Correlation between gene mutation status and molecular subtypes

Breast Invasive Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

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 (2016): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C16H4GQT

Overview

Introduction

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

Summary

Testing the association between mutation status of 79 genes and 12 molecular subtypes across 977 patients, 99 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'.
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'.
GATA3 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
MAP3K1 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
CDH1 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 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
RUNX1 mutation correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
CDKN1B mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
MAP2K4 mutation correlated to 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
FOXA1 mutation correlated to 'CN_CNMF'.
GPS2 mutation correlated to 'MRNA_CNMF' and 'CN_CNMF'.
RB1 mutation correlated to 'RPPA_CNMF' and 'MIRSEQ_MATURE_CNMF'.
CTCF mutation correlated to 'CN_CNMF'.
RBMX mutation correlated to 'MRNASEQ_CNMF'.
NCOR1 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.
ERBB2 mutation correlated to 'RPPA_CNMF'.
RAB42 mutation correlated to 'MRNA_CHIERARCHICAL'.
NBPF9 mutation correlated to 'CN_CNMF'.
MYB mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
TGS1 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.
USP36 mutation correlated to 'MRNA_CHIERARCHICAL'.
EYS mutation correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
ZFP36L1 mutation correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
ACTL6B mutation correlated to 'CN_CNMF'.
ZFP36L2 mutation correlated to 'CN_CNMF'.
MED23 mutation correlated to 'MIRSEQ_CNMF'.
ANKRD20A4 mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
DLG1 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.
GPRASP2 mutation correlated to 'MIRSEQ_CNMF'.
CCDC82 mutation correlated to 'RPPA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 79 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, 99 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
PIK3CA	316 (32%)	661	0.00805 (0.0978)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	3e-05 (0.000694)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	3e-05 (0.000694)	1e-05 (0.000256)
TP53	296 (30%)	681	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)
CDH1	107 (11%)	870	0.00207 (0.0322)	0.00102 (0.0173)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)
GATA3	97 (10%)	880	0.00876 (0.105)	9e-05 (0.00198)	0.00012 (0.00253)	7e-05 (0.00158)	0.00023 (0.00445)	1e-05 (0.000256)	1e-05 (0.000256)	1e-05 (0.000256)	0.00024 (0.00446)	1e-05 (0.000256)	1e-05 (0.000256)	0.0736 (0.421)
MAP3K1	71 (7%)	906	0.00168 (0.0275)	0.00203 (0.0321)	3e-05 (0.000694)	0.0243 (0.235)	0.00022 (0.00434)	1e-05 (0.000256)	0.00022 (0.00434)	0.00031 (0.00565)	0.0004 (0.00715)	0.00013 (0.00268)	0.00448 (0.0616)	0.0999 (0.504)
