Correlation between gene mutation status and molecular subtypes

Breast Invasive Carcinoma (Primary solid tumor)

15 January 2014 | analyses__2014_01_15

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1TD9VVM

Overview

Introduction

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

Summary

Testing the association between mutation status of 73 genes and 12 molecular subtypes across 975 patients, 53 significant findings detected with P value < 0.05 and Q value < 0.25.

PIK3CA mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
CBFB mutation correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
GATA3 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
TP53 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
CDH1 mutation correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
MAP2K4 mutation correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
MAP3K1 mutation correlated to 'MRNA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
CCL13 mutation correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 73 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 53 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Chi-square test	Fisher's exact test	Chi-square test	Chi-square 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
PIK3CA	316 (32%)	659	7.32e-13 (5.87e-10)	3.48e-10 (2.78e-07)	2.65e-12 (2.11e-09)	2.46e-14 (1.98e-11)	0.00017 (0.132)	5.38e-06 (0.00424)	1.36e-14 (1.09e-11)	8.71e-19 (7.04e-16)	1.1e-12 (8.8e-10)	4.22e-20 (3.42e-17)	5.38e-09 (4.27e-06)	1.29e-12 (1.03e-09)
TP53	295 (30%)	680	2.35e-31 (1.92e-28)	2.14e-29 (1.75e-26)	6.94e-52 (5.71e-49)	3.91e-31 (3.19e-28)	4.63e-23 (3.77e-20)	2.58e-23 (2.1e-20)	1.62e-64 (1.33e-61)	2.86e-61 (2.36e-58)	1.99e-49 (1.63e-46)	1.45e-59 (1.19e-56)	1.32e-41 (1.08e-38)	1.63e-34 (1.33e-31)
CDH1	105 (11%)	870	0.000174 (0.135)	0.00336 (1.00)	6.87e-14 (5.52e-11)	5.89e-09 (4.68e-06)	0.00404 (1.00)	0.0106 (1.00)	8.36e-15 (6.74e-12)	3.7e-18 (2.98e-15)	6.42e-25 (5.23e-22)	3.04e-22 (2.47e-19)	5e-21 (4.05e-18)	2.06e-18 (1.67e-15)
GATA3	77 (8%)	898	4.42e-06 (0.00349)	1.16e-06 (0.000915)	0.00052 (0.402)	0.00341 (1.00)	0.218 (1.00)	0.0388 (1.00)	7.88e-10 (6.27e-07)	9.96e-13 (7.98e-10)	3.34e-05 (0.0263)	3.15e-07 (0.000249)	5.91e-05 (0.0463)	5.39e-08 (4.28e-05)
MAP3K1	70 (7%)	905	9.82e-05 (0.0768)	0.000689 (0.53)	0.00782 (1.00)	0.0184 (1.00)	0.00069 (0.531)	3.81e-05 (0.0299)	0.000304 (0.236)	0.000319 (0.247)	5.84e-05 (0.0458)	0.000725 (0.557)	0.000281 (0.218)	0.0188 (1.00)
MAP2K4	32 (3%)	943	0.123 (1.00)	0.00395 (1.00)	0.0722 (1.00)	0.0169 (1.00)	0.00262 (1.00)	0.0298 (1.00)	0.000681 (0.525)	0.000308 (0.238)	0.000237 (0.184)	0.00228 (1.00)	2.83e-05 (0.0222)	0.0137 (1.00)
CBFB	23 (2%)	952	0.134 (1.00)	0.925 (1.00)	0.039 (1.00)	0.00016 (0.124)	0.124 (1.00)	0.513 (1.00)	0.0904 (1.00)	0.149 (1.00)	0.0649 (1.00)	1.73e-05 (0.0136)	0.00395 (1.00)	0.00481 (1.00)
CCL13	4 (0%)	971			0.000151 (0.118)	0.306 (1.00)			0.312 (1.00)	0.565 (1.00)	0.311 (1.00)	0.48 (1.00)
FOXA1	23 (2%)	952	0.356 (1.00)	0.238 (1.00)	0.248 (1.00)	0.0448 (1.00)	0.894 (1.00)	0.309 (1.00)	0.0155 (1.00)	0.0481 (1.00)	0.126 (1.00)	0.0411 (1.00)	0.0705 (1.00)	0.58 (1.00)
SF3B1	16 (2%)	959	0.815 (1.00)	0.298 (1.00)	0.433 (1.00)	0.155 (1.00)	0.45 (1.00)	0.0246 (1.00)	0.125 (1.00)	0.265 (1.00)	0.0497 (1.00)	0.901 (1.00)	0.67 (1.00)	0.2 (1.00)
RUNX1	29 (3%)	946	0.0149 (1.00)	0.0452 (1.00)	0.00905 (1.00)	0.0346 (1.00)	1 (1.00)	0.285 (1.00)	0.0621 (1.00)	0.00493 (1.00)	0.0057 (1.00)	0.00213 (1.00)	0.183 (1.00)	0.0593 (1.00)
PTEN	35 (4%)	940	0.28 (1.00)	0.658 (1.00)	0.17 (1.00)	0.327 (1.00)	0.922 (1.00)	0.667 (1.00)	0.967 (1.00)	0.969 (1.00)	0.655 (1.00)	0.81 (1.00)	0.438 (1.00)	0.72 (1.00)
TBX3	27 (3%)	948	0.428 (1.00)	0.307 (1.00)	0.446 (1.00)	0.0578 (1.00)	0.083 (1.00)	0.609 (1.00)	0.0506 (1.00)	0.0891 (1.00)	0.159 (1.00)	0.0963 (1.00)	0.315 (1.00)	0.3 (1.00)
MLL3	69 (7%)	906	0.598 (1.00)	0.688 (1.00)	0.596 (1.00)	0.292 (1.00)	0.597 (1.00)	0.865 (1.00)	0.0568 (1.00)	0.127 (1.00)	0.0859 (1.00)	0.0716 (1.00)	0.462 (1.00)	0.566 (1.00)
NCOR1	41 (4%)	934	0.571 (1.00)	0.954 (1.00)	0.934 (1.00)	0.823 (1.00)	0.435 (1.00)	0.167 (1.00)	0.847 (1.00)	0.883 (1.00)	0.699 (1.00)	0.666 (1.00)	0.794 (1.00)	0.677 (1.00)
RB1	19 (2%)	956	0.666 (1.00)	0.403 (1.00)	0.153 (1.00)	0.0639 (1.00)	0.482 (1.00)	0.763 (1.00)	0.0233 (1.00)	0.0707 (1.00)	0.0591 (1.00)	0.0756 (1.00)	0.0116 (1.00)	0.287 (1.00)
CTCF	17 (2%)	958	0.0331 (1.00)	0.322 (1.00)	0.0145 (1.00)	0.00413 (1.00)	0.0685 (1.00)	0.297 (1.00)	0.119 (1.00)	0.195 (1.00)	0.0428 (1.00)	0.063 (1.00)	0.699 (1.00)	0.444 (1.00)
THEM5	11 (1%)	964	0.231 (1.00)	0.441 (1.00)	0.231 (1.00)	0.488 (1.00)	0.209 (1.00)	0.0398 (1.00)	0.631 (1.00)	0.559 (1.00)	1 (1.00)	0.562 (1.00)	1 (1.00)	0.186 (1.00)
GPS2	10 (1%)	965	0.00133 (1.00)	0.00592 (1.00)	0.0682 (1.00)	0.375 (1.00)	0.268 (1.00)	0.315 (1.00)	0.172 (1.00)	0.253 (1.00)	0.379 (1.00)	0.0083 (1.00)	1 (1.00)	0.259 (1.00)
RPGR	18 (2%)	957	0.99 (1.00)	0.664 (1.00)	0.872 (1.00)	0.667 (1.00)	0.767 (1.00)	0.695 (1.00)	0.804 (1.00)	0.9 (1.00)	0.917 (1.00)	0.574 (1.00)	0.908 (1.00)	0.451 (1.00)
DNAH12	17 (2%)	958	0.973 (1.00)	0.158 (1.00)	0.574 (1.00)	0.631 (1.00)	0.45 (1.00)	0.627 (1.00)	0.946 (1.00)	0.377 (1.00)	0.283 (1.00)	0.798 (1.00)	0.4 (1.00)	0.164 (1.00)
CDKN1B	10 (1%)	965	0.634 (1.00)	0.178 (1.00)	0.0062 (1.00)	0.0724 (1.00)	0.741 (1.00)	0.28 (1.00)	0.0966 (1.00)	0.193 (1.00)	0.0294 (1.00)	0.107 (1.00)	0.331 (1.00)	0.561 (1.00)
ZFP36L1	9 (1%)	966	0.57 (1.00)	0.441 (1.00)	0.0208 (1.00)	0.244 (1.00)	0.0266 (1.00)	0.0233 (1.00)	0.282 (1.00)	0.324 (1.00)	0.534 (1.00)	0.912 (1.00)	0.865 (1.00)	0.716 (1.00)
ASB10	8 (1%)	967	0.869 (1.00)	0.811 (1.00)	0.978 (1.00)	0.738 (1.00)			0.501 (1.00)	0.908 (1.00)	0.0926 (1.00)	0.74 (1.00)	0.865 (1.00)	1 (1.00)
HIST1H3B	11 (1%)	964	0.638 (1.00)	1 (1.00)	0.917 (1.00)	0.733 (1.00)	0.631 (1.00)	1 (1.00)	0.918 (1.00)	0.467 (1.00)	0.694 (1.00)	0.588 (1.00)	0.88 (1.00)	0.872 (1.00)
FAM86B1	8 (1%)	967			0.738 (1.00)	0.891 (1.00)			0.894 (1.00)	0.533 (1.00)	0.227 (1.00)	0.6 (1.00)	0.892 (1.00)	0.596 (1.00)
PIK3R1	15 (2%)	960	0.0266 (1.00)	0.722 (1.00)	0.88 (1.00)	0.0868 (1.00)	0.631 (1.00)	0.452 (1.00)	0.142 (1.00)	0.53 (1.00)	0.0548 (1.00)	1 (1.00)	0.14 (1.00)	0.436 (1.00)
MYH9	19 (2%)	956	0.711 (1.00)	0.182 (1.00)	0.228 (1.00)	0.437 (1.00)	0.822 (1.00)	0.606 (1.00)	0.873 (1.00)	0.507 (1.00)	0.614 (1.00)	0.0668 (1.00)	0.652 (1.00)	0.137 (1.00)
CASP8	12 (1%)	963	0.423 (1.00)	0.358 (1.00)	0.387 (1.00)	0.372 (1.00)	0.531 (1.00)	0.739 (1.00)	1 (1.00)	1 (1.00)	0.402 (1.00)	0.458 (1.00)	0.74 (1.00)	0.451 (1.00)
COL6A5	25 (3%)	950	0.144 (1.00)	0.44 (1.00)	0.631 (1.00)	0.342 (1.00)	0.075 (1.00)	0.076 (1.00)	0.217 (1.00)	0.112 (1.00)	0.0347 (1.00)	0.297 (1.00)	0.0448 (1.00)	0.0244 (1.00)
TBL1XR1	10 (1%)	965	0.123 (1.00)	0.238 (1.00)	0.0446 (1.00)	0.44 (1.00)	0.451 (1.00)	0.568 (1.00)	0.426 (1.00)	0.143 (1.00)	0.175 (1.00)	0.0499 (1.00)	0.642 (1.00)	0.239 (1.00)
ASXL2	16 (2%)	959	0.403 (1.00)	0.0975 (1.00)	0.894 (1.00)	0.868 (1.00)	0.281 (1.00)	0.00505 (1.00)	0.334 (1.00)	0.408 (1.00)	1 (1.00)	0.144 (1.00)	0.74 (1.00)	0.252 (1.00)
ARID1A	27 (3%)	948	0.135 (1.00)	0.943 (1.00)	0.0552 (1.00)	0.104 (1.00)	1 (1.00)	0.475 (1.00)	0.206 (1.00)	0.295 (1.00)	0.201 (1.00)	0.13 (1.00)	0.307 (1.00)	0.877 (1.00)
AQP12A	6 (1%)	969	0.715 (1.00)	0.203 (1.00)	0.23 (1.00)	0.0317 (1.00)	0.201 (1.00)	0.115 (1.00)	0.867 (1.00)	0.584 (1.00)	0.777 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
EPDR1	5 (1%)	970	0.379 (1.00)	1 (1.00)	0.719 (1.00)		0.557 (1.00)	0.468 (1.00)	0.715 (1.00)	1 (1.00)	0.823 (1.00)	1 (1.00)	0.289 (1.00)	1 (1.00)
ERBB2	21 (2%)	954	0.886 (1.00)	0.349 (1.00)	0.109 (1.00)	0.0134 (1.00)	0.549 (1.00)	0.906 (1.00)	0.256 (1.00)	0.377 (1.00)	0.0155 (1.00)	0.000788 (0.604)	0.666 (1.00)	0.396 (1.00)
MYB	12 (1%)	963	0.631 (1.00)	1 (1.00)	0.208 (1.00)	0.512 (1.00)	1 (1.00)	0.862 (1.00)	1 (1.00)	0.87 (1.00)	0.469 (1.00)	0.87 (1.00)	0.454 (1.00)	0.36 (1.00)
TMEM151B	6 (1%)	969	0.915 (1.00)	0.297 (1.00)	0.306 (1.00)	0.52 (1.00)	0.0266 (1.00)	0.195 (1.00)	0.343 (1.00)	0.0298 (1.00)	0.283 (1.00)	0.132 (1.00)	0.389 (1.00)	0.785 (1.00)
GALNTL6	5 (1%)	970	0.921 (1.00)	1 (1.00)	0.211 (1.00)	0.0124 (1.00)			0.0402 (1.00)	0.102 (1.00)	0.572 (1.00)	0.165 (1.00)	0.389 (1.00)	0.179 (1.00)
AKD1	18 (2%)	957	0.44 (1.00)	0.598 (1.00)	0.322 (1.00)	0.545 (1.00)	0.235 (1.00)	0.124 (1.00)	0.282 (1.00)	0.0769 (1.00)	0.216 (1.00)	0.582 (1.00)	0.111 (1.00)	0.339 (1.00)
AARS	9 (1%)	966	0.403 (1.00)	0.0107 (1.00)	0.742 (1.00)	0.509 (1.00)	0.836 (1.00)	0.563 (1.00)	0.0571 (1.00)	0.109 (1.00)	0.242 (1.00)	0.359 (1.00)	0.0398 (1.00)	0.837 (1.00)
HLA-C	9 (1%)	966	0.316 (1.00)	0.203 (1.00)	0.551 (1.00)	0.0926 (1.00)	0.399 (1.00)	0.634 (1.00)	0.0806 (1.00)	0.392 (1.00)	0.267 (1.00)	0.143 (1.00)	0.167 (1.00)	0.0247 (1.00)
GPRIN2	11 (1%)	964	0.655 (1.00)	0.465 (1.00)	0.927 (1.00)	0.655 (1.00)	0.877 (1.00)	0.33 (1.00)	0.461 (1.00)	0.395 (1.00)	0.67 (1.00)	0.331 (1.00)	0.642 (1.00)	0.288 (1.00)
TRPM5	11 (1%)	964	0.237 (1.00)	0.615 (1.00)	0.606 (1.00)	0.033 (1.00)	0.778 (1.00)	0.782 (1.00)	0.0408 (1.00)	0.0603 (1.00)	0.0933 (1.00)	0.0937 (1.00)	0.0216 (1.00)	0.0383 (1.00)
ANKRD12	18 (2%)	957	0.178 (1.00)	0.115 (1.00)	0.603 (1.00)	0.897 (1.00)	0.385 (1.00)	0.518 (1.00)	0.464 (1.00)	0.0343 (1.00)	0.539 (1.00)	0.332 (1.00)	1 (1.00)	0.491 (1.00)
FBXW7	15 (2%)	960	0.818 (1.00)	0.64 (1.00)	0.0642 (1.00)	0.00296 (1.00)	0.778 (1.00)	0.782 (1.00)	0.222 (1.00)	0.13 (1.00)	0.398 (1.00)	0.144 (1.00)	0.411 (1.00)	0.0968 (1.00)
PRICKLE3	11 (1%)	964	0.335 (1.00)	0.282 (1.00)	0.941 (1.00)	0.645 (1.00)	0.509 (1.00)	0.891 (1.00)	0.17 (1.00)	0.431 (1.00)	0.801 (1.00)	0.0864 (1.00)	0.594 (1.00)	0.639 (1.00)
WDR52	16 (2%)	959	0.768 (1.00)	0.0565 (1.00)	0.318 (1.00)	0.165 (1.00)	0.00424 (1.00)	0.137 (1.00)	0.0119 (1.00)	0.366 (1.00)	0.00958 (1.00)	0.369 (1.00)	0.0448 (1.00)	1 (1.00)
CDC42EP1	5 (1%)	970	0.579 (1.00)	0.452 (1.00)	0.607 (1.00)	0.252 (1.00)	0.836 (1.00)	0.829 (1.00)	0.839 (1.00)	0.531 (1.00)	0.618 (1.00)	0.132 (1.00)
ERBB3	18 (2%)	957	0.412 (1.00)	0.225 (1.00)	0.803 (1.00)	0.192 (1.00)	0.335 (1.00)	0.298 (1.00)	0.168 (1.00)	0.0986 (1.00)	0.925 (1.00)	0.777 (1.00)	1 (1.00)	1 (1.00)
FHOD3	13 (1%)	962	0.0431 (1.00)	0.0205 (1.00)	0.0649 (1.00)	0.0907 (1.00)	0.385 (1.00)	0.0261 (1.00)	0.0215 (1.00)	0.00208 (1.00)	0.0829 (1.00)	0.00313 (1.00)	0.642 (1.00)	0.235 (1.00)
PTHLH	7 (1%)	968	0.442 (1.00)	0.358 (1.00)	0.0276 (1.00)	0.00411 (1.00)	0.69 (1.00)	0.392 (1.00)	0.164 (1.00)	0.295 (1.00)	0.114 (1.00)	0.214 (1.00)
SHISA4	5 (1%)	970	0.0213 (1.00)	0.203 (1.00)	0.188 (1.00)	0.413 (1.00)			0.839 (1.00)	0.453 (1.00)	0.342 (1.00)	1 (1.00)
KCNN3	9 (1%)	966	0.321 (1.00)	0.839 (1.00)	0.207 (1.00)	0.289 (1.00)	0.328 (1.00)	0.144 (1.00)	0.248 (1.00)	0.213 (1.00)	0.242 (1.00)	0.763 (1.00)	0.162 (1.00)	0.616 (1.00)
FGFR2	11 (1%)	964	0.841 (1.00)	0.876 (1.00)	0.323 (1.00)	0.24 (1.00)	1 (1.00)	1 (1.00)	0.85 (1.00)	0.797 (1.00)	0.548 (1.00)	0.863 (1.00)	0.802 (1.00)	0.363 (1.00)
HLA-DRB5	6 (1%)	969	0.00723 (1.00)	0.0135 (1.00)	0.127 (1.00)	0.654 (1.00)			0.645 (1.00)	0.77 (1.00)	0.26 (1.00)	0.127 (1.00)	0.781 (1.00)	1 (1.00)
ICOSLG	6 (1%)	969	0.693 (1.00)	1 (1.00)	0.161 (1.00)	0.654 (1.00)			0.554 (1.00)	1 (1.00)	0.886 (1.00)	0.772 (1.00)	1 (1.00)	1 (1.00)
GYG2	8 (1%)	967	0.703 (1.00)	1 (1.00)	0.189 (1.00)	0.719 (1.00)	0.156 (1.00)	0.0398 (1.00)	1 (1.00)	0.433 (1.00)	0.403 (1.00)	0.904 (1.00)	0.389 (1.00)	0.179 (1.00)
PPEF1	11 (1%)	964	0.84 (1.00)	1 (1.00)	0.0771 (1.00)	0.36 (1.00)	1 (1.00)	1 (1.00)	0.249 (1.00)	0.928 (1.00)	0.801 (1.00)	0.505 (1.00)	1 (1.00)	0.317 (1.00)
MAP4K1	10 (1%)	965	0.828 (1.00)	0.452 (1.00)	0.232 (1.00)	0.599 (1.00)	1 (1.00)	0.782 (1.00)	0.357 (1.00)	0.0488 (1.00)	0.443 (1.00)	0.662 (1.00)	0.274 (1.00)	0.202 (1.00)
ZNF41	11 (1%)	964	0.81 (1.00)	0.465 (1.00)	0.602 (1.00)	0.244 (1.00)	0.877 (1.00)	0.291 (1.00)	0.187 (1.00)	0.431 (1.00)	0.37 (1.00)	0.863 (1.00)	0.0918 (1.00)	0.109 (1.00)
FBXO17	5 (1%)	970			0.831 (1.00)	0.433 (1.00)			0.401 (1.00)	0.622 (1.00)	0.74 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
HRNR	31 (3%)	944	0.892 (1.00)	0.46 (1.00)	0.225 (1.00)	0.944 (1.00)	0.587 (1.00)	0.588 (1.00)	0.577 (1.00)	0.436 (1.00)	0.3 (1.00)	0.677 (1.00)	0.693 (1.00)	1 (1.00)
STAG2	13 (1%)	962	0.357 (1.00)	1 (1.00)	0.294 (1.00)	0.373 (1.00)	0.877 (1.00)	0.676 (1.00)	0.526 (1.00)	0.936 (1.00)	0.194 (1.00)	0.595 (1.00)	0.507 (1.00)	0.883 (1.00)
CEP57	6 (1%)	969	0.324 (1.00)	1 (1.00)	0.406 (1.00)	0.145 (1.00)			0.554 (1.00)	1 (1.00)	0.0731 (1.00)	0.772 (1.00)	0.0581 (1.00)	0.027 (1.00)
SPRR2B	3 (0%)	972			0.734 (1.00)				0.432 (1.00)	0.798 (1.00)	0.633 (1.00)	0.793 (1.00)
ZFP36L2	7 (1%)	968	0.437 (1.00)	1 (1.00)	0.0108 (1.00)	0.787 (1.00)	1 (1.00)	1 (1.00)	0.345 (1.00)	0.442 (1.00)	0.654 (1.00)	0.891 (1.00)	1 (1.00)	0.837 (1.00)
DMXL2	19 (2%)	956	0.697 (1.00)	0.182 (1.00)	0.0376 (1.00)	0.263 (1.00)	0.107 (1.00)	0.0727 (1.00)	0.0464 (1.00)	0.0566 (1.00)	0.0168 (1.00)	0.192 (1.00)	0.0713 (1.00)	0.102 (1.00)
ZBTB7C	5 (1%)	970			0.673 (1.00)	0.752 (1.00)			0.264 (1.00)	0.381 (1.00)	0.868 (1.00)	1 (1.00)	0.781 (1.00)	1 (1.00)
MUC5B	33 (3%)	942	0.694 (1.00)	0.879 (1.00)	0.444 (1.00)	0.371 (1.00)	0.915 (1.00)	0.695 (1.00)	0.329 (1.00)	0.771 (1.00)	0.533 (1.00)	0.729 (1.00)	0.818 (1.00)	0.86 (1.00)
XBP1	4 (0%)	971			0.0199 (1.00)	0.386 (1.00)			1 (1.00)	0.823 (1.00)	0.481 (1.00)	0.693 (1.00)	0.393 (1.00)	0.814 (1.00)
FXYD5	5 (1%)	970	0.693 (1.00)	0.615 (1.00)	0.259 (1.00)		0.643 (1.00)	1 (1.00)	0.0797 (1.00)	0.453 (1.00)	0.401 (1.00)	0.862 (1.00)
ATXN2	15 (2%)	960	0.837 (1.00)	0.366 (1.00)	0.38 (1.00)	0.701 (1.00)	0.234 (1.00)	0.0766 (1.00)	0.603 (1.00)	0.345 (1.00)	0.846 (1.00)	1 (1.00)	0.856 (1.00)	0.916 (1.00)

