	0	1	3
GSX2 WILD-TYPE	47	41	55

'GSX2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S486. Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
GSX2 MUTATED	0	2	2
GSX2 WILD-TYPE	54	46	43

'GSX2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S487. Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
GSX2 MUTATED	1	0	3	0
GSX2 WILD-TYPE	46	14	31	21

'GSX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.31

Table S488. Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
GSX2 MUTATED	1	3	0
GSX2 WILD-TYPE	48	21	43

Figure S53. Get High-res Image Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'GSX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S489. Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
GSX2 MUTATED	1	1	2
GSX2 WILD-TYPE	67	39	37

'GSX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S490. Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
GSX2 MUTATED	0	1	1	2	0	0	0
GSX2 WILD-TYPE	42	25	11	22	8	23	12

'GSX2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0666 (Fisher's exact test), Q value = 0.55

Table S491. Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
GSX2 MUTATED	1	0	3
GSX2 WILD-TYPE	50	56	37

'GSX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 0.83

Table S492. Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
GSX2 MUTATED	1	0	3
GSX2 WILD-TYPE	67	38	38

'GSX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.813 (Fisher's exact test), Q value = 1

Table S493. Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
GSX2 MUTATED	1	1	2
GSX2 WILD-TYPE	66	35	42

'GSX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S494. Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
GSX2 MUTATED	0	1	1	2
GSX2 WILD-TYPE	36	31	37	39

'AHDC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S495. Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
AHDC1 MUTATED	2	0	2
AHDC1 WILD-TYPE	45	42	56

'AHDC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00792 (Fisher's exact test), Q value = 0.19

Table S496. Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
AHDC1 MUTATED	0	0	4
AHDC1 WILD-TYPE	54	48	41

Figure S54. Get High-res Image Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'AHDC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0619 (Fisher's exact test), Q value = 0.53

Table S497. Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
AHDC1 MUTATED	0	1	3	0
AHDC1 WILD-TYPE	47	13	31	21

'AHDC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 0.69

Table S498. Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
AHDC1 MUTATED	0	2	2
AHDC1 WILD-TYPE	49	22	41

'AHDC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00412 (Fisher's exact test), Q value = 0.13

Table S499. Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
AHDC1 MUTATED	0	0	4
AHDC1 WILD-TYPE	68	40	35

Figure S55. Get High-res Image Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'AHDC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.31

Table S500. Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
AHDC1 MUTATED	0	0	0	2	0	0	2
AHDC1 WILD-TYPE	42	26	12	22	8	23	10

Figure S56. Get High-res Image Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'AHDC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00496 (Fisher's exact test), Q value = 0.14

Table S501. Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
AHDC1 MUTATED	0	0	4
AHDC1 WILD-TYPE	51	56	36

Figure S57. Get High-res Image Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'AHDC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00955 (Fisher's exact test), Q value = 0.19

Table S502. Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
AHDC1 MUTATED	0	0	4
AHDC1 WILD-TYPE	68	38	37

Figure S58. Get High-res Image Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'AHDC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.2

Table S503. Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
AHDC1 MUTATED	0	0	4
AHDC1 WILD-TYPE	67	36	40

Figure S59. Get High-res Image Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'AHDC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.24

Table S504. Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
AHDC1 MUTATED	0	0	0	4
AHDC1 WILD-TYPE	36	32	38	37

Figure S60. Get High-res Image Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RFC3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S505. Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
RFC3 MUTATED	1	1	1
RFC3 WILD-TYPE	46	41	57

'RFC3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.52 (Fisher's exact test), Q value = 1

Table S506. Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
RFC3 MUTATED	1	2	0
RFC3 WILD-TYPE	53	46	45

'RFC3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.528 (Fisher's exact test), Q value = 1

Table S507. Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
RFC3 MUTATED	1	1	1	0
RFC3 WILD-TYPE	46	13	33	21

'RFC3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S508. Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
RFC3 MUTATED	1	0	2
RFC3 WILD-TYPE	48	24	41

'RFC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S509. Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
RFC3 MUTATED	1	2	0
RFC3 WILD-TYPE	67	38	39

'RFC3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S510. Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
RFC3 MUTATED	0	1	1	0	0	1	0
RFC3 WILD-TYPE	42	25	11	24	8	22	12