MAP2K4	32 (3%)	945	0.066 (0.409)	0.0692 (0.415)	0.0522 (0.375)	0.0321 (0.287)	0.0357 (0.307)	0.0113 (0.128)	0.00796 (0.0978)	0.0037 (0.0524)	0.00216 (0.033)	0.00024 (0.00446)	0.0334 (0.293)	0.00066 (0.0116)
CBFB	22 (2%)	955	0.662 (0.966)	0.468 (0.867)	0.00069 (0.0119)	0.0612 (0.403)	0.0491 (0.364)	0.202 (0.64)	2e-05 (0.000499)	0.613 (0.938)	0.0496 (0.364)	0.00011 (0.00237)	0.00577 (0.076)	0.00224 (0.0337)
RUNX1	29 (3%)	948	0.246 (0.701)	0.0413 (0.324)	0.0306 (0.276)	0.318 (0.777)	0.428 (0.837)	0.412 (0.835)	0.068 (0.414)	0.011 (0.125)	0.00467 (0.0632)	0.00362 (0.052)	0.374 (0.829)	0.373 (0.829)
GPS2	10 (1%)	967	0.00643 (0.0824)	0.607 (0.936)	0.00725 (0.0916)	0.392 (0.834)	0.072 (0.421)	0.886 (1.00)	0.484 (0.868)	0.0667 (0.409)	0.332 (0.789)	0.595 (0.931)	0.327 (0.788)	0.0379 (0.321)
RB1	19 (2%)	958	0.189 (0.631)	0.265 (0.712)	0.15 (0.586)	0.123 (0.565)	0.00738 (0.0921)	0.16 (0.595)	0.217 (0.655)	0.261 (0.709)	0.289 (0.753)	0.118 (0.565)	0.0235 (0.231)	0.263 (0.709)
EYS	21 (2%)	956	0.19 (0.631)	0.178 (0.624)	0.151 (0.586)	0.484 (0.868)	0.0409 (0.324)	0.0785 (0.438)	0.0108 (0.125)	0.201 (0.64)	0.0368 (0.314)	0.0146 (0.159)	0.199 (0.64)	0.0885 (0.458)
ZFP36L1	8 (1%)	969	0.204 (0.641)	0.581 (0.928)	0.00105 (0.0175)	0.418 (0.837)	0.954 (1.00)	0.434 (0.84)	0.239 (0.689)	0.732 (0.989)	0.0206 (0.215)	0.538 (0.903)	0.71 (0.978)	0.818 (1.00)
CCDC82	6 (1%)	971	0.217 (0.655)	0.302 (0.769)	0.91 (1.00)		0.013 (0.143)	0.586 (0.928)	0.412 (0.835)	0.00255 (0.0378)	0.387 (0.831)	0.0592 (0.402)	0.896 (1.00)	1 (1.00)
CDKN1B	10 (1%)	967	1 (1.00)	0.33 (0.789)	0.117 (0.565)	0.324 (0.785)	0.792 (1.00)	0.148 (0.586)	0.0821 (0.445)	0.464 (0.867)	0.107 (0.528)	0.316 (0.775)	0.328 (0.789)	0.017 (0.181)
FOXA1	23 (2%)	954	0.0748 (0.424)	0.341 (0.794)	0.0233 (0.231)	0.0795 (0.441)	0.569 (0.919)	0.0873 (0.455)	0.0505 (0.368)	0.16 (0.595)	0.258 (0.709)	0.6 (0.932)	0.226 (0.674)	0.491 (0.868)
CTCF	16 (2%)	961	0.0479 (0.358)	0.0596 (0.402)	0.0108 (0.125)	0.0996 (0.504)	0.667 (0.969)	0.202 (0.64)	0.295 (0.763)	0.489 (0.868)	0.118 (0.565)	0.0598 (0.402)	0.972 (1.00)	0.751 (1.00)
RBMX	13 (1%)	964	0.771 (1.00)	0.127 (0.568)	0.14 (0.582)	0.135 (0.571)	0.0848 (0.451)	0.18 (0.626)	0.0236 (0.231)	0.0283 (0.264)	0.681 (0.969)	0.616 (0.94)	0.229 (0.678)	1 (1.00)
NCOR1	40 (4%)	937	0.907 (1.00)	0.947 (1.00)	0.849 (1.00)	0.304 (0.772)	0.352 (0.81)	0.944 (1.00)	0.313 (0.773)	0.532 (0.898)	0.896 (1.00)	0.0208 (0.215)	0.423 (0.837)	0.714 (0.98)
ERBB2	20 (2%)	957	0.2 (0.64)	0.167 (0.608)	0.38 (0.829)	0.156 (0.592)	0.0191 (0.201)	0.359 (0.812)	0.0689 (0.415)	0.133 (0.57)	0.0551 (0.388)	0.0569 (0.397)	0.919 (1.00)	0.497 (0.869)
RAB42	4 (0%)	973	0.82 (1.00)	0.026 (0.249)	0.292 (0.757)		0.402 (0.835)	0.119 (0.565)	0.212 (0.654)	0.157 (0.592)	0.447 (0.848)	0.344 (0.798)
NBPF9	5 (1%)	972	0.315 (0.775)	0.849 (1.00)	0.00409 (0.057)		0.937 (1.00)	1 (1.00)	0.952 (1.00)	0.155 (0.592)	0.353 (0.81)	0.561 (0.918)
MYB	12 (1%)	965	0.386 (0.831)	0.587 (0.928)	0.151 (0.586)	0.555 (0.918)	0.151 (0.586)	1 (1.00)	0.895 (1.00)	0.899 (1.00)	0.245 (0.698)	0.313 (0.773)	0.0866 (0.455)	0.00177 (0.0284)
TGS1	13 (1%)	964	0.21 (0.649)	0.262 (0.709)	0.625 (0.946)	0.285 (0.752)	0.835 (1.00)	0.564 (0.918)	0.745 (0.999)	0.249 (0.703)	0.689 (0.969)	0.0235 (0.231)	0.0869 (0.455)	0.319 (0.777)