'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 7.32e-13 (Chi-square test), Q value = 5.9e-10

Table S1. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
PIK3CA MUTATED	7	13	23	8	61	23	8	21
PIK3CA WILD-TYPE	14	25	91	89	47	50	11	18

Figure S1. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 3.48e-10 (Fisher's exact test), Q value = 2.8e-07

Table S2. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
PIK3CA MUTATED	62	16	86
PIK3CA WILD-TYPE	60	110	175

Figure S2. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 2.65e-12 (Chi-square test), Q value = 2.1e-09

Table S3. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
PIK3CA MUTATED	143	62	53	45	11
PIK3CA WILD-TYPE	215	184	37	180	31

Figure S3. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.46e-14 (Chi-square test), Q value = 2e-11

Table S4. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
PIK3CA MUTATED	5	78	41	32	19	33
PIK3CA WILD-TYPE	106	72	58	95	35	73

Figure S4. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.13

Table S5. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
PIK3CA MUTATED	27	49	46
PIK3CA WILD-TYPE	118	81	72

Figure S5. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 5.38e-06 (Fisher's exact test), Q value = 0.0042

Table S6. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
PIK3CA MUTATED	52	50	20
PIK3CA WILD-TYPE	102	63	106

Figure S6. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.36e-14 (Fisher's exact test), Q value = 1.1e-11

Table S7. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
PIK3CA MUTATED	39	85	191
PIK3CA WILD-TYPE	228	99	327

Figure S7. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.71e-19 (Fisher's exact test), Q value = 7e-16

Table S8. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
PIK3CA MUTATED	25	142	148
PIK3CA WILD-TYPE	201	282	171

Figure S8. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.1e-12 (Fisher's exact test), Q value = 8.8e-10

Table S9. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
PIK3CA MUTATED	147	120	47
PIK3CA WILD-TYPE	249	156	237

Figure S9. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.22e-20 (Fisher's exact test), Q value = 3.4e-17

Table S10. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
PIK3CA MUTATED	37	75	202
PIK3CA WILD-TYPE	209	216	217

Figure S10. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.38e-09 (Fisher's exact test), Q value = 4.3e-06

Table S11. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
PIK3CA MUTATED	96	85	30
PIK3CA WILD-TYPE	154	124	162

Figure S11. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.29e-12 (Fisher's exact test), Q value = 1e-09

Table S12. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
PIK3CA MUTATED	13	76	122
PIK3CA WILD-TYPE	127	93	220

Figure S12. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CBFB MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.134 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
CBFB MUTATED	1	1	0	1	6	2	0	0
CBFB WILD-TYPE	20	37	114	96	102	71	19	39

'CBFB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.925 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
CBFB MUTATED	3	2	6
CBFB WILD-TYPE	119	124	255

'CBFB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.039 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
CBFB MUTATED	12	5	5	1	0
CBFB WILD-TYPE	346	241	85	224	42

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

'CBFB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00016 (Chi-square test), Q value = 0.12

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
CBFB MUTATED	0	11	3	0	0	1
CBFB WILD-TYPE	111	139	96	127	54	105

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

'CBFB MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
CBFB MUTATED	1	6	3
CBFB WILD-TYPE	144	124	115

'CBFB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
CBFB MUTATED	6	2	2
CBFB WILD-TYPE	148	111	124

'CBFB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0904 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
CBFB MUTATED	2	5	16
CBFB WILD-TYPE	265	179	502

'CBFB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
CBFB MUTATED	2	14	7
CBFB WILD-TYPE	224	410	312

'CBFB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0649 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
CBFB MUTATED	11	9	2
CBFB WILD-TYPE	385	267	282

'CBFB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.73e-05 (Fisher's exact test), Q value = 0.014

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
CBFB MUTATED	0	2	20
CBFB WILD-TYPE	246	289	399

Figure S15. Get High-res Image Gene #2: 'CBFB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CBFB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00395 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
CBFB MUTATED	11	4	0
CBFB WILD-TYPE	239	205	192

Figure S16. Get High-res Image Gene #2: 'CBFB MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CBFB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00481 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
CBFB MUTATED	0	1	14
CBFB WILD-TYPE	140	168	328

Figure S17. Get High-res Image Gene #2: 'CBFB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 4.42e-06 (Chi-square test), Q value = 0.0035

Table S25. Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
GATA3 MUTATED	1	5	26	2	9	4	1	0
GATA3 WILD-TYPE	20	33	88	95	99	69	18	39

Figure S18. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00091

Table S26. Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
GATA3 MUTATED	7	1	40
GATA3 WILD-TYPE	115	125	221

Figure S19. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00052 (Chi-square test), Q value = 0.4

Table S27. Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
GATA3 MUTATED	29	33	6	8	0
GATA3 WILD-TYPE	329	213	84	217	42

Figure S20. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'GATA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00341 (Chi-square test), Q value = 1

Table S28. Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
GATA3 MUTATED	0	12	8	15	7	4
GATA3 WILD-TYPE	111	138	91	112	47	102

Figure S21. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'GATA3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S29. Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
GATA3 MUTATED	12	17	8
GATA3 WILD-TYPE	133	113	110

'GATA3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 1

Table S30. Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
GATA3 MUTATED	21	10	6
GATA3 WILD-TYPE	133	103	120

Figure S22. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 7.88e-10 (Fisher's exact test), Q value = 6.3e-07

Table S31. Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
GATA3 MUTATED	2	11	64
GATA3 WILD-TYPE	265	173	454

Figure S23. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.96e-13 (Fisher's exact test), Q value = 8e-10

Table S32. Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
GATA3 MUTATED	0	60	17
GATA3 WILD-TYPE	226	364	302

Figure S24. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.026

Table S33. Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
GATA3 MUTATED	50	13	12
GATA3 WILD-TYPE	346	263	272

Figure S25. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.15e-07 (Fisher's exact test), Q value = 0.00025

Table S34. Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
GATA3 MUTATED	4	40	31
GATA3 WILD-TYPE	242	251	388

Figure S26. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.91e-05 (Fisher's exact test), Q value = 0.046

Table S35. Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
GATA3 MUTATED	32	13	4
GATA3 WILD-TYPE	218	196	188

Figure S27. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.39e-08 (Fisher's exact test), Q value = 4.3e-05

Table S36. Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
GATA3 MUTATED	0	6	43
GATA3 WILD-TYPE	140	163	299

Figure S28. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.356 (Chi-square test), Q value = 1

Table S37. Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
FOXA1 MUTATED	0	0	3	0	1	2	0	2
FOXA1 WILD-TYPE	21	38	111	97	107	71	19	37

'FOXA1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S38. Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
FOXA1 MUTATED	2	0	6
FOXA1 WILD-TYPE	120	126	255

'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.248 (Chi-square test), Q value = 1

Table S39. Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
FOXA1 MUTATED	12	6	3	1	1
FOXA1 WILD-TYPE	346	240	87	224	41

'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0448 (Chi-square test), Q value = 1

Table S40. Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
FOXA1 MUTATED	0	3	7	4	1	2
FOXA1 WILD-TYPE	111	147	92	123	53	104

Figure S29. Get High-res Image Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S41. Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
FOXA1 MUTATED	2	3	2
FOXA1 WILD-TYPE	143	127	116

'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.309 (Fisher's exact test), Q value = 1

Table S42. Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
FOXA1 MUTATED	5	1	1
FOXA1 WILD-TYPE	149	112	125

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S43. Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
FOXA1 MUTATED	1	7	15
FOXA1 WILD-TYPE	266	177	503

Figure S30. Get High-res Image Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0481 (Fisher's exact test), Q value = 1

Table S44. Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
FOXA1 MUTATED	1	11	11
FOXA1 WILD-TYPE	225	413	308

Figure S31. Get High-res Image Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S45. Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
FOXA1 MUTATED	10	10	3
FOXA1 WILD-TYPE	386	266	281

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0411 (Fisher's exact test), Q value = 1

Table S46. Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
FOXA1 MUTATED	2	5	16
FOXA1 WILD-TYPE	244	286	403

Figure S32. Get High-res Image Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0705 (Fisher's exact test), Q value = 1

Table S47. Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
FOXA1 MUTATED	9	7	1
FOXA1 WILD-TYPE	241	202	191

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S48. Gene #4: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
FOXA1 MUTATED	2	4	11
FOXA1 WILD-TYPE	138	165	331

'SF3B1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.815 (Chi-square test), Q value = 1

Table S49. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
SF3B1 MUTATED	0	0	1	1	3	2	0	1
SF3B1 WILD-TYPE	21	38	113	96	105	71	19	38

'SF3B1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S50. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
SF3B1 MUTATED	4	1	3
SF3B1 WILD-TYPE	118	125	258

'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.433 (Chi-square test), Q value = 1

Table S51. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
SF3B1 MUTATED	6	7	1	2	0
SF3B1 WILD-TYPE	352	239	89	223	42

'SF3B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.155 (Chi-square test), Q value = 1

Table S52. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
SF3B1 MUTATED	0	5	3	5	1	0
SF3B1 WILD-TYPE	111	145	96	122	53	106

'SF3B1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S53. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
SF3B1 MUTATED	1	1	3
SF3B1 WILD-TYPE	144	129	115

'SF3B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 1

Table S54. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
SF3B1 MUTATED	0	4	1
SF3B1 WILD-TYPE	154	109	125

Figure S33. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 1

Table S55. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
SF3B1 MUTATED	1	3	12
SF3B1 WILD-TYPE	266	181	506

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.265 (Fisher's exact test), Q value = 1

Table S56. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
SF3B1 MUTATED	1	9	6
SF3B1 WILD-TYPE	225	415	313

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 1

Table S57. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
SF3B1 MUTATED	7	8	1
SF3B1 WILD-TYPE	389	268	283

Figure S34. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.901 (Fisher's exact test), Q value = 1

Table S58. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
SF3B1 MUTATED	3	5	8
SF3B1 WILD-TYPE	243	286	411

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.67 (Fisher's exact test), Q value = 1

Table S59. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
SF3B1 MUTATED	4	3	1
SF3B1 WILD-TYPE	246	206	191

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.2 (Fisher's exact test), Q value = 1

Table S60. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
SF3B1 MUTATED	0	4	4
SF3B1 WILD-TYPE	140	165	338

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 2.35e-31 (Chi-square test), Q value = 1.9e-28

Table S61. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
TP53 MUTATED	7	6	18	73	6	41	7	6
TP53 WILD-TYPE	14	32	96	24	102	32	12	33

Figure S35. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 2.14e-29 (Fisher's exact test), Q value = 1.7e-26

Table S62. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
TP53 MUTATED	15	93	56
TP53 WILD-TYPE	107	33	205

Figure S36. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 6.94e-52 (Chi-square test), Q value = 5.7e-49

Table S63. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
TP53 MUTATED	51	60	10	161	10
TP53 WILD-TYPE	307	186	80	64	32

Figure S37. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.91e-31 (Chi-square test), Q value = 3.2e-28

Table S64. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
TP53 MUTATED	82	9	29	31	8	31
TP53 WILD-TYPE	29	141	70	96	46	75

Figure S38. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 4.63e-23 (Fisher's exact test), Q value = 3.8e-20

Table S65. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
TP53 MUTATED	93	11	33
TP53 WILD-TYPE	52	119	85

Figure S39. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 2.58e-23 (Fisher's exact test), Q value = 2.1e-20

Table S66. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
TP53 MUTATED	30	18	89
TP53 WILD-TYPE	124	95	37

Figure S40. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.62e-64 (Fisher's exact test), Q value = 1.3e-61

Table S67. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
TP53 MUTATED	191	16	86
TP53 WILD-TYPE	76	168	432

Figure S41. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.86e-61 (Fisher's exact test), Q value = 2.4e-58

Table S68. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
TP53 MUTATED	169	91	33
TP53 WILD-TYPE	57	333	286

Figure S42. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.99e-49 (Fisher's exact test), Q value = 1.6e-46

Table S69. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
TP53 MUTATED	74	31	183
TP53 WILD-TYPE	322	245	101

Figure S43. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.45e-59 (Fisher's exact test), Q value = 1.2e-56

Table S70. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
TP53 MUTATED	176	64	48
TP53 WILD-TYPE	70	227	371

Figure S44. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.32e-41 (Fisher's exact test), Q value = 1.1e-38

Table S71. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
TP53 MUTATED	45	20	131
TP53 WILD-TYPE	205	189	61

Figure S45. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.63e-34 (Fisher's exact test), Q value = 1.3e-31

Table S72. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
TP53 MUTATED	103	21	72
TP53 WILD-TYPE	37	148	270

Figure S46. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.000174 (Chi-square test), Q value = 0.14

Table S73. Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
CDH1 MUTATED	0	6	1	1	10	6	1	7
CDH1 WILD-TYPE	21	32	113	96	98	67	18	32

Figure S47. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00336 (Fisher's exact test), Q value = 1

Table S74. Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
CDH1 MUTATED	16	4	12
CDH1 WILD-TYPE	106	122	249

Figure S48. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 6.87e-14 (Chi-square test), Q value = 5.5e-11

Table S75. Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
CDH1 MUTATED	59	14	24	1	5
CDH1 WILD-TYPE	299	232	66	224	37

Figure S49. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 5.89e-09 (Chi-square test), Q value = 4.7e-06

Table S76. Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
CDH1 MUTATED	0	31	20	3	7	21
CDH1 WILD-TYPE	111	119	79	124	47	85

Figure S50. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00404 (Fisher's exact test), Q value = 1

Table S77. Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
CDH1 MUTATED	4	4	14
CDH1 WILD-TYPE	141	126	104

Figure S51. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 1

Table S78. Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
CDH1 MUTATED	5	13	4
CDH1 WILD-TYPE	149	100	122

Figure S52. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 8.36e-15 (Fisher's exact test), Q value = 6.7e-12

Table S79. Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
CDH1 MUTATED	7	50	48
CDH1 WILD-TYPE	260	134	470

Figure S53. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.7e-18 (Fisher's exact test), Q value = 3e-15

Table S80. Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
CDH1 MUTATED	4	26	75
CDH1 WILD-TYPE	222	398	244

Figure S54. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 6.42e-25 (Fisher's exact test), Q value = 5.2e-22

Table S81. Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
CDH1 MUTATED	21	77	5
CDH1 WILD-TYPE	375	199	279

Figure S55. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.04e-22 (Fisher's exact test), Q value = 2.5e-19

Table S82. Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
CDH1 MUTATED	4	8	91
CDH1 WILD-TYPE	242	283	328

Figure S56. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-21 (Fisher's exact test), Q value = 4.1e-18

Table S83. Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
CDH1 MUTATED	13	64	3
CDH1 WILD-TYPE	237	145	189

Figure S57. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.06e-18 (Fisher's exact test), Q value = 1.7e-15

Table S84. Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
CDH1 MUTATED	2	55	23
CDH1 WILD-TYPE	138	114	319

Figure S58. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0149 (Chi-square test), Q value = 1

Table S85. Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
RUNX1 MUTATED	3	1	3	0	5	2	0	4
RUNX1 WILD-TYPE	18	37	111	97	103	71	19	35