'RFC3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S511. Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
RFC3 MUTATED	1	2	0
RFC3 WILD-TYPE	50	54	40

'RFC3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.244 (Fisher's exact test), Q value = 1

Table S512. Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
RFC3 MUTATED	1	2	0
RFC3 WILD-TYPE	67	36	41

'RFC3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S513. Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
RFC3 MUTATED	1	1	1
RFC3 WILD-TYPE	66	35	43

'RFC3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 1

Table S514. Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
RFC3 MUTATED	0	1	2	0
RFC3 WILD-TYPE	36	31	36	41

'CHD4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S515. Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
CHD4 MUTATED	1	1	2
CHD4 WILD-TYPE	46	41	56

'CHD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S516. Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
CHD4 MUTATED	1	1	2
CHD4 WILD-TYPE	53	47	43

'CHD4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S517. Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
CHD4 MUTATED	2	0	1	1
CHD4 WILD-TYPE	45	14	33	20

'CHD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.831 (Fisher's exact test), Q value = 1

Table S518. Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
CHD4 MUTATED	2	0	2
CHD4 WILD-TYPE	47	24	41

'CHD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S519. Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
CHD4 MUTATED	2	1	1
CHD4 WILD-TYPE	66	39	38

'CHD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 1

Table S520. Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
CHD4 MUTATED	1	1	1	0	0	0	1
CHD4 WILD-TYPE	41	25	11	24	8	23	11

'CHD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S521. Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
CHD4 MUTATED	1	2	1
CHD4 WILD-TYPE	50	54	39

'CHD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S522. Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
CHD4 MUTATED	2	1	1
CHD4 WILD-TYPE	66	37	40

'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.576 (Fisher's exact test), Q value = 1

Table S523. Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
CHD4 MUTATED	2	0	2
CHD4 WILD-TYPE	65	36	42

'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S524. Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
CHD4 MUTATED	1	1	1	1
CHD4 WILD-TYPE	35	31	37	40

'RUNX2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S525. Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
RUNX2 MUTATED	1	1	2
RUNX2 WILD-TYPE	46	41	56

'RUNX2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 1

Table S526. Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
RUNX2 MUTATED	1	1	2
RUNX2 WILD-TYPE	53	47	43

'RUNX2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S527. Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
RUNX2 MUTATED	1	0	1	1
RUNX2 WILD-TYPE	46	14	33	20

'RUNX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S528. Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
RUNX2 MUTATED	1	0	2
RUNX2 WILD-TYPE	48	24	41

'RUNX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S529. Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
RUNX2 MUTATED	2	1	1
RUNX2 WILD-TYPE	66	39	38

'RUNX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S530. Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
RUNX2 MUTATED	1	1	0	1	0	1	0
RUNX2 WILD-TYPE	41	25	12	23	8	22	12

'RUNX2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S531. Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
RUNX2 MUTATED	2	1	1
RUNX2 WILD-TYPE	49	55	39

'RUNX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S532. Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
RUNX2 MUTATED	2	1	1
RUNX2 WILD-TYPE	66	37	40

'RUNX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S533. Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
RUNX2 MUTATED	2	1	1
RUNX2 WILD-TYPE	65	35	43

'RUNX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S534. Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
RUNX2 MUTATED	0	2	1	1
RUNX2 WILD-TYPE	36	30	37	40

'SP4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 1

Table S535. Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
SP4 MUTATED	0	1	3
SP4 WILD-TYPE	47	41	55

'SP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.26

Table S536. Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
SP4 MUTATED	0	4	0
SP4 WILD-TYPE	54	44	45

Figure S61. Get High-res Image Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0503 (Fisher's exact test), Q value = 0.48

Table S537. Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
SP4 MUTATED	0	3	1
SP4 WILD-TYPE	68	37	38

'SP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 0.7

Table S538. Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
SP4 MUTATED	0	0	1	1	1	1	0
SP4 WILD-TYPE	42	26	11	23	7	22	12

'SP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.252 (Fisher's exact test), Q value = 1

Table S539. Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
SP4 MUTATED	0	3	1
SP4 WILD-TYPE	51	53	39

'SP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.31

Table S540. Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
SP4 MUTATED	0	3	1
SP4 WILD-TYPE	68	35	40

Figure S62. Get High-res Image Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.31

Table S541. Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
SP4 MUTATED	0	3	1
SP4 WILD-TYPE	67	33	43