USP36	8 (1%)	969	0.336 (0.792)	0.006 (0.0779)	0.882 (1.00)	0.927 (1.00)	0.454 (0.857)	0.499 (0.869)	0.409 (0.835)	0.0759 (0.428)	0.596 (0.931)	0.749 (1.00)
ACTL6B	10 (1%)	967	0.676 (0.969)	0.4 (0.835)	0.00576 (0.076)	0.312 (0.773)	0.163 (0.601)	0.566 (0.918)	0.686 (0.969)	0.197 (0.638)	0.782 (1.00)	0.913 (1.00)	0.515 (0.882)	0.848 (1.00)
ZFP36L2	7 (1%)	970	0.82 (1.00)	1 (1.00)	0.0107 (0.125)	0.42 (0.837)	0.654 (0.96)	0.442 (0.84)	0.688 (0.969)	0.568 (0.918)	0.614 (0.938)	0.737 (0.993)	0.316 (0.775)	0.85 (1.00)
MED23	14 (1%)	963	0.388 (0.831)	0.251 (0.706)	0.274 (0.727)	0.198 (0.639)	0.17 (0.612)	0.0577 (0.399)	0.184 (0.631)	0.0737 (0.421)	0.0164 (0.177)	0.117 (0.565)	0.267 (0.713)	0.534 (0.899)
ANKRD20A4	7 (1%)	970	0.607 (0.936)	1 (1.00)	0.606 (0.936)	0.408 (0.835)	0.922 (1.00)	0.882 (1.00)	0.0725 (0.421)	0.332 (0.789)	0.847 (1.00)	0.813 (1.00)	0.688 (0.969)	0.0236 (0.231)
DLG1	13 (1%)	964	0.795 (1.00)	0.249 (0.703)	0.872 (1.00)	0.13 (0.57)	0.634 (0.951)	0.827 (1.00)	0.262 (0.709)	0.189 (0.631)	0.919 (1.00)	0.0117 (0.13)	0.436 (0.84)	1 (1.00)
GPRASP2	10 (1%)	967	0.433 (0.84)	0.33 (0.789)	0.66 (0.966)	0.655 (0.96)	0.397 (0.835)	0.44 (0.84)	0.146 (0.585)	0.253 (0.709)	0.00291 (0.0424)	0.231 (0.678)	0.379 (0.829)	0.672 (0.969)
PTEN	35 (4%)	942	1 (1.00)	0.695 (0.969)	0.276 (0.731)	0.321 (0.78)	0.206 (0.641)	0.726 (0.988)	0.289 (0.753)	0.573 (0.923)	0.15 (0.586)	0.153 (0.587)	0.421 (0.837)	0.549 (0.915)
MLL3	70 (7%)	907	0.634 (0.951)	0.781 (1.00)	0.168 (0.608)	0.236 (0.687)	0.674 (0.969)	0.109 (0.531)	0.0306 (0.276)	0.415 (0.837)	0.0389 (0.323)	0.121 (0.565)	0.336 (0.792)	0.661 (0.966)
ARID1A	27 (3%)	950	1 (1.00)	1 (1.00)	0.21 (0.649)	0.494 (0.868)	0.384 (0.831)	0.485 (0.868)	0.141 (0.582)	0.644 (0.956)	0.441 (0.84)	0.363 (0.82)	0.196 (0.638)	0.311 (0.773)
TBX3	27 (3%)	950	0.187 (0.631)	0.518 (0.883)	0.0428 (0.33)	0.424 (0.837)	0.14 (0.582)	0.0648 (0.409)	0.081 (0.445)	0.134 (0.57)	0.0602 (0.402)	0.133 (0.57)	0.83 (1.00)	0.594 (0.931)
HRNR	31 (3%)	946	0.874 (1.00)	0.646 (0.956)	0.216 (0.655)	0.516 (0.882)	0.626 (0.947)	0.393 (0.835)	0.99 (1.00)	0.677 (0.969)	0.643 (0.956)	0.835 (1.00)	0.621 (0.945)	0.743 (0.998)
ZMYM3	15 (2%)	962	0.323 (0.783)	0.253 (0.709)	0.397 (0.835)	0.679 (0.969)	0.497 (0.869)	0.0475 (0.358)	0.398 (0.835)	0.487 (0.868)	0.48 (0.868)	0.425 (0.837)	0.714 (0.98)	0.85 (1.00)
GPRIN2	11 (1%)	966	0.792 (1.00)	0.69 (0.969)	0.961 (1.00)	0.61 (0.937)	0.933 (1.00)	0.263 (0.709)	0.771 (1.00)	0.425 (0.837)	0.67 (0.969)	0.248 (0.703)	0.56 (0.918)	1 (1.00)
SPEN	32 (3%)	945	0.877 (1.00)	0.53 (0.896)	0.507 (0.876)	0.421 (0.837)	0.945 (1.00)	1 (1.00)	0.209 (0.649)	0.12 (0.565)	0.0666 (0.409)	0.204 (0.641)	0.526 (0.891)	0.541 (0.905)
NF1	28 (3%)	949	1 (1.00)	0.94 (1.00)	0.139 (0.582)	0.216 (0.655)	0.441 (0.84)	0.866 (1.00)	0.128 (0.568)	0.418 (0.837)	0.29 (0.753)	0.556 (0.918)	0.915 (1.00)	0.787 (1.00)
TCP11	6 (1%)	971	0.872 (1.00)	1 (1.00)	0.46 (0.866)		0.789 (1.00)	1 (1.00)	0.762 (1.00)	0.376 (0.829)	0.647 (0.956)	0.399 (0.835)