Figure S59. Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 1

Table S86. Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
RUNX1 MUTATED	8	1	9
RUNX1 WILD-TYPE	114	125	252

Figure S60. Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00905 (Chi-square test), Q value = 1

Table S87. Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
RUNX1 MUTATED	16	4	6	2	0
RUNX1 WILD-TYPE	342	242	84	223	42

Figure S61. Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0346 (Chi-square test), Q value = 1

Table S88. Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
RUNX1 MUTATED	1	4	5	0	4	5
RUNX1 WILD-TYPE	110	146	94	127	50	101

Figure S62. Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'RUNX1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S89. Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
RUNX1 MUTATED	4	3	3
RUNX1 WILD-TYPE	141	127	115

'RUNX1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.285 (Fisher's exact test), Q value = 1

Table S90. Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
RUNX1 MUTATED	5	4	1
RUNX1 WILD-TYPE	149	109	125

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0621 (Fisher's exact test), Q value = 1

Table S91. Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
RUNX1 MUTATED	4	10	15
RUNX1 WILD-TYPE	263	174	503

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00493 (Fisher's exact test), Q value = 1

Table S92. Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
RUNX1 MUTATED	1	12	16
RUNX1 WILD-TYPE	225	412	303

Figure S63. Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0057 (Fisher's exact test), Q value = 1

Table S93. Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
RUNX1 MUTATED	13	14	2
RUNX1 WILD-TYPE	383	262	282

Figure S64. Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00213 (Fisher's exact test), Q value = 1

Table S94. Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
RUNX1 MUTATED	4	3	22
RUNX1 WILD-TYPE	242	288	397

Figure S65. Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S95. Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
RUNX1 MUTATED	7	10	3
RUNX1 WILD-TYPE	243	199	189

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0593 (Fisher's exact test), Q value = 1

Table S96. Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
RUNX1 MUTATED	1	9	10
RUNX1 WILD-TYPE	139	160	332

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.28 (Chi-square test), Q value = 1

Table S97. Gene #9: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
PTEN MUTATED	2	2	3	1	4	1	0	0
PTEN WILD-TYPE	19	36	111	96	104	72	19	39

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.658 (Fisher's exact test), Q value = 1

Table S98. Gene #9: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
PTEN MUTATED	4	2	7
PTEN WILD-TYPE	118	124	254

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.17 (Chi-square test), Q value = 1

Table S99. Gene #9: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
PTEN MUTATED	13	7	7	8	0
PTEN WILD-TYPE	345	239	83	217	42

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.327 (Chi-square test), Q value = 1

Table S100. Gene #9: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
PTEN MUTATED	6	7	6	3	0	7
PTEN WILD-TYPE	105	143	93	124	54	99

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S101. Gene #9: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
PTEN MUTATED	3	4	3
PTEN WILD-TYPE	142	126	115

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.667 (Fisher's exact test), Q value = 1

Table S102. Gene #9: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
PTEN MUTATED	5	3	2
PTEN WILD-TYPE	149	110	124

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S103. Gene #9: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
PTEN MUTATED	9	7	19
PTEN WILD-TYPE	258	177	499

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S104. Gene #9: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
PTEN MUTATED	8	16	11
PTEN WILD-TYPE	218	408	308

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S105. Gene #9: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
PTEN MUTATED	16	11	8
PTEN WILD-TYPE	380	265	276

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S106. Gene #9: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
PTEN MUTATED	9	9	17
PTEN WILD-TYPE	237	282	402

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S107. Gene #9: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
PTEN MUTATED	7	10	9
PTEN WILD-TYPE	243	199	183

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S108. Gene #9: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
PTEN MUTATED	6	8	12
PTEN WILD-TYPE	134	161	330

'TBX3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.428 (Chi-square test), Q value = 1

Table S109. Gene #10: 'TBX3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
TBX3 MUTATED	0	1	3	2	7	1	0	2
TBX3 WILD-TYPE	21	37	111	95	101	72	19	37

'TBX3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 1

Table S110. Gene #10: 'TBX3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
TBX3 MUTATED	6	2	8
TBX3 WILD-TYPE	116	124	253

'TBX3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.446 (Chi-square test), Q value = 1

Table S111. Gene #10: 'TBX3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
TBX3 MUTATED	13	6	4	3	1
TBX3 WILD-TYPE	345	240	86	222	41

'TBX3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0578 (Chi-square test), Q value = 1

Table S112. Gene #10: 'TBX3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
TBX3 MUTATED	1	9	2	1	1	2
TBX3 WILD-TYPE	110	141	97	126	53	104

'TBX3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.083 (Fisher's exact test), Q value = 1

Table S113. Gene #10: 'TBX3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
TBX3 MUTATED	1	3	6
TBX3 WILD-TYPE	144	127	112

'TBX3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S114. Gene #10: 'TBX3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
TBX3 MUTATED	4	4	2
TBX3 WILD-TYPE	150	109	124

'TBX3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0506 (Fisher's exact test), Q value = 1

Table S115. Gene #10: 'TBX3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
TBX3 MUTATED	3	9	15
TBX3 WILD-TYPE	264	175	503

'TBX3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S116. Gene #10: 'TBX3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
TBX3 MUTATED	3	10	14
TBX3 WILD-TYPE	223	414	305

'TBX3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S117. Gene #10: 'TBX3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
TBX3 MUTATED	12	11	4
TBX3 WILD-TYPE	384	265	280

'TBX3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0963 (Fisher's exact test), Q value = 1

Table S118. Gene #10: 'TBX3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
TBX3 MUTATED	3	7	17
TBX3 WILD-TYPE	243	284	402

'TBX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 1

Table S119. Gene #10: 'TBX3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
TBX3 MUTATED	6	7	2
TBX3 WILD-TYPE	244	202	190

'TBX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S120. Gene #10: 'TBX3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
TBX3 MUTATED	1	6	8
TBX3 WILD-TYPE	139	163	334

'MAP2K4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.123 (Chi-square test), Q value = 1

Table S121. Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
MAP2K4 MUTATED	0	3	3	0	8	2	1	2
MAP2K4 WILD-TYPE	21	35	111	97	100	71	18	37

'MAP2K4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00395 (Fisher's exact test), Q value = 1

Table S122. Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
MAP2K4 MUTATED	9	0	10
MAP2K4 WILD-TYPE	113	126	251

Figure S66. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0722 (Chi-square test), Q value = 1

Table S123. Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
MAP2K4 MUTATED	12	8	7	3	2
MAP2K4 WILD-TYPE	346	238	83	222	40

'MAP2K4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0169 (Chi-square test), Q value = 1

Table S124. Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
MAP2K4 MUTATED	0	10	3	9	2	1
MAP2K4 WILD-TYPE	111	140	96	118	52	105

Figure S67. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MAP2K4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 1

Table S125. Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
MAP2K4 MUTATED	0	5	8
MAP2K4 WILD-TYPE	145	125	110

Figure S68. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MAP2K4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S126. Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
MAP2K4 MUTATED	4	8	1
MAP2K4 WILD-TYPE	150	105	125

Figure S69. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000681 (Fisher's exact test), Q value = 0.53

Table S127. Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
MAP2K4 MUTATED	1	5	26
MAP2K4 WILD-TYPE	266	179	492

Figure S70. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000308 (Fisher's exact test), Q value = 0.24

Table S128. Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
MAP2K4 MUTATED	0	22	10
MAP2K4 WILD-TYPE	226	402	309

Figure S71. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.18

Table S129. Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
MAP2K4 MUTATED	24	6	2
MAP2K4 WILD-TYPE	372	270	282

Figure S72. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00228 (Fisher's exact test), Q value = 1

Table S130. Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
MAP2K4 MUTATED	1	15	16
MAP2K4 WILD-TYPE	245	276	403

Figure S73. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.83e-05 (Fisher's exact test), Q value = 0.022

Table S131. Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
MAP2K4 MUTATED	17	3	0
MAP2K4 WILD-TYPE	233	206	192

Figure S74. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 1

Table S132. Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
MAP2K4 MUTATED	1	2	17
MAP2K4 WILD-TYPE	139	167	325

Figure S75. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MLL3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.598 (Chi-square test), Q value = 1

Table S133. Gene #12: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
MLL3 MUTATED	1	1	8	5	12	4	1	4
MLL3 WILD-TYPE	20	37	106	92	96	69	18	35

'MLL3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.688 (Fisher's exact test), Q value = 1

Table S134. Gene #12: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
MLL3 MUTATED	8	7	21
MLL3 WILD-TYPE	114	119	240

'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.596 (Chi-square test), Q value = 1

Table S135. Gene #12: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
MLL3 MUTATED	30	16	7	11	3
MLL3 WILD-TYPE	328	230	83	214	39

'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.292 (Chi-square test), Q value = 1

Table S136. Gene #12: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
MLL3 MUTATED	5	15	11	11	3	5
MLL3 WILD-TYPE	106	135	88	116	51	101

'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S137. Gene #12: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
MLL3 MUTATED	10	6	9
MLL3 WILD-TYPE	135	124	109

'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S138. Gene #12: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
MLL3 MUTATED	10	6	9
MLL3 WILD-TYPE	144	107	117

'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0568 (Fisher's exact test), Q value = 1

Table S139. Gene #12: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
MLL3 MUTATED	11	13	45
MLL3 WILD-TYPE	256	171	473

'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 1

Table S140. Gene #12: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
MLL3 MUTATED	11	38	20
MLL3 WILD-TYPE	215	386	299

'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0859 (Fisher's exact test), Q value = 1

Table S141. Gene #12: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
MLL3 MUTATED	33	21	12
MLL3 WILD-TYPE	363	255	272

'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0716 (Fisher's exact test), Q value = 1

Table S142. Gene #12: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
MLL3 MUTATED	12	16	38
MLL3 WILD-TYPE	234	275	381

'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S143. Gene #12: 'MLL3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
MLL3 MUTATED	19	13	9
MLL3 WILD-TYPE	231	196	183

'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S144. Gene #12: 'MLL3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
MLL3 MUTATED	6	11	24
MLL3 WILD-TYPE	134	158	318

'MAP3K1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 9.82e-05 (Chi-square test), Q value = 0.077

Table S145. Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
MAP3K1 MUTATED	5	1	12	1	16	1	0	3
MAP3K1 WILD-TYPE	16	37	102	96	92	72	19	36

Figure S76. Get High-res Image Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000689 (Fisher's exact test), Q value = 0.53

Table S146. Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
MAP3K1 MUTATED	12	1	26
MAP3K1 WILD-TYPE	110	125	235

Figure S77. Get High-res Image Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00782 (Chi-square test), Q value = 1

Table S147. Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
MAP3K1 MUTATED	38	15	7	6	4
MAP3K1 WILD-TYPE	320	231	83	219	38

Figure S78. Get High-res Image Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MAP3K1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0184 (Chi-square test), Q value = 1

Table S148. Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
MAP3K1 MUTATED	2	14	1	11	2	8
MAP3K1 WILD-TYPE	109	136	98	116	52	98

Figure S79. Get High-res Image Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MAP3K1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.53

Table S149. Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
MAP3K1 MUTATED	4	20	12
MAP3K1 WILD-TYPE	141	110	106

Figure S80. Get High-res Image Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MAP3K1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 3.81e-05 (Fisher's exact test), Q value = 0.03

Table S150. Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
MAP3K1 MUTATED	20	15	1
MAP3K1 WILD-TYPE	134	98	125

Figure S81. Get High-res Image Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000304 (Fisher's exact test), Q value = 0.24

Table S151. Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
MAP3K1 MUTATED	6	16	48
MAP3K1 WILD-TYPE	261	168	470

Figure S82. Get High-res Image Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000319 (Fisher's exact test), Q value = 0.25

Table S152. Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
MAP3K1 MUTATED	4	37	29
MAP3K1 WILD-TYPE	222	387	290

Figure S83. Get High-res Image Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 5.84e-05 (Fisher's exact test), Q value = 0.046

Table S153. Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
MAP3K1 MUTATED	39	25	6
MAP3K1 WILD-TYPE	357	251	278

Figure S84. Get High-res Image Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000725 (Fisher's exact test), Q value = 0.56

Table S154. Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
MAP3K1 MUTATED	6	23	41
MAP3K1 WILD-TYPE	240	268	378

Figure S85. Get High-res Image Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000281 (Fisher's exact test), Q value = 0.22

Table S155. Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
MAP3K1 MUTATED	26	18	3
MAP3K1 WILD-TYPE	224	191	189

Figure S86. Get High-res Image Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 1

Table S156. Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
MAP3K1 MUTATED	3	14	30
MAP3K1 WILD-TYPE	137	155	312

Figure S87. Get High-res Image Gene #13: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NCOR1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.571 (Chi-square test), Q value = 1

Table S157. Gene #14: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
NCOR1 MUTATED	0	2	4	3	7	3	0	0
NCOR1 WILD-TYPE	21	36	110	94	101	70	19	39

'NCOR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S158. Gene #14: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
NCOR1 MUTATED	5	4	10
NCOR1 WILD-TYPE	117	122	251

'NCOR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.934 (Chi-square test), Q value = 1

Table S159. Gene #14: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
NCOR1 MUTATED	16	11	3	8	1
NCOR1 WILD-TYPE	342	235	87	217	41

'NCOR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.823 (Chi-square test), Q value = 1

Table S160. Gene #14: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
NCOR1 MUTATED	4	8	7	5	2	4
NCOR1 WILD-TYPE	107	142	92	122	52	102

'NCOR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 1

Table S161. Gene #14: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
NCOR1 MUTATED	5	2	5
NCOR1 WILD-TYPE	140	128	113

'NCOR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 1

Table S162. Gene #14: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
NCOR1 MUTATED	2	6	4
NCOR1 WILD-TYPE	152	107	122

'NCOR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S163. Gene #14: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
NCOR1 MUTATED	10	7	24
NCOR1 WILD-TYPE	257	177	494

'NCOR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.883 (Fisher's exact test), Q value = 1

Table S164. Gene #14: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
NCOR1 MUTATED	8	19	14
NCOR1 WILD-TYPE	218	405	305

'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S165. Gene #14: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
NCOR1 MUTATED	15	14	12
NCOR1 WILD-TYPE	381	262	272

'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.666 (Fisher's exact test), Q value = 1

Table S166. Gene #14: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
NCOR1 MUTATED	8	13	20
NCOR1 WILD-TYPE	238	278	399

'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S167. Gene #14: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
NCOR1 MUTATED	8	9	7
NCOR1 WILD-TYPE	242	200	185

'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.677 (Fisher's exact test), Q value = 1

Table S168. Gene #14: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
NCOR1 MUTATED	5	8	11
NCOR1 WILD-TYPE	135	161	331

'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.666 (Chi-square test), Q value = 1

Table S169. Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
RB1 MUTATED	0	0	2	4	2	2	0	0
RB1 WILD-TYPE	21	38	112	93	106	71	19	39

'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.403 (Fisher's exact test), Q value = 1

Table S170. Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
RB1 MUTATED	1	4	5
RB1 WILD-TYPE	121	122	256

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.153 (Chi-square test), Q value = 1

Table S171. Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
RB1 MUTATED	4	4	4	7	0
RB1 WILD-TYPE	354	242	86	218	42

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0639 (Chi-square test), Q value = 1

Table S172. Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
RB1 MUTATED	5	2	3	0	1	0
RB1 WILD-TYPE	106	148	96	127	53	106

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 1

Table S173. Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
RB1 MUTATED	4	4	1
RB1 WILD-TYPE	141	126	117

'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.763 (Fisher's exact test), Q value = 1

Table S174. Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
RB1 MUTATED	3	2	4
RB1 WILD-TYPE	151	111	122

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 1

Table S175. Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
RB1 MUTATED	9	0	10
RB1 WILD-TYPE	258	184	508

Figure S88. Get High-res Image Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0707 (Fisher's exact test), Q value = 1

Table S176. Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
RB1 MUTATED	7	10	2
RB1 WILD-TYPE	219	414	317

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0591 (Fisher's exact test), Q value = 1

Table S177. Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
RB1 MUTATED	7	1	8
RB1 WILD-TYPE	389	275	276

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0756 (Fisher's exact test), Q value = 1

Table S178. Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
RB1 MUTATED	8	2	6
RB1 WILD-TYPE	238	289	413

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 1

Table S179. Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
RB1 MUTATED	5	0	7
RB1 WILD-TYPE	245	209	185

Figure S89. Get High-res Image Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S180. Gene #15: 'RB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
RB1 MUTATED	4	1	7
RB1 WILD-TYPE	136	168	335

'CTCF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0331 (Chi-square test), Q value = 1

Table S181. Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
CTCF MUTATED	1	0	2	1	8	0	0	1
CTCF WILD-TYPE	20	38	112	96	100	73	19	38

Figure S90. Get High-res Image Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CTCF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.322 (Fisher's exact test), Q value = 1

Table S182. Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
CTCF MUTATED	3	1	9
CTCF WILD-TYPE	119	125	252

'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0145 (Chi-square test), Q value = 1

Table S183. Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
CTCF MUTATED	13	2	0	1	1
CTCF WILD-TYPE	345	244	90	224	41

Figure S91. Get High-res Image Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00413 (Chi-square test), Q value = 1

Table S184. Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
CTCF MUTATED	0	8	1	0	0	2
CTCF WILD-TYPE	111	142	98	127	54	104

Figure S92. Get High-res Image Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CTCF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0685 (Fisher's exact test), Q value = 1

Table S185. Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
CTCF MUTATED	1	7	3
CTCF WILD-TYPE	144	123	115

'CTCF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S186. Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
CTCF MUTATED	7	2	2
CTCF WILD-TYPE	147	111	124

'CTCF MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S187. Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
CTCF MUTATED	1	4	12
CTCF WILD-TYPE	266	180	506

'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S188. Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
CTCF MUTATED	1	10	6
CTCF WILD-TYPE	225	414	313

'CTCF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 1

Table S189. Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
CTCF MUTATED	11	5	1
CTCF WILD-TYPE	385	271	283

Figure S93. Get High-res Image Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.063 (Fisher's exact test), Q value = 1

Table S190. Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
CTCF MUTATED	1	9	7
CTCF WILD-TYPE	245	282	412

'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S191. Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
CTCF MUTATED	5	2	2
CTCF WILD-TYPE	245	207	190

'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S192. Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
CTCF MUTATED	1	1	7
CTCF WILD-TYPE	139	168	335

'THEM5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.231 (Chi-square test), Q value = 1

Table S193. Gene #17: 'THEM5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
THEM5 MUTATED	1	0	1	0	3	0	0	0
THEM5 WILD-TYPE	20	38	113	97	105	73	19	39

'THEM5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S194. Gene #17: 'THEM5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
THEM5 MUTATED	1	0	4
THEM5 WILD-TYPE	121	126	257

'THEM5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.231 (Chi-square test), Q value = 1

Table S195. Gene #17: 'THEM5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
THEM5 MUTATED	2	3	3	2	1
THEM5 WILD-TYPE	356	243	87	223	41

'THEM5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.488 (Chi-square test), Q value = 1

Table S196. Gene #17: 'THEM5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
THEM5 MUTATED	0	2	1	2	0	3
THEM5 WILD-TYPE	111	148	98	125	54	103

'THEM5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S197. Gene #17: 'THEM5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
THEM5 MUTATED	1	3	0
THEM5 WILD-TYPE	144	127	118

'THEM5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0398 (Fisher's exact test), Q value = 1

Table S198. Gene #17: 'THEM5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
THEM5 MUTATED	4	0	0
THEM5 WILD-TYPE	150	113	126

Figure S94. Get High-res Image Gene #17: 'THEM5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'THEM5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S199. Gene #17: 'THEM5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
THEM5 MUTATED	2	3	5
THEM5 WILD-TYPE	265	181	513