Figure S63. Get High-res Image Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.9

Table S542. Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
SP4 MUTATED	0	0	3	1
SP4 WILD-TYPE	36	32	35	40

'DIAPH1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S543. Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
DIAPH1 MUTATED	1	1	1
DIAPH1 WILD-TYPE	46	41	57

'DIAPH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S544. Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
DIAPH1 MUTATED	2	0	1
DIAPH1 WILD-TYPE	52	48	44

'DIAPH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.62 (Fisher's exact test), Q value = 1

Table S545. Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
DIAPH1 MUTATED	2	0	1
DIAPH1 WILD-TYPE	66	40	38

'DIAPH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.813 (Fisher's exact test), Q value = 1

Table S546. Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
DIAPH1 MUTATED	2	0	0	1	0	0	0
DIAPH1 WILD-TYPE	40	26	12	23	8	23	12

'DIAPH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S547. Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
DIAPH1 MUTATED	1	1	1
DIAPH1 WILD-TYPE	50	55	39

'DIAPH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S548. Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
DIAPH1 MUTATED	2	0	1
DIAPH1 WILD-TYPE	66	38	40

'DIAPH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S549. Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
DIAPH1 MUTATED	2	0	1
DIAPH1 WILD-TYPE	65	36	43

'DIAPH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S550. Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
DIAPH1 MUTATED	1	1	0	1
DIAPH1 WILD-TYPE	35	31	38	40

'PLEC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.48

Table S551. Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
PLEC MUTATED	6	0	4
PLEC WILD-TYPE	41	42	54

Figure S64. Get High-res Image Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PLEC MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S552. Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
PLEC MUTATED	5	1	4
PLEC WILD-TYPE	49	47	41

'PLEC MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S553. Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
PLEC MUTATED	2	2	4	1
PLEC WILD-TYPE	45	12	30	20

'PLEC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.83

Table S554. Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
PLEC MUTATED	2	4	3
PLEC WILD-TYPE	47	20	40

'PLEC MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S555. Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
PLEC MUTATED	4	2	4
PLEC WILD-TYPE	64	38	35

'PLEC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.92

Table S556. Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
PLEC MUTATED	4	0	1	2	1	0	2
PLEC WILD-TYPE	38	26	11	22	7	23	10

'PLEC MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S557. Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
PLEC MUTATED	4	2	4
PLEC WILD-TYPE	47	54	36

'PLEC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S558. Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
PLEC MUTATED	4	2	4
PLEC WILD-TYPE	64	36	37

'PLEC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 1

Table S559. Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
PLEC MUTATED	4	1	5
PLEC WILD-TYPE	63	35	39

'PLEC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0854 (Fisher's exact test), Q value = 0.63

Table S560. Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
PLEC MUTATED	4	0	1	5
PLEC WILD-TYPE	32	32	37	36

'NHS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.78 (Fisher's exact test), Q value = 1

Table S561. Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
NHS MUTATED	1	0	2
NHS WILD-TYPE	46	42	56

'NHS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.773 (Fisher's exact test), Q value = 1

Table S562. Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
NHS MUTATED	2	1	0
NHS WILD-TYPE	52	47	45

'NHS MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S563. Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
NHS MUTATED	1	1	0	1
NHS WILD-TYPE	46	13	34	20

'NHS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S564. Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
NHS MUTATED	2	0	1
NHS WILD-TYPE	47	24	42

'NHS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S565. Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
NHS MUTATED	2	1	0
NHS WILD-TYPE	66	39	39

'NHS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.772 (Fisher's exact test), Q value = 1

Table S566. Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
NHS MUTATED	2	0	0	0	0	1	0
NHS WILD-TYPE	40	26	12	24	8	22	12

'NHS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S567. Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
NHS MUTATED	2	1	0
NHS WILD-TYPE	49	55	40

'NHS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S568. Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
NHS MUTATED	2	1	0
NHS WILD-TYPE	66	37	41

'NHS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S569. Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
NHS MUTATED	2	1	0
NHS WILD-TYPE	65	35	44

'NHS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S570. Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
NHS MUTATED	1	1	1	0
NHS WILD-TYPE	35	31	37	41

'PIK3CD MUTATION STATUS' versus 'CN_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 1