SF3B1	16 (2%)	961	0.73 (0.988)	0.453 (0.856)	0.508 (0.876)	0.172 (0.614)	0.174 (0.617)	0.26 (0.709)	0.646 (0.956)	0.354 (0.81)	0.338 (0.792)	0.19 (0.631)	0.624 (0.946)	0.183 (0.63)
CDC42EP1	5 (1%)	972	0.82 (1.00)	0.172 (0.614)	0.174 (0.617)	0.346 (0.799)	0.77 (1.00)	0.739 (0.994)	0.259 (0.709)	0.559 (0.918)	0.692 (0.969)	0.218 (0.655)
KDM6A	15 (2%)	962	0.0841 (0.451)	0.573 (0.923)	0.371 (0.829)	0.348 (0.803)	0.26 (0.709)	0.153 (0.587)	0.54 (0.905)	0.405 (0.835)	0.931 (1.00)	0.987 (1.00)	0.801 (1.00)	0.401 (0.835)
AQP12A	6 (1%)	971	0.467 (0.867)	1 (1.00)	0.562 (0.918)	0.777 (1.00)	0.937 (1.00)	0.185 (0.631)	0.777 (1.00)	1 (1.00)	0.93 (1.00)	0.559 (0.918)	0.202 (0.64)	1 (1.00)
KRAS	6 (1%)	971	0.565 (0.918)	0.826 (1.00)	0.178 (0.624)	0.355 (0.811)	0.632 (0.951)	1 (1.00)	0.565 (0.918)	0.0851 (0.451)	0.693 (0.969)	0.0391 (0.323)	0.722 (0.987)	0.192 (0.631)
ZNF362	5 (1%)	972	0.0996 (0.504)	0.714 (0.98)	0.181 (0.627)		0.776 (1.00)	0.473 (0.868)	0.462 (0.866)	0.909 (1.00)	0.178 (0.624)	0.0701 (0.416)
TBL1XR1	9 (1%)	968	0.0631 (0.407)	0.34 (0.794)	0.0983 (0.504)		0.474 (0.868)	1 (1.00)	0.0417 (0.324)	0.566 (0.918)	0.425 (0.837)	0.2 (0.64)	0.9 (1.00)	0.103 (0.512)
SP3	7 (1%)	970	1 (1.00)	0.3 (0.768)	0.492 (0.868)	0.947 (1.00)	0.836 (1.00)	0.821 (1.00)	0.194 (0.636)	0.442 (0.84)	0.519 (0.883)	0.0652 (0.409)	0.38 (0.829)	1 (1.00)
FGFR2	11 (1%)	966	0.498 (0.869)	1 (1.00)	0.639 (0.953)	0.559 (0.918)	0.0416 (0.324)	0.313 (0.773)	0.194 (0.636)	0.428 (0.837)	0.219 (0.655)	0.0721 (0.421)	0.828 (1.00)	0.673 (0.969)
ZBTB7C	5 (1%)	972			0.126 (0.565)	1 (1.00)	0.704 (0.976)	1 (1.00)	0.881 (1.00)	0.677 (0.969)	0.83 (1.00)	0.597 (0.931)
NCDN	4 (0%)	973	0.8 (1.00)	0.157 (0.592)	0.916 (1.00)		0.952 (1.00)	1 (1.00)	0.88 (1.00)	0.913 (1.00)	0.501 (0.87)	0.468 (0.867)
MUC6	14 (1%)	963	0.631 (0.951)	0.904 (1.00)	0.125 (0.565)	0.135 (0.571)	0.485 (0.868)	0.168 (0.608)	0.0623 (0.405)	0.205 (0.641)	0.492 (0.868)	0.033 (0.292)	0.587 (0.928)	0.052 (0.375)
TFE3	7 (1%)	970	0.192 (0.631)	0.149 (0.586)	0.407 (0.835)	0.694 (0.969)	0.357 (0.812)	1 (1.00)	0.722 (0.987)	0.647 (0.956)	0.958 (1.00)	0.165 (0.605)	1 (1.00)	0.311 (0.773)
IRS4	11 (1%)	966	0.191 (0.631)	0.125 (0.565)	0.231 (0.678)	0.638 (0.953)	0.166 (0.606)	0.0652 (0.409)	0.146 (0.585)	0.47 (0.867)	0.0614 (0.403)	0.815 (1.00)	0.709 (0.978)	0.817 (1.00)
NLGN3	11 (1%)	966	0.242 (0.695)	1 (1.00)	0.791 (1.00)	0.876 (1.00)	0.124 (0.565)	0.396 (0.835)	0.928 (1.00)	0.0819 (0.445)	0.994 (1.00)	0.996 (1.00)	0.375 (0.829)	0.673 (0.969)
IL1RAP	9 (1%)	968			0.427 (0.837)	0.299 (0.767)	0.337 (0.792)	0.312 (0.773)	0.873 (1.00)	0.643 (0.956)	0.575 (0.923)	0.301 (0.768)	0.833 (1.00)	0.611 (0.937)
CASZ1	14 (1%)	963	0.896 (1.00)	0.458 (0.862)	0.972 (1.00)	0.462 (0.866)	0.493 (0.868)	0.098 (0.504)	0.986 (1.00)	0.733 (0.99)	0.483 (0.868)	0.986 (1.00)	0.707 (0.977)	0.809 (1.00)
KCNN3	9 (1%)	968	0.379 (0.829)	0.162 (0.598)	0.386 (0.831)	0.125 (0.565)	0.0406 (0.324)	0.495 (0.868)	0.0729 (0.421)	0.398 (0.835)	0.142 (0.584)	0.487 (0.868)	0.491 (0.868)	0.428 (0.837)
ICOSLG	5 (1%)	972	0.799 (1.00)	0.157 (0.592)	0.47 (0.867)	1 (1.00)	0.102 (0.507)	0.383 (0.831)	0.835 (1.00)	0.968 (1.00)	0.141 (0.582)	0.682 (0.969)