'THEM5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S200. Gene #17: 'THEM5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
THEM5 MUTATED	1	6	3
THEM5 WILD-TYPE	225	418	316

'THEM5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S201. Gene #17: 'THEM5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
THEM5 MUTATED	4	3	3
THEM5 WILD-TYPE	392	273	281

'THEM5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.562 (Fisher's exact test), Q value = 1

Table S202. Gene #17: 'THEM5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
THEM5 MUTATED	1	4	5
THEM5 WILD-TYPE	245	287	414

'THEM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S203. Gene #17: 'THEM5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
THEM5 MUTATED	3	3	3
THEM5 WILD-TYPE	247	206	189

'THEM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S204. Gene #17: 'THEM5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
THEM5 MUTATED	1	5	3
THEM5 WILD-TYPE	139	164	339

'GPS2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00133 (Chi-square test), Q value = 1

Table S205. Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
GPS2 MUTATED	0	4	2	0	1	0	0	1
GPS2 WILD-TYPE	21	34	112	97	107	73	19	38

Figure S95. Get High-res Image Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'GPS2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00592 (Fisher's exact test), Q value = 1

Table S206. Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
GPS2 MUTATED	6	0	2
GPS2 WILD-TYPE	116	126	259

Figure S96. Get High-res Image Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'GPS2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0682 (Chi-square test), Q value = 1

Table S207. Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
GPS2 MUTATED	8	1	1	0	0
GPS2 WILD-TYPE	350	245	89	225	42

'GPS2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.375 (Chi-square test), Q value = 1

Table S208. Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
GPS2 MUTATED	1	1	3	1	1	0
GPS2 WILD-TYPE	110	149	96	126	53	106

'GPS2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S209. Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
GPS2 MUTATED	0	2	2
GPS2 WILD-TYPE	145	128	116

'GPS2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.315 (Fisher's exact test), Q value = 1

Table S210. Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
GPS2 MUTATED	3	1	0
GPS2 WILD-TYPE	151	112	126

'GPS2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S211. Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
GPS2 MUTATED	1	4	5
GPS2 WILD-TYPE	266	180	513

'GPS2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S212. Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
GPS2 MUTATED	1	3	6
GPS2 WILD-TYPE	225	421	313

'GPS2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S213. Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
GPS2 MUTATED	3	5	2
GPS2 WILD-TYPE	393	271	282

'GPS2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0083 (Fisher's exact test), Q value = 1

Table S214. Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
GPS2 MUTATED	1	0	9
GPS2 WILD-TYPE	245	291	410

Figure S97. Get High-res Image Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'GPS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S215. Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
GPS2 MUTATED	2	1	1
GPS2 WILD-TYPE	248	208	191

'GPS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S216. Gene #18: 'GPS2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
GPS2 MUTATED	2	1	1
GPS2 WILD-TYPE	138	168	341

'RPGR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.99 (Chi-square test), Q value = 1

Table S217. Gene #19: 'RPGR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
RPGR MUTATED	0	1	3	2	2	2	0	1
RPGR WILD-TYPE	21	37	111	95	106	71	19	38

'RPGR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S218. Gene #19: 'RPGR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
RPGR MUTATED	4	2	5
RPGR WILD-TYPE	118	124	256

'RPGR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.872 (Chi-square test), Q value = 1

Table S219. Gene #19: 'RPGR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
RPGR MUTATED	6	5	2	3	0
RPGR WILD-TYPE	352	241	88	222	42

'RPGR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.667 (Chi-square test), Q value = 1

Table S220. Gene #19: 'RPGR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
RPGR MUTATED	3	2	1	5	1	2
RPGR WILD-TYPE	108	148	98	122	53	104

'RPGR MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S221. Gene #19: 'RPGR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
RPGR MUTATED	3	4	2
RPGR WILD-TYPE	142	126	116

'RPGR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S222. Gene #19: 'RPGR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
RPGR MUTATED	5	2	2
RPGR WILD-TYPE	149	111	124

'RPGR MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S223. Gene #19: 'RPGR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
RPGR MUTATED	6	3	9
RPGR WILD-TYPE	261	181	509

'RPGR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.9 (Fisher's exact test), Q value = 1

Table S224. Gene #19: 'RPGR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
RPGR MUTATED	5	7	6
RPGR WILD-TYPE	221	417	313

'RPGR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S225. Gene #19: 'RPGR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
RPGR MUTATED	8	4	5
RPGR WILD-TYPE	388	272	279

'RPGR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S226. Gene #19: 'RPGR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
RPGR MUTATED	4	7	6
RPGR WILD-TYPE	242	284	413

'RPGR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S227. Gene #19: 'RPGR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
RPGR MUTATED	3	2	3
RPGR WILD-TYPE	247	207	189

'RPGR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S228. Gene #19: 'RPGR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
RPGR MUTATED	3	2	3
RPGR WILD-TYPE	137	167	339

'DNAH12 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.973 (Chi-square test), Q value = 1

Table S229. Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
DNAH12 MUTATED	0	0	2	2	2	1	0	1
DNAH12 WILD-TYPE	21	38	112	95	106	72	19	38

'DNAH12 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S230. Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
DNAH12 MUTATED	4	2	2
DNAH12 WILD-TYPE	118	124	259

'DNAH12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.574 (Chi-square test), Q value = 1

Table S231. Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
DNAH12 MUTATED	9	3	1	3	0
DNAH12 WILD-TYPE	349	243	89	222	42

'DNAH12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.631 (Chi-square test), Q value = 1

Table S232. Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
DNAH12 MUTATED	1	5	2	2	0	2
DNAH12 WILD-TYPE	110	145	97	125	54	104

'DNAH12 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S233. Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
DNAH12 MUTATED	1	1	3
DNAH12 WILD-TYPE	144	129	115

'DNAH12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S234. Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
DNAH12 MUTATED	1	2	2
DNAH12 WILD-TYPE	153	111	124

'DNAH12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S235. Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
DNAH12 MUTATED	4	3	10
DNAH12 WILD-TYPE	263	181	508

'DNAH12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S236. Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
DNAH12 MUTATED	4	5	8
DNAH12 WILD-TYPE	222	419	311

'DNAH12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S237. Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
DNAH12 MUTATED	4	7	6
DNAH12 WILD-TYPE	392	269	278

'DNAH12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.798 (Fisher's exact test), Q value = 1

Table S238. Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
DNAH12 MUTATED	4	4	9
DNAH12 WILD-TYPE	242	287	410

'DNAH12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S239. Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
DNAH12 MUTATED	2	5	4
DNAH12 WILD-TYPE	248	204	188

'DNAH12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S240. Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
DNAH12 MUTATED	3	5	3
DNAH12 WILD-TYPE	137	164	339

'CDKN1B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.634 (Chi-square test), Q value = 1

Table S241. Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
CDKN1B MUTATED	0	0	1	0	3	1	0	1
CDKN1B WILD-TYPE	21	38	113	97	105	72	19	38

'CDKN1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.178 (Fisher's exact test), Q value = 1

Table S242. Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
CDKN1B MUTATED	3	0	3
CDKN1B WILD-TYPE	119	126	258

'CDKN1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0062 (Chi-square test), Q value = 1

Table S243. Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
CDKN1B MUTATED	5	0	4	1	0
CDKN1B WILD-TYPE	353	246	86	224	42

Figure S98. Get High-res Image Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CDKN1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0724 (Chi-square test), Q value = 1

Table S244. Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
CDKN1B MUTATED	0	4	0	0	0	1
CDKN1B WILD-TYPE	111	146	99	127	54	105

'CDKN1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S245. Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
CDKN1B MUTATED	1	2	2
CDKN1B WILD-TYPE	144	128	116

'CDKN1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 1

Table S246. Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
CDKN1B MUTATED	3	2	0
CDKN1B WILD-TYPE	151	111	126

'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0966 (Fisher's exact test), Q value = 1

Table S247. Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
CDKN1B MUTATED	0	3	7
CDKN1B WILD-TYPE	267	181	511

'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S248. Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
CDKN1B MUTATED	0	6	4
CDKN1B WILD-TYPE	226	418	315

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S249. Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
CDKN1B MUTATED	4	6	0
CDKN1B WILD-TYPE	392	270	284

Figure S99. Get High-res Image Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S250. Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
CDKN1B MUTATED	0	3	7
CDKN1B WILD-TYPE	246	288	412

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S251. Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
CDKN1B MUTATED	3	3	0
CDKN1B WILD-TYPE	247	206	192

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S252. Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
CDKN1B MUTATED	0	2	4
CDKN1B WILD-TYPE	140	167	338

'ZFP36L1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.57 (Chi-square test), Q value = 1

Table S253. Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
ZFP36L1 MUTATED	1	0	1	0	1	1	0	1
ZFP36L1 WILD-TYPE	20	38	113	97	107	72	19	38

'ZFP36L1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S254. Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
ZFP36L1 MUTATED	1	0	4
ZFP36L1 WILD-TYPE	121	126	257

'ZFP36L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0208 (Chi-square test), Q value = 1

Table S255. Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
ZFP36L1 MUTATED	1	4	3	0	1
ZFP36L1 WILD-TYPE	357	242	87	225	41

Figure S100. Get High-res Image Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZFP36L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.244 (Chi-square test), Q value = 1

Table S256. Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
ZFP36L1 MUTATED	1	0	1	3	0	0
ZFP36L1 WILD-TYPE	110	150	98	124	54	106

'ZFP36L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 1

Table S257. Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
ZFP36L1 MUTATED	0	0	3
ZFP36L1 WILD-TYPE	145	130	115

Figure S101. Get High-res Image Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'ZFP36L1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 1

Table S258. Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
ZFP36L1 MUTATED	0	3	0
ZFP36L1 WILD-TYPE	154	110	126

Figure S102. Get High-res Image Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 1

Table S259. Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
ZFP36L1 MUTATED	2	0	7
ZFP36L1 WILD-TYPE	265	184	511

'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S260. Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
ZFP36L1 MUTATED	2	6	1
ZFP36L1 WILD-TYPE	224	418	318

'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S261. Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
ZFP36L1 MUTATED	5	3	1
ZFP36L1 WILD-TYPE	391	273	283

'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S262. Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
ZFP36L1 MUTATED	2	2	5
ZFP36L1 WILD-TYPE	244	289	414

'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S263. Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
ZFP36L1 MUTATED	2	1	2
ZFP36L1 WILD-TYPE	248	208	190

'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.716 (Fisher's exact test), Q value = 1

Table S264. Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
ZFP36L1 MUTATED	2	1	2
ZFP36L1 WILD-TYPE	138	168	340

'ASB10 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.869 (Chi-square test), Q value = 1

Table S265. Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
ASB10 MUTATED	0	0	1	1	2	0	0	0
ASB10 WILD-TYPE	21	38	113	96	106	73	19	39

'ASB10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S266. Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
ASB10 MUTATED	0	1	3
ASB10 WILD-TYPE	122	125	258

'ASB10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.978 (Chi-square test), Q value = 1

Table S267. Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
ASB10 MUTATED	3	2	1	2	0
ASB10 WILD-TYPE	355	244	89	223	42

'ASB10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.738 (Chi-square test), Q value = 1

Table S268. Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
ASB10 MUTATED	2	3	1	1	1	0
ASB10 WILD-TYPE	109	147	98	126	53	106

'ASB10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.501 (Fisher's exact test), Q value = 1

Table S269. Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
ASB10 MUTATED	3	0	5
ASB10 WILD-TYPE	264	184	513

'ASB10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S270. Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
ASB10 MUTATED	2	4	2
ASB10 WILD-TYPE	224	420	317

'ASB10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0926 (Fisher's exact test), Q value = 1

Table S271. Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
ASB10 MUTATED	6	0	2
ASB10 WILD-TYPE	390	276	282

'ASB10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S272. Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
ASB10 MUTATED	3	2	3
ASB10 WILD-TYPE	243	289	416

'ASB10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S273. Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
ASB10 MUTATED	2	1	2
ASB10 WILD-TYPE	248	208	190

'ASB10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S274. Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
ASB10 MUTATED	1	1	3
ASB10 WILD-TYPE	139	168	339

'HIST1H3B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.638 (Chi-square test), Q value = 1

Table S275. Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
HIST1H3B MUTATED	0	0	1	1	0	2	0	1
HIST1H3B WILD-TYPE	21	38	113	96	108	71	19	38

'HIST1H3B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S276. Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
HIST1H3B MUTATED	1	1	3
HIST1H3B WILD-TYPE	121	125	258

'HIST1H3B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.917 (Chi-square test), Q value = 1

Table S277. Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
HIST1H3B MUTATED	3	3	1	3	1
HIST1H3B WILD-TYPE	355	243	89	222	41

'HIST1H3B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.733 (Chi-square test), Q value = 1

Table S278. Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
HIST1H3B MUTATED	2	1	2	3	0	1
HIST1H3B WILD-TYPE	109	149	97	124	54	105

'HIST1H3B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S279. Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
HIST1H3B MUTATED	3	1	1
HIST1H3B WILD-TYPE	142	129	117

'HIST1H3B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S280. Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
HIST1H3B MUTATED	2	1	2
HIST1H3B WILD-TYPE	152	112	124

'HIST1H3B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 1

Table S281. Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
HIST1H3B MUTATED	2	2	7
HIST1H3B WILD-TYPE	265	182	511

'HIST1H3B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.467 (Fisher's exact test), Q value = 1

Table S282. Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
HIST1H3B MUTATED	2	7	2
HIST1H3B WILD-TYPE	224	417	317

'HIST1H3B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S283. Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
HIST1H3B MUTATED	6	2	3
HIST1H3B WILD-TYPE	390	274	281

'HIST1H3B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S284. Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
HIST1H3B MUTATED	2	5	4
HIST1H3B WILD-TYPE	244	286	415

'HIST1H3B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S285. Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
HIST1H3B MUTATED	3	2	1
HIST1H3B WILD-TYPE	247	207	191

'HIST1H3B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S286. Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
HIST1H3B MUTATED	1	2	3
HIST1H3B WILD-TYPE	139	167	339

'FAM86B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.738 (Chi-square test), Q value = 1

Table S287. Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
FAM86B1 MUTATED	3	2	0	2	1
FAM86B1 WILD-TYPE	355	244	90	223	41

'FAM86B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.891 (Chi-square test), Q value = 1

Table S288. Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
FAM86B1 MUTATED	2	1	1	2	0	1
FAM86B1 WILD-TYPE	109	149	98	125	54	105

'FAM86B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S289. Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
FAM86B1 MUTATED	2	2	4
FAM86B1 WILD-TYPE	265	182	514

'FAM86B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S290. Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
FAM86B1 MUTATED	2	2	4
FAM86B1 WILD-TYPE	224	422	315

'FAM86B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S291. Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
FAM86B1 MUTATED	1	4	3
FAM86B1 WILD-TYPE	395	272	281

'FAM86B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.6 (Fisher's exact test), Q value = 1

Table S292. Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
FAM86B1 MUTATED	2	1	5
FAM86B1 WILD-TYPE	244	290	414

'FAM86B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S293. Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
FAM86B1 MUTATED	2	3	2
FAM86B1 WILD-TYPE	248	206	190

'FAM86B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S294. Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
FAM86B1 MUTATED	1	3	3
FAM86B1 WILD-TYPE	139	166	339

'PIK3R1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0266 (Chi-square test), Q value = 1

Table S295. Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
PIK3R1 MUTATED	0	0	1	1	1	5	0	0
PIK3R1 WILD-TYPE	21	38	113	96	107	68	19	39

Figure S103. Get High-res Image Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PIK3R1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S296. Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
PIK3R1 MUTATED	1	3	4
PIK3R1 WILD-TYPE	121	123	257

'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.88 (Chi-square test), Q value = 1

Table S297. Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
PIK3R1 MUTATED	4	5	1	4	1
PIK3R1 WILD-TYPE	354	241	89	221	41

'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0868 (Chi-square test), Q value = 1

Table S298. Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
PIK3R1 MUTATED	3	1	3	0	0	0
PIK3R1 WILD-TYPE	108	149	96	127	54	106

'PIK3R1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S299. Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
PIK3R1 MUTATED	3	1	1
PIK3R1 WILD-TYPE	142	129	117

'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S300. Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
PIK3R1 MUTATED	3	0	2
PIK3R1 WILD-TYPE	151	113	124

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 1

Table S301. Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
PIK3R1 MUTATED	5	0	10
PIK3R1 WILD-TYPE	262	184	508

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.53 (Fisher's exact test), Q value = 1

Table S302. Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
PIK3R1 MUTATED	4	8	3
PIK3R1 WILD-TYPE	222	416	316

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S303. Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
PIK3R1 MUTATED	10	1	3
PIK3R1 WILD-TYPE	386	275	281

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S304. Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
PIK3R1 MUTATED	4	4	6
PIK3R1 WILD-TYPE	242	287	413

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S305. Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
PIK3R1 MUTATED	7	1	3
PIK3R1 WILD-TYPE	243	208	189

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S306. Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
PIK3R1 MUTATED	3	1	7
PIK3R1 WILD-TYPE	137	168	335

'MYH9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.711 (Chi-square test), Q value = 1

Table S307. Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
MYH9 MUTATED	0	1	0	2	2	1	1	1
MYH9 WILD-TYPE	21	37	114	95	106	72	18	38

'MYH9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S308. Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
MYH9 MUTATED	2	4	2
MYH9 WILD-TYPE	120	122	259

'MYH9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.228 (Chi-square test), Q value = 1

Table S309. Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
MYH9 MUTATED	10	5	0	2	0
MYH9 WILD-TYPE	348	241	90	223	42

'MYH9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.437 (Chi-square test), Q value = 1

Table S310. Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
MYH9 MUTATED	2	5	4	2	0	1
MYH9 WILD-TYPE	109	145	95	125	54	105

'MYH9 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S311. Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
MYH9 MUTATED	4	2	2
MYH9 WILD-TYPE	141	128	116

'MYH9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S312. Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
MYH9 MUTATED	2	2	4
MYH9 WILD-TYPE	152	111	122

'MYH9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.873 (Fisher's exact test), Q value = 1

Table S313. Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
MYH9 MUTATED	6	3	10
MYH9 WILD-TYPE	261	181	508

'MYH9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S314. Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
MYH9 MUTATED	5	6	8
MYH9 WILD-TYPE	221	418	311

'MYH9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S315. Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
MYH9 MUTATED	8	7	4
MYH9 WILD-TYPE	388	269	280

'MYH9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0668 (Fisher's exact test), Q value = 1

Table S316. Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
MYH9 MUTATED	4	2	13
MYH9 WILD-TYPE	242	289	406

'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S317. Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
MYH9 MUTATED	4	6	4
MYH9 WILD-TYPE	246	203	188

'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S318. Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
MYH9 MUTATED	2	7	5
MYH9 WILD-TYPE	138	162	337

'CASP8 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.423 (Chi-square test), Q value = 1

Table S319. Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
CASP8 MUTATED	0	0	1	0	3	0	0	1
CASP8 WILD-TYPE	21	38	113	97	105	73	19	38

'CASP8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S320. Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
CASP8 MUTATED	2	0	3
CASP8 WILD-TYPE	120	126	258

'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.387 (Chi-square test), Q value = 1

Table S321. Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
CASP8 MUTATED	4	2	3	3	0
CASP8 WILD-TYPE	354	244	87	222	42

'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.372 (Chi-square test), Q value = 1

Table S322. Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
CASP8 MUTATED	2	4	0	0	1	2
CASP8 WILD-TYPE	109	146	99	127	53	104

'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S323. Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
CASP8 MUTATED	1	3	1
CASP8 WILD-TYPE	144	127	117

'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S324. Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
CASP8 MUTATED	3	1	1
CASP8 WILD-TYPE	151	112	125

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S325. Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
CASP8 MUTATED	3	2	7
CASP8 WILD-TYPE	264	182	511