Table S571. Gene #61: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
PIK3CD MUTATED	3	0	1
PIK3CD WILD-TYPE	44	42	57

'PIK3CD MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 1

Table S572. Gene #61: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
PIK3CD MUTATED	3	0	1
PIK3CD WILD-TYPE	51	48	44

'PIK3CD MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S573. Gene #61: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
PIK3CD MUTATED	3	0	1
PIK3CD WILD-TYPE	65	40	38

'PIK3CD MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S574. Gene #61: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
PIK3CD MUTATED	3	0	0	0	0	0	1
PIK3CD WILD-TYPE	39	26	12	24	8	23	11

'PIK3CD MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.81

Table S575. Gene #61: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
PIK3CD MUTATED	3	0	1
PIK3CD WILD-TYPE	48	56	39

'PIK3CD MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S576. Gene #61: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
PIK3CD MUTATED	3	0	1
PIK3CD WILD-TYPE	65	38	40

'PIK3CD MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S577. Gene #61: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
PIK3CD MUTATED	3	0	1
PIK3CD WILD-TYPE	64	36	43

'PIK3CD MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.102 (Fisher's exact test), Q value = 0.67

Table S578. Gene #61: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
PIK3CD MUTATED	3	0	0	1
PIK3CD WILD-TYPE	33	32	38	40

'EPAS1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S579. Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
EPAS1 MUTATED	2	0	3
EPAS1 WILD-TYPE	45	42	55

'EPAS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S580. Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
EPAS1 MUTATED	2	1	2
EPAS1 WILD-TYPE	52	47	43

'EPAS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 1

Table S581. Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
EPAS1 MUTATED	1	0	2	1
EPAS1 WILD-TYPE	46	14	32	20

'EPAS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S582. Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
EPAS1 MUTATED	1	1	2
EPAS1 WILD-TYPE	48	23	41

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S583. Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
EPAS1 MUTATED	2	1	2
EPAS1 WILD-TYPE	66	39	37

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S584. Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
EPAS1 MUTATED	2	0	0	1	0	1	1
EPAS1 WILD-TYPE	40	26	12	23	8	22	11

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S585. Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
EPAS1 MUTATED	2	1	2
EPAS1 WILD-TYPE	49	55	38

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.853 (Fisher's exact test), Q value = 1

Table S586. Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
EPAS1 MUTATED	2	1	2
EPAS1 WILD-TYPE	66	37	39

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S587. Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
EPAS1 MUTATED	2	1	2
EPAS1 WILD-TYPE	65	35	42

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S588. Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
EPAS1 MUTATED	2	0	1	2
EPAS1 WILD-TYPE	34	32	37	39

'DLC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 1

Table S589. Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	42	58
DLC1 MUTATED	2	1	0
DLC1 WILD-TYPE	45	41	58

'DLC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S590. Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	45
DLC1 MUTATED	1	1	1
DLC1 WILD-TYPE	53	47	44

'DLC1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S591. Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	14	34	21
DLC1 MUTATED	2	0	0	1
DLC1 WILD-TYPE	45	14	34	20

'DLC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S592. Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	24	43
DLC1 MUTATED	2	0	1
DLC1 WILD-TYPE	47	24	42

'DLC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S593. Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	40	39
DLC1 MUTATED	2	1	0
DLC1 WILD-TYPE	66	39	39

'DLC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S594. Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	42	26	12	24	8	23	12
DLC1 MUTATED	1	1	0	0	0	1	0
DLC1 WILD-TYPE	41	25	12	24	8	22	12

'DLC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 1

Table S595. Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	56	40
DLC1 MUTATED	2	1	0
DLC1 WILD-TYPE	49	55	40

'DLC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S596. Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	38	41
DLC1 MUTATED	2	1	0
DLC1 WILD-TYPE	66	37	41

'DLC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S597. Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	36	44
DLC1 MUTATED	2	1	0
DLC1 WILD-TYPE	65	35	44

'DLC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S598. Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	32	38	41
DLC1 MUTATED	1	1	1	0
DLC1 WILD-TYPE	35	31	37	41

Methods & Data

Input

Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/TGCT-TP/15890416/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/TGCT-TP/15111345/TGCT-TP.transferedmergedcluster.txt
Number of patients = 147
Number of significantly mutated genes = 63
Number of Molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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