MYH9	18 (2%)	959	0.478 (0.868)	1 (1.00)	0.144 (0.584)	0.812 (1.00)	0.39 (0.832)	0.412 (0.835)	0.338 (0.792)	0.143 (0.584)	0.633 (0.951)	0.504 (0.873)	0.906 (1.00)	0.171 (0.614)
FBXW7	15 (2%)	962	0.767 (1.00)	0.479 (0.868)	0.133 (0.57)	0.0272 (0.258)	0.263 (0.709)	0.101 (0.507)	0.125 (0.565)	0.148 (0.586)	0.518 (0.883)	0.403 (0.835)	0.034 (0.296)	0.81 (1.00)
FRMPD2	13 (1%)	964	0.441 (0.84)	0.124 (0.565)	0.23 (0.678)	0.135 (0.571)	0.133 (0.57)	0.262 (0.709)	0.575 (0.923)	0.0541 (0.386)	0.435 (0.84)	0.29 (0.753)	0.553 (0.918)	0.579 (0.926)
TPP2	8 (1%)	969	0.358 (0.812)	0.826 (1.00)	0.908 (1.00)	0.635 (0.951)	0.937 (1.00)	1 (1.00)	0.598 (0.931)	0.916 (1.00)	0.595 (0.931)	0.889 (1.00)	0.487 (0.868)	1 (1.00)
C17ORF95	5 (1%)	972	1 (1.00)	1 (1.00)	1 (1.00)				0.953 (1.00)	0.968 (1.00)	0.513 (0.881)	0.429 (0.837)
RUFY1	6 (1%)	971	1 (1.00)	0.298 (0.767)	0.38 (0.829)	0.729 (0.988)	0.07 (0.416)	0.736 (0.993)	0.878 (1.00)	0.239 (0.69)	0.697 (0.969)	0.266 (0.713)	0.369 (0.829)	0.431 (0.839)
PAX2	4 (0%)	973	0.466 (0.867)	0.583 (0.928)	0.839 (1.00)		0.805 (1.00)	0.484 (0.868)	0.376 (0.829)	0.286 (0.752)	0.388 (0.831)	0.337 (0.792)
MED12	21 (2%)	956	0.728 (0.988)	0.512 (0.881)	0.545 (0.91)	0.872 (1.00)	0.697 (0.969)	0.832 (1.00)	0.663 (0.966)	0.41 (0.835)	0.707 (0.977)	0.914 (1.00)	0.537 (0.903)	0.481 (0.868)
CHD4	19 (2%)	958	0.76 (1.00)	0.494 (0.868)	0.231 (0.678)	0.0616 (0.403)	0.715 (0.98)	1 (1.00)	0.0297 (0.274)	0.269 (0.716)	0.873 (1.00)	0.0669 (0.409)	0.818 (1.00)	0.308 (0.773)
PFKP	6 (1%)	971	0.123 (0.565)	0.0587 (0.402)	0.697 (0.969)		0.306 (0.773)	0.687 (0.969)	0.587 (0.928)	0.302 (0.769)	0.427 (0.837)	0.131 (0.57)
RHBG	4 (0%)	973			1 (1.00)				0.219 (0.655)	0.107 (0.528)	0.679 (0.969)	0.289 (0.753)
PSIP1	8 (1%)	969	0.692 (0.969)	1 (1.00)	0.652 (0.96)	0.902 (1.00)	0.592 (0.931)	0.585 (0.928)	0.556 (0.918)	0.935 (1.00)	0.411 (0.835)	0.909 (1.00)	0.915 (1.00)	0.429 (0.837)
LRIG2	7 (1%)	970	0.564 (0.918)	0.0643 (0.409)	0.624 (0.946)	0.59 (0.931)	0.406 (0.835)	0.584 (0.928)	0.368 (0.829)	0.885 (1.00)	0.331 (0.789)	0.93 (1.00)	1 (1.00)	1 (1.00)
RIBC1	4 (0%)	973	0.357 (0.812)	0.653 (0.96)	0.7 (0.972)	0.0395 (0.323)			0.685 (0.969)	0.608 (0.936)	0.388 (0.831)	0.412 (0.835)
PLK2	9 (1%)	968	0.606 (0.936)	0.442 (0.84)	1 (1.00)	0.922 (1.00)	0.342 (0.796)	1 (1.00)	0.908 (1.00)	0.797 (1.00)	0.982 (1.00)	0.596 (0.931)	0.829 (1.00)	0.671 (0.969)
PHACTR1	7 (1%)	970	0.121 (0.565)	1 (1.00)	0.869 (1.00)	0.237 (0.687)	0.191 (0.631)	0.0851 (0.451)	0.132 (0.57)	0.0784 (0.438)	0.757 (1.00)	0.0417 (0.324)	0.897 (1.00)	1 (1.00)
CCDC27	7 (1%)	970	0.216 (0.655)	0.402 (0.835)	0.129 (0.57)	0.0284 (0.264)	0.0813 (0.445)	0.143 (0.584)	0.0382 (0.321)	0.263 (0.709)	0.214 (0.655)	0.0553 (0.388)	0.232 (0.678)	0.312 (0.773)
RHOA	6 (1%)	971	0.0459 (0.348)	0.439 (0.84)	0.526 (0.891)	0.236 (0.687)	0.481 (0.868)	0.508 (0.876)	0.889 (1.00)	0.261 (0.709)	0.727 (0.988)	0.374 (0.829)
MAMLD1	10 (1%)	967	0.371 (0.829)	0.189 (0.631)	0.601 (0.932)	0.467 (0.867)	0.158 (0.593)	0.5 (0.869)	0.621 (0.945)	0.653 (0.96)	0.757 (1.00)	0.727 (0.988)	0.671 (0.969)	1 (1.00)
OR8D1	5 (1%)	972	0.692 (0.969)	0.0446 (0.341)	0.769 (1.00)	0.522 (0.888)	0.188 (0.631)	0.146 (0.585)	0.243 (0.695)	0.18 (0.627)	0.475 (0.868)	1 (1.00)