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S326. Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
CASP8 MUTATED	3	5	4
CASP8 WILD-TYPE	223	419	315

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.402 (Fisher's exact test), Q value = 1

Table S327. Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
CASP8 MUTATED	3	5	4
CASP8 WILD-TYPE	393	271	280

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S328. Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
CASP8 MUTATED	5	2	5
CASP8 WILD-TYPE	241	289	414

'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S329. Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
CASP8 MUTATED	2	3	3
CASP8 WILD-TYPE	248	206	189

'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S330. Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
CASP8 MUTATED	3	2	3
CASP8 WILD-TYPE	137	167	339

'COL6A5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.144 (Chi-square test), Q value = 1

Table S331. Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
COL6A5 MUTATED	0	1	1	4	6	0	0	0
COL6A5 WILD-TYPE	21	37	113	93	102	73	19	39

'COL6A5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.44 (Fisher's exact test), Q value = 1

Table S332. Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
COL6A5 MUTATED	2	5	5
COL6A5 WILD-TYPE	120	121	256

'COL6A5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.631 (Chi-square test), Q value = 1

Table S333. Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
COL6A5 MUTATED	10	4	3	7	0
COL6A5 WILD-TYPE	348	242	87	218	42

'COL6A5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.342 (Chi-square test), Q value = 1

Table S334. Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
COL6A5 MUTATED	5	4	1	6	1	1
COL6A5 WILD-TYPE	106	146	98	121	53	105

'COL6A5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.075 (Fisher's exact test), Q value = 1

Table S335. Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
COL6A5 MUTATED	5	5	0
COL6A5 WILD-TYPE	140	125	118

'COL6A5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.076 (Fisher's exact test), Q value = 1

Table S336. Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
COL6A5 MUTATED	5	0	5
COL6A5 WILD-TYPE	149	113	121

'COL6A5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S337. Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
COL6A5 MUTATED	10	2	13
COL6A5 WILD-TYPE	257	182	505

'COL6A5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S338. Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
COL6A5 MUTATED	9	12	4
COL6A5 WILD-TYPE	217	412	315

'COL6A5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 1

Table S339. Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
COL6A5 MUTATED	12	2	11
COL6A5 WILD-TYPE	384	274	273

Figure S104. Get High-res Image Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'COL6A5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S340. Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
COL6A5 MUTATED	10	6	9
COL6A5 WILD-TYPE	236	285	410

'COL6A5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 1

Table S341. Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
COL6A5 MUTATED	7	2	10
COL6A5 WILD-TYPE	243	207	182

Figure S105. Get High-res Image Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'COL6A5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 1

Table S342. Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
COL6A5 MUTATED	9	2	8
COL6A5 WILD-TYPE	131	167	334

Figure S106. Get High-res Image Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TBL1XR1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.123 (Chi-square test), Q value = 1

Table S343. Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
TBL1XR1 MUTATED	1	0	1	0	5	1	0	0
TBL1XR1 WILD-TYPE	20	38	113	97	103	72	19	39

'TBL1XR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S344. Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
TBL1XR1 MUTATED	2	0	6
TBL1XR1 WILD-TYPE	120	126	255

'TBL1XR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0446 (Chi-square test), Q value = 1

Table S345. Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
TBL1XR1 MUTATED	6	1	3	0	0
TBL1XR1 WILD-TYPE	352	245	87	225	42

Figure S107. Get High-res Image Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TBL1XR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.44 (Chi-square test), Q value = 1

Table S346. Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
TBL1XR1 MUTATED	0	2	0	0	0	1
TBL1XR1 WILD-TYPE	111	148	99	127	54	105

'TBL1XR1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S347. Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
TBL1XR1 MUTATED	2	4	1
TBL1XR1 WILD-TYPE	143	126	117

'TBL1XR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S348. Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
TBL1XR1 MUTATED	4	2	1
TBL1XR1 WILD-TYPE	150	111	125

'TBL1XR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.426 (Fisher's exact test), Q value = 1

Table S349. Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
TBL1XR1 MUTATED	1	3	6
TBL1XR1 WILD-TYPE	266	181	512

'TBL1XR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S350. Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
TBL1XR1 MUTATED	0	5	5
TBL1XR1 WILD-TYPE	226	419	314

'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 1

Table S351. Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
TBL1XR1 MUTATED	7	2	1
TBL1XR1 WILD-TYPE	389	274	283

'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0499 (Fisher's exact test), Q value = 1

Table S352. Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
TBL1XR1 MUTATED	0	2	8
TBL1XR1 WILD-TYPE	246	289	411

Figure S108. Get High-res Image Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S353. Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
TBL1XR1 MUTATED	4	2	1
TBL1XR1 WILD-TYPE	246	207	191

'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.239 (Fisher's exact test), Q value = 1

Table S354. Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
TBL1XR1 MUTATED	0	1	6
TBL1XR1 WILD-TYPE	140	168	336

'ASXL2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.403 (Chi-square test), Q value = 1

Table S355. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
ASXL2 MUTATED	1	1	1	5	2	1	0	0
ASXL2 WILD-TYPE	20	37	113	92	106	72	19	39

'ASXL2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0975 (Fisher's exact test), Q value = 1

Table S356. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
ASXL2 MUTATED	2	6	3
ASXL2 WILD-TYPE	120	120	258

'ASXL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.894 (Chi-square test), Q value = 1

Table S357. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
ASXL2 MUTATED	6	5	1	4	0
ASXL2 WILD-TYPE	352	241	89	221	42

'ASXL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.868 (Chi-square test), Q value = 1

Table S358. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
ASXL2 MUTATED	1	2	2	1	0	2
ASXL2 WILD-TYPE	110	148	97	126	54	104

'ASXL2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S359. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
ASXL2 MUTATED	3	0	2
ASXL2 WILD-TYPE	142	130	116

'ASXL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00505 (Fisher's exact test), Q value = 1

Table S360. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
ASXL2 MUTATED	0	0	5
ASXL2 WILD-TYPE	154	113	121

Figure S109. Get High-res Image Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.334 (Fisher's exact test), Q value = 1

Table S361. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
ASXL2 MUTATED	7	2	7
ASXL2 WILD-TYPE	260	182	511

'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S362. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
ASXL2 MUTATED	6	6	4
ASXL2 WILD-TYPE	220	418	315

'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S363. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
ASXL2 MUTATED	6	4	5
ASXL2 WILD-TYPE	390	272	279

'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S364. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
ASXL2 MUTATED	7	2	6
ASXL2 WILD-TYPE	239	289	413

'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S365. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
ASXL2 MUTATED	2	3	3
ASXL2 WILD-TYPE	248	206	189

'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 1

Table S366. Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
ASXL2 MUTATED	3	3	2
ASXL2 WILD-TYPE	137	166	340

'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.135 (Chi-square test), Q value = 1

Table S367. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
ARID1A MUTATED	3	1	4	2	3	1	0	1
ARID1A WILD-TYPE	18	37	110	95	105	72	19	38

'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.943 (Fisher's exact test), Q value = 1

Table S368. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
ARID1A MUTATED	4	3	8
ARID1A WILD-TYPE	118	123	253

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0552 (Chi-square test), Q value = 1

Table S369. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
ARID1A MUTATED	9	12	0	3	2
ARID1A WILD-TYPE	349	234	90	222	40

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.104 (Chi-square test), Q value = 1

Table S370. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
ARID1A MUTATED	1	5	2	8	1	1
ARID1A WILD-TYPE	110	145	97	119	53	105

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S371. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
ARID1A MUTATED	4	3	3
ARID1A WILD-TYPE	141	127	115

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S372. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
ARID1A MUTATED	5	1	4
ARID1A WILD-TYPE	149	112	122

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S373. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
ARID1A MUTATED	4	4	19
ARID1A WILD-TYPE	263	180	499

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S374. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
ARID1A MUTATED	3	13	11
ARID1A WILD-TYPE	223	411	308

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S375. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
ARID1A MUTATED	14	9	4
ARID1A WILD-TYPE	382	267	280

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.13 (Fisher's exact test), Q value = 1

Table S376. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
ARID1A MUTATED	6	13	8
ARID1A WILD-TYPE	240	278	411

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 1

Table S377. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
ARID1A MUTATED	5	7	2
ARID1A WILD-TYPE	245	202	190

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S378. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
ARID1A MUTATED	2	4	8
ARID1A WILD-TYPE	138	165	334

'AQP12A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.715 (Chi-square test), Q value = 1

Table S379. Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
AQP12A MUTATED	0	1	1	0	1	0	0	0
AQP12A WILD-TYPE	21	37	113	97	107	73	19	39

'AQP12A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S380. Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
AQP12A MUTATED	2	0	1
AQP12A WILD-TYPE	120	126	260

'AQP12A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.23 (Chi-square test), Q value = 1

Table S381. Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
AQP12A MUTATED	1	4	0	1	0
AQP12A WILD-TYPE	357	242	90	224	42

'AQP12A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0317 (Chi-square test), Q value = 1

Table S382. Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
AQP12A MUTATED	1	0	3	0	0	0
AQP12A WILD-TYPE	110	150	96	127	54	106

Figure S110. Get High-res Image Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'AQP12A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S383. Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
AQP12A MUTATED	0	1	2
AQP12A WILD-TYPE	145	129	116

'AQP12A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 1

Table S384. Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
AQP12A MUTATED	3	0	0
AQP12A WILD-TYPE	151	113	126

'AQP12A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S385. Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
AQP12A MUTATED	1	1	4
AQP12A WILD-TYPE	266	183	514

'AQP12A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S386. Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
AQP12A MUTATED	1	4	1
AQP12A WILD-TYPE	225	420	318

'AQP12A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S387. Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
AQP12A MUTATED	3	2	1
AQP12A WILD-TYPE	393	274	283

'AQP12A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S388. Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
AQP12A MUTATED	1	2	3
AQP12A WILD-TYPE	245	289	416

'AQP12A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S389. Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
AQP12A MUTATED	2	1	1
AQP12A WILD-TYPE	248	208	191

'AQP12A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S390. Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
AQP12A MUTATED	1	1	2
AQP12A WILD-TYPE	139	168	340

'EPDR1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.379 (Chi-square test), Q value = 1

Table S391. Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
EPDR1 MUTATED	0	1	1	0	0	2	0	0
EPDR1 WILD-TYPE	21	37	113	97	108	71	19	39

'EPDR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S392. Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
EPDR1 MUTATED	1	1	2
EPDR1 WILD-TYPE	121	125	259

'EPDR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.719 (Chi-square test), Q value = 1

Table S393. Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
EPDR1 MUTATED	1	2	0	2	0
EPDR1 WILD-TYPE	357	244	90	223	42

'EPDR1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S394. Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
EPDR1 MUTATED	2	2	0
EPDR1 WILD-TYPE	143	128	118

'EPDR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S395. Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
EPDR1 MUTATED	3	0	1
EPDR1 WILD-TYPE	151	113	125

'EPDR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S396. Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
EPDR1 MUTATED	2	0	3
EPDR1 WILD-TYPE	265	184	515

'EPDR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S397. Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
EPDR1 MUTATED	1	2	2
EPDR1 WILD-TYPE	225	422	317

'EPDR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S398. Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
EPDR1 MUTATED	1	1	2
EPDR1 WILD-TYPE	395	275	282

'EPDR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S399. Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
EPDR1 MUTATED	1	1	2
EPDR1 WILD-TYPE	245	290	417

'EPDR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 1

Table S400. Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
EPDR1 MUTATED	0	2	1
EPDR1 WILD-TYPE	250	207	191

'EPDR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S401. Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
EPDR1 MUTATED	0	1	2
EPDR1 WILD-TYPE	140	168	340

'ERBB2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.886 (Chi-square test), Q value = 1

Table S402. Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
ERBB2 MUTATED	1	1	2	1	3	3	0	1
ERBB2 WILD-TYPE	20	37	112	96	105	70	19	38

'ERBB2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.349 (Fisher's exact test), Q value = 1

Table S403. Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
ERBB2 MUTATED	5	2	5
ERBB2 WILD-TYPE	117	124	256

'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.109 (Chi-square test), Q value = 1

Table S404. Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
ERBB2 MUTATED	11	3	4	2	0
ERBB2 WILD-TYPE	347	243	86	223	42

'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0134 (Chi-square test), Q value = 1

Table S405. Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
ERBB2 MUTATED	0	1	5	0	2	4
ERBB2 WILD-TYPE	111	149	94	127	52	102

Figure S111. Get High-res Image Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 1

Table S406. Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
ERBB2 MUTATED	2	2	4
ERBB2 WILD-TYPE	143	128	114

'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S407. Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
ERBB2 MUTATED	4	2	2
ERBB2 WILD-TYPE	150	111	124

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 1

Table S408. Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
ERBB2 MUTATED	4	7	10
ERBB2 WILD-TYPE	263	177	508

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S409. Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
ERBB2 MUTATED	4	7	10
ERBB2 WILD-TYPE	222	417	309

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S410. Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
ERBB2 MUTATED	9	10	1
ERBB2 WILD-TYPE	387	266	283

Figure S112. Get High-res Image Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000788 (Fisher's exact test), Q value = 0.6

Table S411. Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
ERBB2 MUTATED	2	1	17
ERBB2 WILD-TYPE	244	290	402

Figure S113. Get High-res Image Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.666 (Fisher's exact test), Q value = 1

Table S412. Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
ERBB2 MUTATED	5	5	2
ERBB2 WILD-TYPE	245	204	190

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.396 (Fisher's exact test), Q value = 1

Table S413. Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
ERBB2 MUTATED	1	5	6
ERBB2 WILD-TYPE	139	164	336

'MYB MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.631 (Chi-square test), Q value = 1

Table S414. Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
MYB MUTATED	0	0	2	2	4	0	0	1
MYB WILD-TYPE	21	38	112	95	104	73	19	38

'MYB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S415. Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
MYB MUTATED	2	2	5
MYB WILD-TYPE	120	124	256

'MYB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.208 (Chi-square test), Q value = 1

Table S416. Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
MYB MUTATED	6	1	3	2	0
MYB WILD-TYPE	352	245	87	223	42

'MYB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.512 (Chi-square test), Q value = 1

Table S417. Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
MYB MUTATED	2	1	1	0	1	0
MYB WILD-TYPE	109	149	98	127	53	106

'MYB MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S418. Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
MYB MUTATED	2	2	1
MYB WILD-TYPE	143	128	117

'MYB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.862 (Fisher's exact test), Q value = 1

Table S419. Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
MYB MUTATED	2	2	1
MYB WILD-TYPE	152	111	125

'MYB MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S420. Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
MYB MUTATED	3	2	7
MYB WILD-TYPE	264	182	511

'MYB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S421. Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
MYB MUTATED	3	6	3
MYB WILD-TYPE	223	418	316

'MYB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 1

Table S422. Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
MYB MUTATED	7	3	2
MYB WILD-TYPE	389	273	282

'MYB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S423. Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
MYB MUTATED	2	4	6
MYB WILD-TYPE	244	287	413

'MYB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 1

Table S424. Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
MYB MUTATED	4	1	1
MYB WILD-TYPE	246	208	191

'MYB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S425. Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
MYB MUTATED	2	0	4
MYB WILD-TYPE	138	169	338

'TMEM151B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.915 (Chi-square test), Q value = 1

Table S426. Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
TMEM151B MUTATED	0	0	0	1	1	1	0	0
TMEM151B WILD-TYPE	21	38	114	96	107	72	19	39

'TMEM151B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S427. Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
TMEM151B MUTATED	0	2	1
TMEM151B WILD-TYPE	122	124	260

'TMEM151B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.306 (Chi-square test), Q value = 1

Table S428. Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
TMEM151B MUTATED	0	2	1	3	0
TMEM151B WILD-TYPE	358	244	89	222	42

'TMEM151B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.52 (Chi-square test), Q value = 1

Table S429. Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
TMEM151B MUTATED	2	1	0	1	0	0
TMEM151B WILD-TYPE	109	149	99	126	54	106

'TMEM151B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 1

Table S430. Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
TMEM151B MUTATED	0	0	3
TMEM151B WILD-TYPE	145	130	115

Figure S114. Get High-res Image Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TMEM151B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S431. Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
TMEM151B MUTATED	0	2	1
TMEM151B WILD-TYPE	154	111	125

'TMEM151B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 1

Table S432. Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
TMEM151B MUTATED	3	0	3
TMEM151B WILD-TYPE	264	184	515

'TMEM151B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S433. Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
TMEM151B MUTATED	4	2	0
TMEM151B WILD-TYPE	222	422	319

Figure S115. Get High-res Image Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TMEM151B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S434. Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
TMEM151B MUTATED	2	0	3
TMEM151B WILD-TYPE	394	276	281

'TMEM151B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 1

Table S435. Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
TMEM151B MUTATED	3	0	2
TMEM151B WILD-TYPE	243	291	417

'TMEM151B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 1

Table S436. Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
TMEM151B MUTATED	1	0	2
TMEM151B WILD-TYPE	249	209	190

'TMEM151B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S437. Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
TMEM151B MUTATED	1	0	2
TMEM151B WILD-TYPE	139	169	340

'GALNTL6 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.921 (Chi-square test), Q value = 1

Table S438. Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
GALNTL6 MUTATED	0	0	1	1	0	1	0	0
GALNTL6 WILD-TYPE	21	38	113	96	108	72	19	39

'GALNTL6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S439. Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
GALNTL6 MUTATED	0	1	2
GALNTL6 WILD-TYPE	122	125	259

'GALNTL6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.211 (Chi-square test), Q value = 1

Table S440. Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
GALNTL6 MUTATED	0	2	0	3	0
GALNTL6 WILD-TYPE	358	244	90	222	42

'GALNTL6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0124 (Chi-square test), Q value = 1

Table S441. Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
GALNTL6 MUTATED	3	0	0	0	0	0
GALNTL6 WILD-TYPE	108	150	99	127	54	106

Figure S116. Get High-res Image Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'GALNTL6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 1

Table S442. Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
GALNTL6 MUTATED	4	0	1
GALNTL6 WILD-TYPE	263	184	517

Figure S117. Get High-res Image Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'GALNTL6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.102 (Fisher's exact test), Q value = 1

Table S443. Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
GALNTL6 MUTATED	3	2	0
GALNTL6 WILD-TYPE	223	422	319

'GALNTL6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S444. Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
GALNTL6 MUTATED	2	0	2
GALNTL6 WILD-TYPE	394	276	282

'GALNTL6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.165 (Fisher's exact test), Q value = 1

Table S445. Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
GALNTL6 MUTATED	2	2	0
GALNTL6 WILD-TYPE	244	289	419

'GALNTL6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 1

Table S446. Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
GALNTL6 MUTATED	1	0	2
GALNTL6 WILD-TYPE	249	209	190

'GALNTL6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S447. Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
GALNTL6 MUTATED	2	0	1
GALNTL6 WILD-TYPE	138	169	341

'AKD1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.44 (Chi-square test), Q value = 1

Table S448. Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
AKD1 MUTATED	0	0	0	3	3	1	0	0
AKD1 WILD-TYPE	21	38	114	94	105	72	19	39

'AKD1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S449. Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
AKD1 MUTATED	1	3	3
AKD1 WILD-TYPE	121	123	258

'AKD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.322 (Chi-square test), Q value = 1

Table S450. Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
AKD1 MUTATED	6	2	3	5	2
AKD1 WILD-TYPE	352	244	87	220	40

'AKD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.545 (Chi-square test), Q value = 1

Table S451. Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
AKD1 MUTATED	4	1	3	3	1	1
AKD1 WILD-TYPE	107	149	96	124	53	105

'AKD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 1

Table S452. Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
AKD1 MUTATED	2	0	3
AKD1 WILD-TYPE	143	130	115