'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00805 (Fisher's exact test), Q value = 0.098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
PIK3CA MUTATED	83	43	38
PIK3CA WILD-TYPE	144	74	127

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 = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
PIK3CA MUTATED	51	108	5
PIK3CA WILD-TYPE	104	157	84

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 = 1e-05 (Fisher's exact test), Q value = 0.00026

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	292	118	267	261	25
PIK3CA MUTATED	81	65	104	54	10
PIK3CA WILD-TYPE	211	53	163	207	15

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 = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
PIK3CA MUTATED	83	52	41	8	32
PIK3CA WILD-TYPE	110	98	81	111	48

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 = 3e-05 (Fisher's exact test), Q value = 0.00069

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
PIK3CA MUTATED	26	75	12	81	35	22	1
PIK3CA WILD-TYPE	126	139	17	118	88	45	9

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 = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
PIK3CA MUTATED	28	124	100
PIK3CA WILD-TYPE	187	206	149

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 = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
PIK3CA MUTATED	45	57	60	115	12	17	10
PIK3CA WILD-TYPE	188	102	70	90	172	28	8

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 = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
PIK3CA MUTATED	79	55	34	125	7	16
PIK3CA WILD-TYPE	184	96	45	136	161	36

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 = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
PIK3CA MUTATED	33	45	68	74	76	18
PIK3CA WILD-TYPE	96	198	109	110	108	23

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 = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
PIK3CA MUTATED	7	49	74	54	38	45	7	22	18
PIK3CA WILD-TYPE	57	70	82	113	31	66	138	32	55

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 = 3e-05 (Fisher's exact test), Q value = 0.00069

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
PIK3CA MUTATED	32	26	22	47	17	38
PIK3CA WILD-TYPE	82	37	28	73	105	61

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 = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
PIK3CA MUTATED	51	71	60
PIK3CA WILD-TYPE	230	100	56

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

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
TP53 MUTATED	23	26	116
TP53 WILD-TYPE	204	91	49

Figure S13. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
TP53 MUTATED	11	85	69
TP53 WILD-TYPE	144	180	20

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

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
TP53 MUTATED	63	14	25	187	4
TP53 WILD-TYPE	229	104	242	74	21

Figure S15. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
TP53 MUTATED	21	46	34	90	6
TP53 WILD-TYPE	172	104	88	29	74

Figure S16. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
TP53 MUTATED	107	18	8	33	44	32	6
TP53 WILD-TYPE	45	196	21	166	79	35	4

Figure S17. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
TP53 MUTATED	153	54	41
TP53 WILD-TYPE	62	276	208

Figure S18. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
TP53 MUTATED	31	87	10	17	136	7	7
TP53 WILD-TYPE	202	72	120	188	48	38	11

Figure S19. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
TP53 MUTATED	25	64	3	37	126	40
TP53 WILD-TYPE	238	87	76	224	42	12

Figure S20. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
TP53 MUTATED	36	166	14	28	38	7
TP53 WILD-TYPE	93	77	163	156	146	34

Figure S21. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
TP53 MUTATED	11	62	14	15	14	19	106	7	41
TP53 WILD-TYPE	53	57	142	152	55	92	39	47	32

Figure S22. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
TP53 MUTATED	15	11	14	23	93	16
TP53 WILD-TYPE	99	52	36	97	29	83

Figure S23. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
TP53 MUTATED	124	32	16
TP53 WILD-TYPE	157	139	100

Figure S24. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00876 (Fisher's exact test), Q value = 0.11

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
GATA3 MUTATED	38	10	12
GATA3 WILD-TYPE	189	107	153

Figure S25. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.002

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
GATA3 MUTATED	29	30	1
GATA3 WILD-TYPE	126	235	88

Figure S26. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0025

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	292	118	267	261	25
GATA3 MUTATED	38	15	33	8	2
GATA3 WILD-TYPE	254	103	234	253	23

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

'GATA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
GATA3 MUTATED	24	18	5	1	11
GATA3 WILD-TYPE	169	132	117	118	69

Figure S28. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'GATA3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0044

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
GATA3 MUTATED	7	40	1	12	14	8	1
GATA3 WILD-TYPE	145	174	28	187	109	59	9

Figure S29. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'GATA3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
GATA3 MUTATED	4	58	21
GATA3 WILD-TYPE	211	272	228

Figure S30. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
GATA3 MUTATED	40	8	13	33	1	1	0
GATA3 WILD-TYPE	193	151	117	172	183	44	18

Figure S31. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
GATA3 MUTATED	46	14	3	33	0	0
GATA3 WILD-TYPE	217	137	76	228	168	52

Figure S32. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0045

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
GATA3 MUTATED	22	9	20	15	23	6
GATA3 WILD-TYPE	107	234	157	169	161	35

Figure S33. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
GATA3 MUTATED	16	8	11	24	15	11	0	4	6
GATA3 WILD-TYPE	48	111	145	143	54	100	145	50	67

Figure S34. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
GATA3 MUTATED	23	3	5	20	0	6
GATA3 WILD-TYPE	91	60	45	100	122	93

Figure S35. 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 = 0.0736 (Fisher's exact test), Q value = 0.42

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
GATA3 MUTATED	29	11	17
GATA3 WILD-TYPE	252	160	99

'MAP3K1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.027

Table S37. Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
MAP3K1 MUTATED	27	9	4
MAP3K1 WILD-TYPE	200	108	161

Figure S36. Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00203 (Fisher's exact test), Q value = 0.032

Table S38. Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
MAP3K1 MUTATED	20	19	1
MAP3K1 WILD-TYPE	135	246	88

Figure S37. Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00069

Table S39. Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
MAP3K1 MUTATED	16	11	33	6	5
MAP3K1 WILD-TYPE	276	107	234	255	20

Figure S38. Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MAP3K1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.23

Table S40. Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
MAP3K1 MUTATED	19	4	9	3	5
MAP3K1 WILD-TYPE	174	146	113	116	75

Figure S39. Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MAP3K1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0043

Table S41. Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
MAP3K1 MUTATED	3	25	4	21	3	2	0
MAP3K1 WILD-TYPE	149	189	25	178	120	65	10

Figure S40. Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MAP3K1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S42. Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
MAP3K1 MUTATED	1	34	23
MAP3K1 WILD-TYPE	214	296	226

Figure S41. Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0043

Table S43. Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
MAP3K1 MUTATED	21	4	16	23	4	3	0
MAP3K1 WILD-TYPE	212	155	114	182	180	42	18

Figure S42. Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0057

Table S44. Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
MAP3K1 MUTATED	31	8	7	22	3	0
MAP3K1 WILD-TYPE	232	143	72	239	165	52