'AKD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S453. Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
AKD1 MUTATED	0	2	3
AKD1 WILD-TYPE	154	111	123

'AKD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 1

Table S454. Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
AKD1 MUTATED	7	1	10
AKD1 WILD-TYPE	260	183	508

'AKD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0769 (Fisher's exact test), Q value = 1

Table S455. Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
AKD1 MUTATED	7	9	2
AKD1 WILD-TYPE	219	415	317

'AKD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 1

Table S456. Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
AKD1 MUTATED	10	2	6
AKD1 WILD-TYPE	386	274	278

'AKD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.582 (Fisher's exact test), Q value = 1

Table S457. Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
AKD1 MUTATED	6	6	6
AKD1 WILD-TYPE	240	285	413

'AKD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 1

Table S458. Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
AKD1 MUTATED	6	1	6
AKD1 WILD-TYPE	244	208	186

'AKD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.339 (Fisher's exact test), Q value = 1

Table S459. Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
AKD1 MUTATED	5	3	5
AKD1 WILD-TYPE	135	166	337

'AARS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.403 (Chi-square test), Q value = 1

Table S460. Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
AARS MUTATED	0	1	2	2	0	0	1	0
AARS WILD-TYPE	21	37	112	95	108	73	18	39

'AARS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 1

Table S461. Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
AARS MUTATED	4	2	0
AARS WILD-TYPE	118	124	261

Figure S118. Get High-res Image Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'AARS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.742 (Chi-square test), Q value = 1

Table S462. Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
AARS MUTATED	4	2	0	2	1
AARS WILD-TYPE	354	244	90	223	41

'AARS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.509 (Chi-square test), Q value = 1

Table S463. Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
AARS MUTATED	1	0	2	1	0	2
AARS WILD-TYPE	110	150	97	126	54	104

'AARS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S464. Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
AARS MUTATED	1	2	1
AARS WILD-TYPE	144	128	117

'AARS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.563 (Fisher's exact test), Q value = 1

Table S465. Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
AARS MUTATED	2	0	2
AARS WILD-TYPE	152	113	124

'AARS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S466. Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
AARS MUTATED	3	4	2
AARS WILD-TYPE	264	180	516

'AARS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S467. Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
AARS MUTATED	3	1	5
AARS WILD-TYPE	223	423	314

'AARS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S468. Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
AARS MUTATED	3	1	5
AARS WILD-TYPE	393	275	279

'AARS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.359 (Fisher's exact test), Q value = 1

Table S469. Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
AARS MUTATED	3	4	2
AARS WILD-TYPE	243	287	417

'AARS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 1

Table S470. Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
AARS MUTATED	1	0	4
AARS WILD-TYPE	249	209	188

Figure S119. Get High-res Image Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'AARS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S471. Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
AARS MUTATED	1	2	2
AARS WILD-TYPE	139	167	340

'HLA-C MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.316 (Chi-square test), Q value = 1

Table S472. Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
HLA-C MUTATED	0	1	0	0	0	1	0	1
HLA-C WILD-TYPE	21	37	114	97	108	72	19	38

'HLA-C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S473. Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
HLA-C MUTATED	2	0	1
HLA-C WILD-TYPE	120	126	260

'HLA-C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.551 (Chi-square test), Q value = 1

Table S474. Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
HLA-C MUTATED	3	2	0	4	0
HLA-C WILD-TYPE	355	244	90	221	42

'HLA-C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0926 (Chi-square test), Q value = 1

Table S475. Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
HLA-C MUTATED	4	3	1	0	0	0
HLA-C WILD-TYPE	107	147	98	127	54	106

'HLA-C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.399 (Fisher's exact test), Q value = 1

Table S476. Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
HLA-C MUTATED	1	0	2
HLA-C WILD-TYPE	144	130	116

'HLA-C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S477. Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
HLA-C MUTATED	2	1	0
HLA-C WILD-TYPE	152	112	126

'HLA-C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0806 (Fisher's exact test), Q value = 1

Table S478. Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
HLA-C MUTATED	5	2	2
HLA-C WILD-TYPE	262	182	516

'HLA-C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S479. Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
HLA-C MUTATED	4	3	2
HLA-C WILD-TYPE	222	421	317

'HLA-C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 1

Table S480. Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
HLA-C MUTATED	2	2	5
HLA-C WILD-TYPE	394	274	279

'HLA-C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S481. Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
HLA-C MUTATED	5	1	3
HLA-C WILD-TYPE	241	290	416

'HLA-C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 1

Table S482. Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
HLA-C MUTATED	1	1	4
HLA-C WILD-TYPE	249	208	188

'HLA-C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 1

Table S483. Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
HLA-C MUTATED	4	1	1
HLA-C WILD-TYPE	136	168	341

Figure S120. Get High-res Image Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GPRIN2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.655 (Chi-square test), Q value = 1

Table S484. Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
GPRIN2 MUTATED	0	1	0	2	3	1	0	0
GPRIN2 WILD-TYPE	21	37	114	95	105	72	19	39

'GPRIN2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S485. Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
GPRIN2 MUTATED	2	3	2
GPRIN2 WILD-TYPE	120	123	259

'GPRIN2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.927 (Chi-square test), Q value = 1

Table S486. Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
GPRIN2 MUTATED	4	2	1	3	1
GPRIN2 WILD-TYPE	354	244	89	222	41

'GPRIN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.655 (Chi-square test), Q value = 1

Table S487. Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
GPRIN2 MUTATED	2	2	2	1	0	0
GPRIN2 WILD-TYPE	109	148	97	126	54	106

'GPRIN2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S488. Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
GPRIN2 MUTATED	3	2	1
GPRIN2 WILD-TYPE	142	128	117

'GPRIN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S489. Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
GPRIN2 MUTATED	3	0	3
GPRIN2 WILD-TYPE	151	113	123

'GPRIN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S490. Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
GPRIN2 MUTATED	5	1	5
GPRIN2 WILD-TYPE	262	183	513

'GPRIN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 1

Table S491. Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
GPRIN2 MUTATED	4	3	4
GPRIN2 WILD-TYPE	222	421	315

'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.67 (Fisher's exact test), Q value = 1

Table S492. Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
GPRIN2 MUTATED	3	3	4
GPRIN2 WILD-TYPE	393	273	280

'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S493. Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
GPRIN2 MUTATED	4	1	5
GPRIN2 WILD-TYPE	242	290	414

'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S494. Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
GPRIN2 MUTATED	3	2	4
GPRIN2 WILD-TYPE	247	207	188

'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S495. Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
GPRIN2 MUTATED	4	1	4
GPRIN2 WILD-TYPE	136	168	338

'TRPM5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.237 (Chi-square test), Q value = 1

Table S496. Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
TRPM5 MUTATED	0	0	1	1	0	0	1	0
TRPM5 WILD-TYPE	21	38	113	96	108	73	18	39

'TRPM5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S497. Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
TRPM5 MUTATED	1	1	1
TRPM5 WILD-TYPE	121	125	260

'TRPM5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.606 (Chi-square test), Q value = 1

Table S498. Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
TRPM5 MUTATED	3	3	0	4	1
TRPM5 WILD-TYPE	355	243	90	221	41

'TRPM5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.033 (Chi-square test), Q value = 1

Table S499. Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
TRPM5 MUTATED	5	0	1	0	1	2
TRPM5 WILD-TYPE	106	150	98	127	53	104

Figure S121. Get High-res Image Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TRPM5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S500. Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
TRPM5 MUTATED	2	1	0
TRPM5 WILD-TYPE	143	129	118

'TRPM5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S501. Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
TRPM5 MUTATED	2	0	1
TRPM5 WILD-TYPE	152	113	125

'TRPM5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 1

Table S502. Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
TRPM5 MUTATED	7	1	3
TRPM5 WILD-TYPE	260	183	515

Figure S122. Get High-res Image Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TRPM5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0603 (Fisher's exact test), Q value = 1

Table S503. Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
TRPM5 MUTATED	6	2	3
TRPM5 WILD-TYPE	220	422	316

'TRPM5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0933 (Fisher's exact test), Q value = 1

Table S504. Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
TRPM5 MUTATED	2	2	7
TRPM5 WILD-TYPE	394	274	277

'TRPM5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0937 (Fisher's exact test), Q value = 1

Table S505. Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
TRPM5 MUTATED	6	1	4
TRPM5 WILD-TYPE	240	290	415

'TRPM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 1

Table S506. Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
TRPM5 MUTATED	1	2	7
TRPM5 WILD-TYPE	249	207	185

Figure S123. Get High-res Image Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TRPM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 1

Table S507. Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
TRPM5 MUTATED	5	3	2
TRPM5 WILD-TYPE	135	166	340

Figure S124. Get High-res Image Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ANKRD12 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.178 (Chi-square test), Q value = 1

Table S508. Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
ANKRD12 MUTATED	0	1	6	0	2	1	0	0
ANKRD12 WILD-TYPE	21	37	108	97	106	72	19	39

'ANKRD12 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 1

Table S509. Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
ANKRD12 MUTATED	4	0	6
ANKRD12 WILD-TYPE	118	126	255

'ANKRD12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.603 (Chi-square test), Q value = 1

Table S510. Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
ANKRD12 MUTATED	6	3	3	5	0
ANKRD12 WILD-TYPE	352	243	87	220	42

'ANKRD12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.897 (Chi-square test), Q value = 1

Table S511. Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
ANKRD12 MUTATED	1	2	3	2	1	2
ANKRD12 WILD-TYPE	110	148	96	125	53	104

'ANKRD12 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S512. Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
ANKRD12 MUTATED	4	1	1
ANKRD12 WILD-TYPE	141	129	117

'ANKRD12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S513. Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
ANKRD12 MUTATED	4	1	1
ANKRD12 WILD-TYPE	150	112	125

'ANKRD12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S514. Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
ANKRD12 MUTATED	3	5	10
ANKRD12 WILD-TYPE	264	179	508

'ANKRD12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 1

Table S515. Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
ANKRD12 MUTATED	1	6	11
ANKRD12 WILD-TYPE	225	418	308

Figure S125. Get High-res Image Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ANKRD12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 1

Table S516. Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
ANKRD12 MUTATED	10	4	4
ANKRD12 WILD-TYPE	386	272	280

'ANKRD12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.332 (Fisher's exact test), Q value = 1

Table S517. Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
ANKRD12 MUTATED	2	7	9
ANKRD12 WILD-TYPE	244	284	410

'ANKRD12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S518. Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
ANKRD12 MUTATED	3	3	3
ANKRD12 WILD-TYPE	247	206	189

'ANKRD12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.491 (Fisher's exact test), Q value = 1

Table S519. Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
ANKRD12 MUTATED	1	4	4
ANKRD12 WILD-TYPE	139	165	338

'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.818 (Chi-square test), Q value = 1

Table S520. Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
FBXW7 MUTATED	0	1	1	2	2	0	0	0
FBXW7 WILD-TYPE	21	37	113	95	106	73	19	39

'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S521. Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
FBXW7 MUTATED	2	2	2
FBXW7 WILD-TYPE	120	124	259

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0642 (Chi-square test), Q value = 1

Table S522. Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
FBXW7 MUTATED	5	2	0	8	0
FBXW7 WILD-TYPE	353	244	90	217	42

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00296 (Chi-square test), Q value = 1

Table S523. Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
FBXW7 MUTATED	7	2	1	0	0	1
FBXW7 WILD-TYPE	104	148	98	127	54	105

Figure S126. Get High-res Image Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S524. Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
FBXW7 MUTATED	2	1	0
FBXW7 WILD-TYPE	143	129	118

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S525. Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
FBXW7 MUTATED	2	0	1
FBXW7 WILD-TYPE	152	113	125

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.222 (Fisher's exact test), Q value = 1

Table S526. Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
FBXW7 MUTATED	7	1	7
FBXW7 WILD-TYPE	260	183	511

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.13 (Fisher's exact test), Q value = 1

Table S527. Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
FBXW7 MUTATED	7	5	3
FBXW7 WILD-TYPE	219	419	316

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.398 (Fisher's exact test), Q value = 1

Table S528. Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
FBXW7 MUTATED	5	3	7
FBXW7 WILD-TYPE	391	273	277

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S529. Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
FBXW7 MUTATED	7	2	6
FBXW7 WILD-TYPE	239	289	413

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.411 (Fisher's exact test), Q value = 1

Table S530. Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
FBXW7 MUTATED	3	2	5
FBXW7 WILD-TYPE	247	207	187

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0968 (Fisher's exact test), Q value = 1

Table S531. Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
FBXW7 MUTATED	5	2	3
FBXW7 WILD-TYPE	135	167	339

'PRICKLE3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.335 (Chi-square test), Q value = 1

Table S532. Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
PRICKLE3 MUTATED	1	0	0	3	1	2	0	0
PRICKLE3 WILD-TYPE	20	38	114	94	107	71	19	39

'PRICKLE3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 1

Table S533. Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
PRICKLE3 MUTATED	0	3	4
PRICKLE3 WILD-TYPE	122	123	257

'PRICKLE3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.941 (Chi-square test), Q value = 1

Table S534. Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
PRICKLE3 MUTATED	4	2	1	3	0
PRICKLE3 WILD-TYPE	354	244	89	222	42

'PRICKLE3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.645 (Chi-square test), Q value = 1

Table S535. Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
PRICKLE3 MUTATED	0	1	2	1	0	1
PRICKLE3 WILD-TYPE	111	149	97	126	54	105

'PRICKLE3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S536. Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
PRICKLE3 MUTATED	4	1	2
PRICKLE3 WILD-TYPE	141	129	116

'PRICKLE3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S537. Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
PRICKLE3 MUTATED	2	2	3
PRICKLE3 WILD-TYPE	152	111	123

'PRICKLE3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 1

Table S538. Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
PRICKLE3 MUTATED	6	1	4
PRICKLE3 WILD-TYPE	261	183	514

'PRICKLE3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S539. Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
PRICKLE3 MUTATED	4	5	2
PRICKLE3 WILD-TYPE	222	419	317

'PRICKLE3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S540. Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
PRICKLE3 MUTATED	5	2	4
PRICKLE3 WILD-TYPE	391	274	280

'PRICKLE3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0864 (Fisher's exact test), Q value = 1

Table S541. Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
PRICKLE3 MUTATED	6	3	2
PRICKLE3 WILD-TYPE	240	288	417

'PRICKLE3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.594 (Fisher's exact test), Q value = 1

Table S542. Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
PRICKLE3 MUTATED	2	1	3
PRICKLE3 WILD-TYPE	248	208	189

'PRICKLE3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S543. Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
PRICKLE3 MUTATED	2	2	2
PRICKLE3 WILD-TYPE	138	167	340

'WDR52 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.768 (Chi-square test), Q value = 1

Table S544. Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
WDR52 MUTATED	0	1	1	2	1	1	1	0
WDR52 WILD-TYPE	21	37	113	95	107	72	18	39

'WDR52 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0565 (Fisher's exact test), Q value = 1

Table S545. Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
WDR52 MUTATED	2	4	1
WDR52 WILD-TYPE	120	122	260

'WDR52 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.318 (Chi-square test), Q value = 1

Table S546. Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
WDR52 MUTATED	4	3	2	7	0
WDR52 WILD-TYPE	354	243	88	218	42

'WDR52 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.165 (Chi-square test), Q value = 1

Table S547. Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
WDR52 MUTATED	4	0	2	3	1	0
WDR52 WILD-TYPE	107	150	97	124	53	106

'WDR52 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00424 (Fisher's exact test), Q value = 1

Table S548. Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
WDR52 MUTATED	6	0	0
WDR52 WILD-TYPE	139	130	118

Figure S127. Get High-res Image Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'WDR52 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S549. Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
WDR52 MUTATED	2	0	4
WDR52 WILD-TYPE	152	113	122

'WDR52 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S550. Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
WDR52 MUTATED	10	1	5
WDR52 WILD-TYPE	257	183	513

Figure S128. Get High-res Image Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'WDR52 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S551. Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
WDR52 MUTATED	6	5	5
WDR52 WILD-TYPE	220	419	314

'WDR52 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00958 (Fisher's exact test), Q value = 1

Table S552. Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
WDR52 MUTATED	4	1	10
WDR52 WILD-TYPE	392	275	274

Figure S129. Get High-res Image Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'WDR52 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S553. Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
WDR52 MUTATED	5	6	4
WDR52 WILD-TYPE	241	285	415

'WDR52 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 1

Table S554. Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
WDR52 MUTATED	4	0	5
WDR52 WILD-TYPE	246	209	187

Figure S130. Get High-res Image Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'WDR52 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S555. Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
WDR52 MUTATED	2	2	5
WDR52 WILD-TYPE	138	167	337

'CDC42EP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.579 (Chi-square test), Q value = 1

Table S556. Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
CDC42EP1 MUTATED	0	0	1	2	0	0	0	1
CDC42EP1 WILD-TYPE	21	38	113	95	108	73	19	38

'CDC42EP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S557. Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
CDC42EP1 MUTATED	1	2	1
CDC42EP1 WILD-TYPE	121	124	260

'CDC42EP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.607 (Chi-square test), Q value = 1

Table S558. Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
CDC42EP1 MUTATED	2	0	1	2	0
CDC42EP1 WILD-TYPE	356	246	89	223	42

'CDC42EP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.252 (Chi-square test), Q value = 1

Table S559. Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
CDC42EP1 MUTATED	0	1	0	0	0	2
CDC42EP1 WILD-TYPE	111	149	99	127	54	104

'CDC42EP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S560. Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
CDC42EP1 MUTATED	1	2	1
CDC42EP1 WILD-TYPE	144	128	117

'CDC42EP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S561. Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
CDC42EP1 MUTATED	1	1	2
CDC42EP1 WILD-TYPE	153	112	124

'CDC42EP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S562. Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
CDC42EP1 MUTATED	2	1	2
CDC42EP1 WILD-TYPE	265	183	516

'CDC42EP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S563. Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
CDC42EP1 MUTATED	2	1	2
CDC42EP1 WILD-TYPE	224	423	317

'CDC42EP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S564. Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
CDC42EP1 MUTATED	1	2	2
CDC42EP1 WILD-TYPE	395	274	282

'CDC42EP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 1

Table S565. Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
CDC42EP1 MUTATED	3	0	2
CDC42EP1 WILD-TYPE	243	291	417

'ERBB3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.412 (Chi-square test), Q value = 1

Table S566. Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
ERBB3 MUTATED	1	0	1	3	1	3	1	0
ERBB3 WILD-TYPE	20	38	113	94	107	70	18	39

'ERBB3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S567. Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
ERBB3 MUTATED	2	5	3
ERBB3 WILD-TYPE	120	121	258

'ERBB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.803 (Chi-square test), Q value = 1

Table S568. Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
ERBB3 MUTATED	6	6	1	4	0
ERBB3 WILD-TYPE	352	240	89	221	42

'ERBB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.192 (Chi-square test), Q value = 1

Table S569. Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
ERBB3 MUTATED	1	0	3	3	1	0
ERBB3 WILD-TYPE	110	150	96	124	53	106

'ERBB3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S570. Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
ERBB3 MUTATED	5	1	3
ERBB3 WILD-TYPE	140	129	115

'ERBB3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S571. Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
ERBB3 MUTATED	3	1	5
ERBB3 WILD-TYPE	151	112	121

'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S572. Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
ERBB3 MUTATED	8	1	9
ERBB3 WILD-TYPE	259	183	509

'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0986 (Fisher's exact test), Q value = 1

Table S573. Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
ERBB3 MUTATED	6	10	2
ERBB3 WILD-TYPE	220	414	317

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.925 (Fisher's exact test), Q value = 1

Table S574. Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
ERBB3 MUTATED	7	6	5
ERBB3 WILD-TYPE	389	270	279

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S575. Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
ERBB3 MUTATED	6	5	7
ERBB3 WILD-TYPE	240	286	412

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S576. Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
ERBB3 MUTATED	5	4	4
ERBB3 WILD-TYPE	245	205	188

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S577. Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
ERBB3 MUTATED	3	3	7
ERBB3 WILD-TYPE	137	166	335

'FHOD3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0431 (Chi-square test), Q value = 1

Table S578. Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
FHOD3 MUTATED	0	1	1	5	0	0	0	0
FHOD3 WILD-TYPE	21	37	113	92	108	73	19	39

Figure S131. Get High-res Image Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'FHOD3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 1

Table S579. Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
FHOD3 MUTATED	1	5	1
FHOD3 WILD-TYPE	121	121	260

Figure S132. Get High-res Image Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FHOD3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0649 (Chi-square test), Q value = 1

Table S580. Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
FHOD3 MUTATED	2	4	0	7	0
FHOD3 WILD-TYPE	356	242	90	218	42

'FHOD3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0907 (Chi-square test), Q value = 1

Table S581. Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
FHOD3 MUTATED	3	0	3	0	2	1
FHOD3 WILD-TYPE	108	150	96	127	52	105

'FHOD3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S582. Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
FHOD3 MUTATED	4	1	1
FHOD3 WILD-TYPE	141	129	117

'FHOD3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 1

Table S583. Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
FHOD3 MUTATED	1	0	5
FHOD3 WILD-TYPE	153	113	121

Figure S133. Get High-res Image Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'FHOD3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 1

Table S584. Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
FHOD3 MUTATED	8	2	3
FHOD3 WILD-TYPE	259	182	515

Figure S134. Get High-res Image Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FHOD3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00208 (Fisher's exact test), Q value = 1

Table S585. Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
FHOD3 MUTATED	8	1	4
FHOD3 WILD-TYPE	218	423	315

Figure S135. Get High-res Image Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FHOD3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0829 (Fisher's exact test), Q value = 1

Table S586. Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
FHOD3 MUTATED	2	4	7
FHOD3 WILD-TYPE	394	272	277

'FHOD3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00313 (Fisher's exact test), Q value = 1

Table S587. Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
FHOD3 MUTATED	8	0	5
FHOD3 WILD-TYPE	238	291	414

Figure S136. Get High-res Image Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FHOD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S588. Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
FHOD3 MUTATED	3	2	4
FHOD3 WILD-TYPE	247	207	188

'FHOD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 1

Table S589. Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
FHOD3 MUTATED	4	2	3
FHOD3 WILD-TYPE	136	167	339

'PTHLH MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.442 (Chi-square test), Q value = 1

Table S590. Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
PTHLH MUTATED	0	1	0	0	1	2	0	1
PTHLH WILD-TYPE	21	37	114	97	107	71	19	38

'PTHLH MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S591. Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
PTHLH MUTATED	2	0	3
PTHLH WILD-TYPE	120	126	258

'PTHLH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0276 (Chi-square test), Q value = 1

Table S592. Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
PTHLH MUTATED	1	2	1	1	2
PTHLH WILD-TYPE	357	244	89	224	40

Figure S137. Get High-res Image Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PTHLH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00411 (Chi-square test), Q value = 1

Table S593. Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
PTHLH MUTATED	1	0	4	0	0	0
PTHLH WILD-TYPE	110	150	95	127	54	106

Figure S138. Get High-res Image Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PTHLH MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S594. Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
PTHLH MUTATED	1	1	2
PTHLH WILD-TYPE	144	129	116

'PTHLH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S595. Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
PTHLH MUTATED	2	2	0
PTHLH WILD-TYPE	152	111	126

'PTHLH MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S596. Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
PTHLH MUTATED	0	1	6
PTHLH WILD-TYPE	267	183	512

'PTHLH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S597. Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
PTHLH MUTATED	0	5	2
PTHLH WILD-TYPE	226	419	317

'PTHLH MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S598. Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
PTHLH MUTATED	5	1	0
PTHLH WILD-TYPE	391	275	284

'PTHLH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.214 (Fisher's exact test), Q value = 1

Table S599. Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
PTHLH MUTATED	0	1	5
PTHLH WILD-TYPE	246	290	414

'SHISA4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0213 (Chi-square test), Q value = 1

Table S600. Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
SHISA4 MUTATED	0	2	1	0	0	0	0	0
SHISA4 WILD-TYPE	21	36	113	97	108	73	19	39

Figure S139. Get High-res Image Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SHISA4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S601. Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
SHISA4 MUTATED	2	0	1
SHISA4 WILD-TYPE	120	126	260

'SHISA4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.188 (Chi-square test), Q value = 1

Table S602. Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
SHISA4 MUTATED	0	2	0	2	1
SHISA4 WILD-TYPE	358	244	90	223	41

'SHISA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.413 (Chi-square test), Q value = 1

Table S603. Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
SHISA4 MUTATED	2	0	1	0	0	1
SHISA4 WILD-TYPE	109	150	98	127	54	105

'SHISA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S604. Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
SHISA4 MUTATED	2	1	2
SHISA4 WILD-TYPE	265	183	516

'SHISA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S605. Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
SHISA4 MUTATED	1	1	3
SHISA4 WILD-TYPE	225	423	316

'SHISA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 1

Table S606. Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
SHISA4 MUTATED	3	2	0
SHISA4 WILD-TYPE	393	274	284

'SHISA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S607. Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
SHISA4 MUTATED	1	2	2
SHISA4 WILD-TYPE	245	289	417

'KCNN3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.321 (Chi-square test), Q value = 1

Table S608. Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
KCNN3 MUTATED	1	0	0	2	0	1	0	1
KCNN3 WILD-TYPE	20	38	114	95	108	72	19	38

'KCNN3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S609. Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
KCNN3 MUTATED	1	2	2
KCNN3 WILD-TYPE	121	124	259

'KCNN3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.207 (Chi-square test), Q value = 1

Table S610. Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
KCNN3 MUTATED	1	4	0	4	0
KCNN3 WILD-TYPE	357	242	90	221	42

'KCNN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.289 (Chi-square test), Q value = 1

Table S611. Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
KCNN3 MUTATED	2	0	0	2	1	0
KCNN3 WILD-TYPE	109	150	99	125	53	106

'KCNN3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S612. Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
KCNN3 MUTATED	3	0	1
KCNN3 WILD-TYPE	142	130	117

'KCNN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S613. Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
KCNN3 MUTATED	0	1	3
KCNN3 WILD-TYPE	154	112	123

'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 1

Table S614. Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
KCNN3 MUTATED	4	0	5
KCNN3 WILD-TYPE	263	184	513

'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.213 (Fisher's exact test), Q value = 1

Table S615. Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
KCNN3 MUTATED	4	4	1
KCNN3 WILD-TYPE	222	420	318

'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S616. Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
KCNN3 MUTATED	3	1	5
KCNN3 WILD-TYPE	393	275	279

'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.763 (Fisher's exact test), Q value = 1

Table S617. Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
KCNN3 MUTATED	3	3	3
KCNN3 WILD-TYPE	243	288	416

'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 1

Table S618. Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
KCNN3 MUTATED	4	0	1
KCNN3 WILD-TYPE	246	209	191

'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S619. Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
KCNN3 MUTATED	0	1	4
KCNN3 WILD-TYPE	140	168	338

'FGFR2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.841 (Chi-square test), Q value = 1

Table S620. Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
FGFR2 MUTATED	0	0	1	1	2	2	0	0
FGFR2 WILD-TYPE	21	38	113	96	106	71	19	39

'FGFR2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S621. Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
FGFR2 MUTATED	1	2	3
FGFR2 WILD-TYPE	121	124	258

'FGFR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.323 (Chi-square test), Q value = 1

Table S622. Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
FGFR2 MUTATED	4	2	3	2	0
FGFR2 WILD-TYPE	354	244	87	223	42

'FGFR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.24 (Chi-square test), Q value = 1

Table S623. Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
FGFR2 MUTATED	0	0	2	2	1	0
FGFR2 WILD-TYPE	111	150	97	125	53	106

'FGFR2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S624. Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
FGFR2 MUTATED	2	2	1
FGFR2 WILD-TYPE	143	128	117

'FGFR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S625. Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
FGFR2 MUTATED	2	1	2
FGFR2 WILD-TYPE	152	112	124

'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S626. Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
FGFR2 MUTATED	3	1	7
FGFR2 WILD-TYPE	264	183	511

'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S627. Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
FGFR2 MUTATED	2	6	3
FGFR2 WILD-TYPE	224	418	316

'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 1

Table S628. Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
FGFR2 MUTATED	4	2	5
FGFR2 WILD-TYPE	392	274	279

'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S629. Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
FGFR2 MUTATED	3	4	4
FGFR2 WILD-TYPE	243	287	415

'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S630. Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
FGFR2 MUTATED	2	2	3
FGFR2 WILD-TYPE	248	207	189

'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S631. Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
FGFR2 MUTATED	0	3	4
FGFR2 WILD-TYPE	140	166	338

'HLA-DRB5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00723 (Chi-square test), Q value = 1

Table S632. Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
HLA-DRB5 MUTATED	0	2	0	0	0	0	0	1
HLA-DRB5 WILD-TYPE	21	36	114	97	108	73	19	38

Figure S140. Get High-res Image Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'HLA-DRB5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 1

Table S633. Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
HLA-DRB5 MUTATED	3	0	0
HLA-DRB5 WILD-TYPE	119	126	261

Figure S141. Get High-res Image Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'HLA-DRB5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.127 (Chi-square test), Q value = 1

Table S634. Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
HLA-DRB5 MUTATED	1	3	0	0	1
HLA-DRB5 WILD-TYPE	357	243	90	225	41

'HLA-DRB5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.654 (Chi-square test), Q value = 1

Table S635. Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
HLA-DRB5 MUTATED	1	1	2	1	0	0
HLA-DRB5 WILD-TYPE	110	149	97	126	54	106

'HLA-DRB5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S636. Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
HLA-DRB5 MUTATED	1	2	3
HLA-DRB5 WILD-TYPE	266	182	515

'HLA-DRB5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S637. Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
HLA-DRB5 MUTATED	1	2	3
HLA-DRB5 WILD-TYPE	225	422	316

'HLA-DRB5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S638. Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
HLA-DRB5 MUTATED	4	2	0
HLA-DRB5 WILD-TYPE	392	274	284

'HLA-DRB5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 1

Table S639. Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
HLA-DRB5 MUTATED	1	0	5
HLA-DRB5 WILD-TYPE	245	291	414

'HLA-DRB5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S640. Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
HLA-DRB5 MUTATED	2	1	0
HLA-DRB5 WILD-TYPE	248	208	192

'HLA-DRB5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S641. Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
HLA-DRB5 MUTATED	0	1	2
HLA-DRB5 WILD-TYPE	140	168	340

'ICOSLG MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.693 (Chi-square test), Q value = 1

Table S642. Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
ICOSLG MUTATED	0	0	2	1	0	0	0	0
ICOSLG WILD-TYPE	21	38	112	96	108	73	19	39

'ICOSLG MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S643. Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
ICOSLG MUTATED	0	1	2
ICOSLG WILD-TYPE	122	125	259

'ICOSLG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.161 (Chi-square test), Q value = 1

Table S644. Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
ICOSLG MUTATED	0	3	0	2	1
ICOSLG WILD-TYPE	358	243	90	223	41

'ICOSLG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.654 (Chi-square test), Q value = 1

Table S645. Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
ICOSLG MUTATED	1	1	2	1	0	0
ICOSLG WILD-TYPE	110	149	97	126	54	106

'ICOSLG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 1

Table S646. Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
ICOSLG MUTATED	1	0	5
ICOSLG WILD-TYPE	266	184	513

'ICOSLG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S647. Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
ICOSLG MUTATED	1	3	2
ICOSLG WILD-TYPE	225	421	317

'ICOSLG MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S648. Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
ICOSLG MUTATED	3	1	2
ICOSLG WILD-TYPE	393	275	282

'ICOSLG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.772 (Fisher's exact test), Q value = 1

Table S649. Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
ICOSLG MUTATED	2	1	3
ICOSLG WILD-TYPE	244	290	416

'ICOSLG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S650. Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
ICOSLG MUTATED	1	1	1
ICOSLG WILD-TYPE	249	208	191

'ICOSLG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S651. Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
ICOSLG MUTATED	0	1	2
ICOSLG WILD-TYPE	140	168	340

'GYG2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.703 (Chi-square test), Q value = 1

Table S652. Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
GYG2 MUTATED	0	1	3	1	1	0	0	0
GYG2 WILD-TYPE	21	37	111	96	107	73	19	39

'GYG2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S653. Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
GYG2 MUTATED	1	1	4
GYG2 WILD-TYPE	121	125	257

'GYG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.189 (Chi-square test), Q value = 1

Table S654. Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
GYG2 MUTATED	2	5	0	1	0
GYG2 WILD-TYPE	356	241	90	224	42

'GYG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.719 (Chi-square test), Q value = 1

Table S655. Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
GYG2 MUTATED	2	1	1	1	0	0
GYG2 WILD-TYPE	109	149	98	126	54	106

'GYG2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S656. Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
GYG2 MUTATED	0	3	1
GYG2 WILD-TYPE	145	127	117

'GYG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0398 (Fisher's exact test), Q value = 1

Table S657. Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
GYG2 MUTATED	4	0	0
GYG2 WILD-TYPE	150	113	126

Figure S142. Get High-res Image Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'GYG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S658. Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
GYG2 MUTATED	2	1	5
GYG2 WILD-TYPE	265	183	513

'GYG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S659. Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
GYG2 MUTATED	2	5	1
GYG2 WILD-TYPE	224	419	318

'GYG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 1

Table S660. Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
GYG2 MUTATED	3	1	4
GYG2 WILD-TYPE	393	275	280

'GYG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S661. Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
GYG2 MUTATED	2	3	3
GYG2 WILD-TYPE	244	288	416

'GYG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 1

Table S662. Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
GYG2 MUTATED	1	0	2
GYG2 WILD-TYPE	249	209	190

'GYG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S663. Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
GYG2 MUTATED	2	0	1
GYG2 WILD-TYPE	138	169	341

'PPEF1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.84 (Chi-square test), Q value = 1

Table S664. Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
PPEF1 MUTATED	0	0	3	2	1	1	0	0
PPEF1 WILD-TYPE	21	38	111	95	107	72	19	39

'PPEF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S665. Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
PPEF1 MUTATED	1	2	4
PPEF1 WILD-TYPE	121	124	257

'PPEF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0771 (Chi-square test), Q value = 1

Table S666. Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
PPEF1 MUTATED	0	6	1	3	1
PPEF1 WILD-TYPE	358	240	89	222	41

'PPEF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.36 (Chi-square test), Q value = 1

Table S667. Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
PPEF1 MUTATED	2	0	2	3	1	0
PPEF1 WILD-TYPE	109	150	97	124	53	106

'PPEF1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S668. Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
PPEF1 MUTATED	2	2	2
PPEF1 WILD-TYPE	143	128	116

'PPEF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S669. Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
PPEF1 MUTATED	2	2	2
PPEF1 WILD-TYPE	152	111	124

'PPEF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.249 (Fisher's exact test), Q value = 1

Table S670. Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
PPEF1 MUTATED	3	0	8
PPEF1 WILD-TYPE	264	184	510

'PPEF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.928 (Fisher's exact test), Q value = 1

Table S671. Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
PPEF1 MUTATED	3	5	3
PPEF1 WILD-TYPE	223	419	316

'PPEF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S672. Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
PPEF1 MUTATED	5	2	4
PPEF1 WILD-TYPE	391	274	280

'PPEF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.505 (Fisher's exact test), Q value = 1

Table S673. Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
PPEF1 MUTATED	4	4	3
PPEF1 WILD-TYPE	242	287	416

'PPEF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S674. Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
PPEF1 MUTATED	3	2	2
PPEF1 WILD-TYPE	247	207	190

'PPEF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S675. Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
PPEF1 MUTATED	3	2	2
PPEF1 WILD-TYPE	137	167	340

'MAP4K1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.828 (Chi-square test), Q value = 1

Table S676. Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
MAP4K1 MUTATED	0	0	1	2	1	0	0	0
MAP4K1 WILD-TYPE	21	38	113	95	107	73	19	39

'MAP4K1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S677. Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
MAP4K1 MUTATED	1	2	1
MAP4K1 WILD-TYPE	121	124	260

'MAP4K1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.232 (Chi-square test), Q value = 1

Table S678. Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
MAP4K1 MUTATED	1	3	1	5	0
MAP4K1 WILD-TYPE	357	243	89	220	42

'MAP4K1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.599 (Chi-square test), Q value = 1

Table S679. Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
MAP4K1 MUTATED	2	2	1	3	0	0
MAP4K1 WILD-TYPE	109	148	98	124	54	106

'MAP4K1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S680. Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
MAP4K1 MUTATED	1	1	1
MAP4K1 WILD-TYPE	144	129	117

'MAP4K1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S681. Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
MAP4K1 MUTATED	2	0	1
MAP4K1 WILD-TYPE	152	113	125

'MAP4K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S682. Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
MAP4K1 MUTATED	3	0	7
MAP4K1 WILD-TYPE	264	184	511

'MAP4K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0488 (Fisher's exact test), Q value = 1

Table S683. Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
MAP4K1 MUTATED	3	7	0
MAP4K1 WILD-TYPE	223	417	319

Figure S143. Get High-res Image Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MAP4K1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.443 (Fisher's exact test), Q value = 1

Table S684. Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
MAP4K1 MUTATED	6	1	3
MAP4K1 WILD-TYPE	390	275	281

'MAP4K1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S685. Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
MAP4K1 MUTATED	3	4	3
MAP4K1 WILD-TYPE	243	287	416

'MAP4K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 1

Table S686. Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
MAP4K1 MUTATED	5	1	1
MAP4K1 WILD-TYPE	245	208	191

'MAP4K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 1

Table S687. Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
MAP4K1 MUTATED	1	0	6
MAP4K1 WILD-TYPE	139	169	336

'ZNF41 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.81 (Chi-square test), Q value = 1

Table S688. Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
ZNF41 MUTATED	1	1	1	2	1	1	0	0
ZNF41 WILD-TYPE	20	37	113	95	107	72	19	39

'ZNF41 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S689. Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
ZNF41 MUTATED	2	3	2
ZNF41 WILD-TYPE	120	123	259

'ZNF41 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.602 (Chi-square test), Q value = 1

Table S690. Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
ZNF41 MUTATED	3	2	2	4	0
ZNF41 WILD-TYPE	355	244	88	221	42

'ZNF41 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.244 (Chi-square test), Q value = 1

Table S691. Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
ZNF41 MUTATED	1	0	3	1	0	1
ZNF41 WILD-TYPE	110	150	96	126	54	105

'ZNF41 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S692. Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
ZNF41 MUTATED	3	2	1
ZNF41 WILD-TYPE	142	128	117

'ZNF41 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S693. Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
ZNF41 MUTATED	4	0	2
ZNF41 WILD-TYPE	150	113	124

'ZNF41 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S694. Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
ZNF41 MUTATED	5	0	6
ZNF41 WILD-TYPE	262	184	512

'ZNF41 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S695. Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
ZNF41 MUTATED	4	5	2
ZNF41 WILD-TYPE	222	419	317

'ZNF41 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.37 (Fisher's exact test), Q value = 1

Table S696. Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
ZNF41 MUTATED	6	1	4
ZNF41 WILD-TYPE	390	275	280

'ZNF41 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S697. Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
ZNF41 MUTATED	3	4	4
ZNF41 WILD-TYPE	243	287	415

'ZNF41 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0918 (Fisher's exact test), Q value = 1

Table S698. Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
ZNF41 MUTATED	4	0	4
ZNF41 WILD-TYPE	246	209	188

'ZNF41 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S699. Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
ZNF41 MUTATED	1	0	7
ZNF41 WILD-TYPE	139	169	335

'FBXO17 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.831 (Chi-square test), Q value = 1

Table S700. Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
FBXO17 MUTATED	3	1	0	1	0
FBXO17 WILD-TYPE	355	245	90	224	42

'FBXO17 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.433 (Chi-square test), Q value = 1

Table S701. Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
FBXO17 MUTATED	0	1	0	2	0	2
FBXO17 WILD-TYPE	111	149	99	125	54	104

'FBXO17 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 1

Table S702. Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
FBXO17 MUTATED	0	1	4
FBXO17 WILD-TYPE	267	183	514

'FBXO17 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S703. Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
FBXO17 MUTATED	0	3	2
FBXO17 WILD-TYPE	226	421	317

'FBXO17 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S704. Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
FBXO17 MUTATED	3	1	1
FBXO17 WILD-TYPE	393	275	283

'FBXO17 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S705. Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
FBXO17 MUTATED	1	2	2
FBXO17 WILD-TYPE	245	289	417

'FBXO17 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S706. Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
FBXO17 MUTATED	1	1	1
FBXO17 WILD-TYPE	249	208	191

'FBXO17 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S707. Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
FBXO17 MUTATED	0	1	2
FBXO17 WILD-TYPE	140	168	340

'HRNR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.892 (Chi-square test), Q value = 1

Table S708. Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
HRNR MUTATED	0	1	5	5	4	4	0	1
HRNR WILD-TYPE	21	37	109	92	104	69	19	38

'HRNR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S709. Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
HRNR MUTATED	5	7	8
HRNR WILD-TYPE	117	119	253

'HRNR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.225 (Chi-square test), Q value = 1

Table S710. Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
HRNR MUTATED	12	4	5	7	3
HRNR WILD-TYPE	346	242	85	218	39

'HRNR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.944 (Chi-square test), Q value = 1

Table S711. Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
HRNR MUTATED	4	6	2	3	2	3
HRNR WILD-TYPE	107	144	97	124	52	103

'HRNR MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S712. Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
HRNR MUTATED	4	6	6
HRNR WILD-TYPE	141	124	112

'HRNR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S713. Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
HRNR MUTATED	8	3	5
HRNR WILD-TYPE	146	110	121

'HRNR MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S714. Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
HRNR MUTATED	10	7	14
HRNR WILD-TYPE	257	177	504

'HRNR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S715. Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
HRNR MUTATED	10	11	10
HRNR WILD-TYPE	216	413	309

'HRNR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S716. Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
HRNR MUTATED	14	5	11
HRNR WILD-TYPE	382	271	273

'HRNR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.677 (Fisher's exact test), Q value = 1

Table S717. Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
HRNR MUTATED	9	10	11
HRNR WILD-TYPE	237	281	408

'HRNR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.693 (Fisher's exact test), Q value = 1

Table S718. Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
HRNR MUTATED	8	4	5
HRNR WILD-TYPE	242	205	187

'HRNR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S719. Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
HRNR MUTATED	4	4	9
HRNR WILD-TYPE	136	165	333

'STAG2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.357 (Chi-square test), Q value = 1

Table S720. Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
STAG2 MUTATED	0	0	0	1	3	2	1	0
STAG2 WILD-TYPE	21	38	114	96	105	71	18	39

'STAG2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S721. Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
STAG2 MUTATED	1	2	4
STAG2 WILD-TYPE	121	124	257

'STAG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.294 (Chi-square test), Q value = 1

Table S722. Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
STAG2 MUTATED	5	3	0	3	2
STAG2 WILD-TYPE	353	243	90	222	40

'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.373 (Chi-square test), Q value = 1

Table S723. Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
STAG2 MUTATED	2	2	1	4	0	0
STAG2 WILD-TYPE	109	148	98	123	54	106

'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S724. Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
STAG2 MUTATED	3	2	1
STAG2 WILD-TYPE	142	128	117

'STAG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.676 (Fisher's exact test), Q value = 1

Table S725. Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
STAG2 MUTATED	2	1	3
STAG2 WILD-TYPE	152	112	123

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S726. Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
STAG2 MUTATED	5	1	7
STAG2 WILD-TYPE	262	183	511

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S727. Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
STAG2 MUTATED	3	5	5
STAG2 WILD-TYPE	223	419	314

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S728. Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
STAG2 MUTATED	6	1	6
STAG2 WILD-TYPE	390	275	278

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.595 (Fisher's exact test), Q value = 1

Table S729. Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
STAG2 MUTATED	5	3	5
STAG2 WILD-TYPE	241	288	414

'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S730. Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
STAG2 MUTATED	4	1	2
STAG2 WILD-TYPE	246	208	190

'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.883 (Fisher's exact test), Q value = 1

Table S731. Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
STAG2 MUTATED	2	1	4
STAG2 WILD-TYPE	138	168	338

'CEP57 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.324 (Chi-square test), Q value = 1

Table S732. Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
CEP57 MUTATED	0	0	0	1	0	2	0	0
CEP57 WILD-TYPE	21	38	114	96	108	71	19	39

'CEP57 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S733. Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
CEP57 MUTATED	0	1	2
CEP57 WILD-TYPE	122	125	259

'CEP57 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.406 (Chi-square test), Q value = 1

Table S734. Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
CEP57 MUTATED	2	0	1	3	0
CEP57 WILD-TYPE	356	246	89	222	42

'CEP57 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.145 (Chi-square test), Q value = 1

Table S735. Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
CEP57 MUTATED	0	1	1	0	0	3
CEP57 WILD-TYPE	111	149	98	127	54	103

'CEP57 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 1

Table S736. Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
CEP57 MUTATED	1	0	5
CEP57 WILD-TYPE	266	184	513

'CEP57 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S737. Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
CEP57 MUTATED	1	3	2
CEP57 WILD-TYPE	225	421	317

'CEP57 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0731 (Fisher's exact test), Q value = 1

Table S738. Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
CEP57 MUTATED	2	4	0
CEP57 WILD-TYPE	394	272	284

'CEP57 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.772 (Fisher's exact test), Q value = 1

Table S739. Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
CEP57 MUTATED	2	1	3
CEP57 WILD-TYPE	244	290	416

'CEP57 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0581 (Fisher's exact test), Q value = 1

Table S740. Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
CEP57 MUTATED	0	3	0
CEP57 WILD-TYPE	250	206	192

'CEP57 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S741. Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
CEP57 MUTATED	0	3	0
CEP57 WILD-TYPE	140	166	342

Figure S144. Get High-res Image Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SPRR2B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.734 (Chi-square test), Q value = 1

Table S742. Gene #65: 'SPRR2B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
SPRR2B MUTATED	2	0	0	1	0
SPRR2B WILD-TYPE	356	246	90	224	42

'SPRR2B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S743. Gene #65: 'SPRR2B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
SPRR2B MUTATED	0	0	3
SPRR2B WILD-TYPE	267	184	515

'SPRR2B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.798 (Fisher's exact test), Q value = 1

Table S744. Gene #65: 'SPRR2B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
SPRR2B MUTATED	0	2	1
SPRR2B WILD-TYPE	226	422	318

'SPRR2B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S745. Gene #65: 'SPRR2B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
SPRR2B MUTATED	2	1	0
SPRR2B WILD-TYPE	394	275	284

'SPRR2B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S746. Gene #65: 'SPRR2B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
SPRR2B MUTATED	0	1	2
SPRR2B WILD-TYPE	246	290	417

'ZFP36L2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.437 (Chi-square test), Q value = 1

Table S747. Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
ZFP36L2 MUTATED	0	0	1	1	0	1	1	0
ZFP36L2 WILD-TYPE	21	38	113	96	108	72	18	39

'ZFP36L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S748. Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
ZFP36L2 MUTATED	1	1	2
ZFP36L2 WILD-TYPE	121	125	259

'ZFP36L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0108 (Chi-square test), Q value = 1

Table S749. Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
ZFP36L2 MUTATED	1	3	1	0	2
ZFP36L2 WILD-TYPE	357	243	89	225	40

Figure S145. Get High-res Image Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZFP36L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.787 (Chi-square test), Q value = 1

Table S750. Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
ZFP36L2 MUTATED	1	1	1	2	0	0
ZFP36L2 WILD-TYPE	110	149	98	125	54	106

'ZFP36L2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S751. Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
ZFP36L2 MUTATED	1	1	1
ZFP36L2 WILD-TYPE	144	129	117

'ZFP36L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S752. Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
ZFP36L2 MUTATED	1	1	1
ZFP36L2 WILD-TYPE	153	112	125

'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S753. Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
ZFP36L2 MUTATED	1	0	6
ZFP36L2 WILD-TYPE	266	184	512

'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S754. Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
ZFP36L2 MUTATED	1	5	1
ZFP36L2 WILD-TYPE	225	419	318

'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S755. Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
ZFP36L2 MUTATED	4	2	1
ZFP36L2 WILD-TYPE	392	274	283

'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S756. Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
ZFP36L2 MUTATED	1	2	4
ZFP36L2 WILD-TYPE	245	289	415

'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S757. Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
ZFP36L2 MUTATED	2	2	1
ZFP36L2 WILD-TYPE	248	207	191

'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S758. Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
ZFP36L2 MUTATED	1	2	2
ZFP36L2 WILD-TYPE	139	167	340

'DMXL2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.697 (Chi-square test), Q value = 1

Table S759. Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
DMXL2 MUTATED	1	1	1	3	1	1	0	0
DMXL2 WILD-TYPE	20	37	113	94	107	72	19	39

'DMXL2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S760. Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
DMXL2 MUTATED	2	4	2
DMXL2 WILD-TYPE	120	122	259

'DMXL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0376 (Chi-square test), Q value = 1

Table S761. Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
DMXL2 MUTATED	2	5	3	9	0
DMXL2 WILD-TYPE	356	241	87	216	42

Figure S146. Get High-res Image Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'DMXL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.263 (Chi-square test), Q value = 1

Table S762. Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
DMXL2 MUTATED	5	0	2	3	1	3
DMXL2 WILD-TYPE	106	150	97	124	53	103

'DMXL2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S763. Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
DMXL2 MUTATED	4	0	1
DMXL2 WILD-TYPE	141	130	117

'DMXL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0727 (Fisher's exact test), Q value = 1

Table S764. Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
DMXL2 MUTATED	1	0	4
DMXL2 WILD-TYPE	153	113	122

'DMXL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 1

Table S765. Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
DMXL2 MUTATED	10	1	8
DMXL2 WILD-TYPE	257	183	510

Figure S147. Get High-res Image Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'DMXL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0566 (Fisher's exact test), Q value = 1

Table S766. Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
DMXL2 MUTATED	9	5	5
DMXL2 WILD-TYPE	217	419	314

'DMXL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 1

Table S767. Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
DMXL2 MUTATED	2	7	9
DMXL2 WILD-TYPE	394	269	275

Figure S148. Get High-res Image Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'DMXL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S768. Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
DMXL2 MUTATED	8	5	5
DMXL2 WILD-TYPE	238	286	414

'DMXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0713 (Fisher's exact test), Q value = 1

Table S769. Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
DMXL2 MUTATED	1	4	6
DMXL2 WILD-TYPE	249	205	186

'DMXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.102 (Fisher's exact test), Q value = 1

Table S770. Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
DMXL2 MUTATED	5	3	3
DMXL2 WILD-TYPE	135	166	339

'ZBTB7C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.673 (Chi-square test), Q value = 1

Table S771. Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
ZBTB7C MUTATED	2	1	1	0	0
ZBTB7C WILD-TYPE	356	245	89	225	42

'ZBTB7C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.752 (Chi-square test), Q value = 1

Table S772. Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
ZBTB7C MUTATED	0	1	1	0	0	1
ZBTB7C WILD-TYPE	111	149	98	127	54	105

'ZBTB7C MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S773. Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
ZBTB7C MUTATED	0	2	3
ZBTB7C WILD-TYPE	267	182	515

'ZBTB7C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S774. Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
ZBTB7C MUTATED	0	2	3
ZBTB7C WILD-TYPE	226	422	316

'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S775. Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
ZBTB7C MUTATED	2	2	1
ZBTB7C WILD-TYPE	394	274	283

'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S776. Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
ZBTB7C MUTATED	1	2	2
ZBTB7C WILD-TYPE	245	289	417

'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S777. Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
ZBTB7C MUTATED	2	1	0
ZBTB7C WILD-TYPE	248	208	192

'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S778. Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
ZBTB7C MUTATED	0	1	2
ZBTB7C WILD-TYPE	140	168	340

'MUC5B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.694 (Chi-square test), Q value = 1

Table S779. Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
MUC5B MUTATED	0	1	6	3	2	1	0	1
MUC5B WILD-TYPE	21	37	108	94	106	72	19	38

'MUC5B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S780. Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
MUC5B MUTATED	4	3	7
MUC5B WILD-TYPE	118	123	254

'MUC5B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.444 (Chi-square test), Q value = 1

Table S781. Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
MUC5B MUTATED	10	7	3	11	0
MUC5B WILD-TYPE	348	239	87	214	42

'MUC5B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.371 (Chi-square test), Q value = 1

Table S782. Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
MUC5B MUTATED	4	3	6	6	0	4
MUC5B WILD-TYPE	107	147	93	121	54	102

'MUC5B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S783. Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
MUC5B MUTATED	4	3	2
MUC5B WILD-TYPE	141	127	116

'MUC5B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S784. Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
MUC5B MUTATED	5	2	2
MUC5B WILD-TYPE	149	111	124

'MUC5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S785. Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
MUC5B MUTATED	6	5	22
MUC5B WILD-TYPE	261	179	496

'MUC5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S786. Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
MUC5B MUTATED	6	16	11
MUC5B WILD-TYPE	220	408	308

'MUC5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S787. Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
MUC5B MUTATED	15	11	7
MUC5B WILD-TYPE	381	265	277

'MUC5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.729 (Fisher's exact test), Q value = 1

Table S788. Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
MUC5B MUTATED	8	12	13
MUC5B WILD-TYPE	238	279	406

'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S789. Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
MUC5B MUTATED	9	8	5
MUC5B WILD-TYPE	241	201	187

'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S790. Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
MUC5B MUTATED	4	5	13
MUC5B WILD-TYPE	136	164	329

'XBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0199 (Chi-square test), Q value = 1

Table S791. Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
XBP1 MUTATED	0	4	0	0	0
XBP1 WILD-TYPE	358	242	90	225	42

Figure S149. Get High-res Image Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'XBP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.386 (Chi-square test), Q value = 1

Table S792. Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
XBP1 MUTATED	0	1	0	2	0	0
XBP1 WILD-TYPE	111	149	99	125	54	106

'XBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S793. Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
XBP1 MUTATED	1	1	2
XBP1 WILD-TYPE	266	183	516

'XBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S794. Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
XBP1 MUTATED	1	1	2
XBP1 WILD-TYPE	225	423	317

'XBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S795. Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
XBP1 MUTATED	2	2	0
XBP1 WILD-TYPE	394	274	284

'XBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 1

Table S796. Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
XBP1 MUTATED	0	2	2
XBP1 WILD-TYPE	246	289	417

'XBP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S797. Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
XBP1 MUTATED	3	1	0
XBP1 WILD-TYPE	247	208	192

'XBP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S798. Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
XBP1 MUTATED	0	1	3
XBP1 WILD-TYPE	140	168	339

'FXYD5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.693 (Chi-square test), Q value = 1

Table S799. Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
FXYD5 MUTATED	0	1	1	1	0	0	0	0
FXYD5 WILD-TYPE	21	37	113	96	108	73	19	39

'FXYD5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S800. Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
FXYD5 MUTATED	1	1	1
FXYD5 WILD-TYPE	121	125	260

'FXYD5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.259 (Chi-square test), Q value = 1

Table S801. Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
FXYD5 MUTATED	3	0	0	1	1
FXYD5 WILD-TYPE	355	246	90	224	41

'FXYD5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S802. Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
FXYD5 MUTATED	2	0	1
FXYD5 WILD-TYPE	143	130	117

'FXYD5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S803. Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
FXYD5 MUTATED	1	1	1
FXYD5 WILD-TYPE	153	112	125

'FXYD5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0797 (Fisher's exact test), Q value = 1

Table S804. Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
FXYD5 MUTATED	1	3	1
FXYD5 WILD-TYPE	266	181	517

'FXYD5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S805. Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
FXYD5 MUTATED	1	1	3
FXYD5 WILD-TYPE	225	423	316

'FXYD5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 1

Table S806. Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
FXYD5 MUTATED	1	3	1
FXYD5 WILD-TYPE	395	273	283

'FXYD5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.862 (Fisher's exact test), Q value = 1

Table S807. Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
FXYD5 MUTATED	1	1	3
FXYD5 WILD-TYPE	245	290	416

'ATXN2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.837 (Chi-square test), Q value = 1

Table S808. Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	38	114	97	108	73	19	39
ATXN2 MUTATED	0	0	2	3	2	2	0	0
ATXN2 WILD-TYPE	21	38	112	94	106	71	19	39

'ATXN2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S809. Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	126	261
ATXN2 MUTATED	2	4	3
ATXN2 WILD-TYPE	120	122	258

'ATXN2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.38 (Chi-square test), Q value = 1

Table S810. Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
ATXN2 MUTATED	7	2	0	5	0
ATXN2 WILD-TYPE	351	244	90	220	42

'ATXN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.701 (Chi-square test), Q value = 1

Table S811. Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
ATXN2 MUTATED	1	1	1	3	1	3
ATXN2 WILD-TYPE	110	149	98	124	53	103

'ATXN2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.234 (Fisher's exact test), Q value = 1

Table S812. Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	130	118
ATXN2 MUTATED	5	1	1
ATXN2 WILD-TYPE	140	129	117

'ATXN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0766 (Fisher's exact test), Q value = 1

Table S813. Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	113	126
ATXN2 MUTATED	2	0	5
ATXN2 WILD-TYPE	152	113	121

'ATXN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S814. Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
ATXN2 MUTATED	6	2	7
ATXN2 WILD-TYPE	261	182	511

'ATXN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S815. Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
ATXN2 MUTATED	6	5	4
ATXN2 WILD-TYPE	220	419	315

'ATXN2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.846 (Fisher's exact test), Q value = 1

Table S816. Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
ATXN2 MUTATED	5	5	5
ATXN2 WILD-TYPE	391	271	279

'ATXN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S817. Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
ATXN2 MUTATED	4	4	7
ATXN2 WILD-TYPE	242	287	412

'ATXN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S818. Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	209	192
ATXN2 MUTATED	4	4	2
ATXN2 WILD-TYPE	246	205	190

'ATXN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S819. Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	169	342
ATXN2 MUTATED	2	3	5
ATXN2 WILD-TYPE	138	166	337

'CCL13 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000151 (Chi-square test), Q value = 0.12

Table S820. Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	358	246	90	225	42
CCL13 MUTATED	0	1	1	0	2
CCL13 WILD-TYPE	358	245	89	225	40

Figure S150. Get High-res Image Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CCL13 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.306 (Chi-square test), Q value = 1

Table S821. Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	111	150	99	127	54	106
CCL13 MUTATED	0	0	1	2	0	0
CCL13 WILD-TYPE	111	150	98	125	54	106

'CCL13 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 1

Table S822. Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	267	184	518
CCL13 MUTATED	0	0	4
CCL13 WILD-TYPE	267	184	514

'CCL13 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S823. Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	424	319
CCL13 MUTATED	0	3	1
CCL13 WILD-TYPE	226	421	318

'CCL13 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S824. Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	396	276	284
CCL13 MUTATED	3	1	0
CCL13 WILD-TYPE	393	275	284

'CCL13 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S825. Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	246	291	419
CCL13 MUTATED	0	1	3
CCL13 WILD-TYPE	246	290	416

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = BRCA-TP.transferedmergedcluster.txt
Number of patients = 975
Number of significantly mutated genes = 73
Number of Molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[2] 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)

[3] 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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