Figure S43. Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0072

Table S45. Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
MAP3K1 MUTATED	10	4	20	17	15	5
MAP3K1 WILD-TYPE	119	239	157	167	169	36

Figure S44. Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0027

Table S46. Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
MAP3K1 MUTATED	1	3	20	19	5	12	2	5	4
MAP3K1 WILD-TYPE	63	116	136	148	64	99	143	49	69

Figure S45. Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.062

Table S47. Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
MAP3K1 MUTATED	16	4	6	5	3	4
MAP3K1 WILD-TYPE	98	59	44	115	119	95

Figure S46. Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0999 (Fisher's exact test), Q value = 0.5

Table S48. Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
MAP3K1 MUTATED	15	10	13
MAP3K1 WILD-TYPE	266	161	103

'CDH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.032

Table S49. Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
CDH1 MUTATED	14	15	4
CDH1 WILD-TYPE	213	102	161

Figure S47. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.017

Table S50. Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
CDH1 MUTATED	5	27	1
CDH1 WILD-TYPE	150	238	88

Figure S48. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S51. Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
CDH1 MUTATED	20	36	42	4	3
CDH1 WILD-TYPE	272	82	225	257	22

Figure S49. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S52. Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
CDH1 MUTATED	28	19	24	0	17
CDH1 WILD-TYPE	165	131	98	119	63

Figure S50. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S53. Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
CDH1 MUTATED	2	21	1	36	11	7	2
CDH1 WILD-TYPE	150	193	28	163	112	60	8

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

'CDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S54. Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
CDH1 MUTATED	5	30	45
CDH1 WILD-TYPE	210	300	204

Figure S52. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S55. Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
CDH1 MUTATED	10	12	32	37	1	14	1
CDH1 WILD-TYPE	223	147	98	168	183	31	17

Figure S53. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S56. Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
CDH1 MUTATED	12	11	29	51	1	3
CDH1 WILD-TYPE	251	140	50	210	167	49

Figure S54. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S57. Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
CDH1 MUTATED	9	2	28	49	11	6
CDH1 WILD-TYPE	120	241	149	135	173	35

Figure S55. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S58. Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
CDH1 MUTATED	2	6	56	11	8	10	0	11	1
CDH1 WILD-TYPE	62	113	100	156	61	101	145	43	72

Figure S56. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S59. Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
CDH1 MUTATED	7	19	7	10	1	31
CDH1 WILD-TYPE	107	44	43	110	121	68

Figure S57. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S60. Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
CDH1 MUTATED	8	56	11
CDH1 WILD-TYPE	273	115	105

Figure S58. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CBFB MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.662 (Fisher's exact test), Q value = 0.97

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
CBFB MUTATED	6	2	2
CBFB WILD-TYPE	221	115	163

'CBFB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.468 (Fisher's exact test), Q value = 0.87

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
CBFB MUTATED	5	4	1
CBFB WILD-TYPE	150	261	88

'CBFB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.012

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
CBFB MUTATED	4	8	7	1	2
CBFB WILD-TYPE	288	110	260	260	23

Figure S59. Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CBFB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0612 (Fisher's exact test), Q value = 0.4

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
CBFB MUTATED	7	3	1	0	4
CBFB WILD-TYPE	186	147	121	119	76

'CBFB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.36

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
CBFB MUTATED	1	4	0	6	3	3	2
CBFB WILD-TYPE	151	210	29	193	120	64	8

Figure S60. Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CBFB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 0.64

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
CBFB MUTATED	2	11	6
CBFB WILD-TYPE	213	319	243

'CBFB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5e-04

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
CBFB MUTATED	0	2	3	16	1	0	0
CBFB WILD-TYPE	233	157	127	189	183	45	18

Figure S61. Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CBFB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.613 (Fisher's exact test), Q value = 0.94

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
CBFB MUTATED	7	3	2	8	1	1
CBFB WILD-TYPE	256	148	77	253	167	51

'CBFB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 0.36

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
CBFB MUTATED	2	1	3	5	8	2
CBFB WILD-TYPE	127	242	174	179	176	39

Figure S62. Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CBFB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0024

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
CBFB MUTATED	0	1	5	1	7	6	0	1	0
CBFB WILD-TYPE	64	118	151	166	62	105	145	53	73

Figure S63. Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CBFB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00577 (Fisher's exact test), Q value = 0.076

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
CBFB MUTATED	2	0	2	8	0	1
CBFB WILD-TYPE	112	63	48	112	122	98

Figure S64. Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CBFB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00224 (Fisher's exact test), Q value = 0.034

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
CBFB MUTATED	4	1	8
CBFB WILD-TYPE	277	170	108

Figure S65. Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
PTEN MUTATED	6	3	4
PTEN WILD-TYPE	221	114	161

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.695 (Fisher's exact test), Q value = 0.97

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
PTEN MUTATED	4	8	1
PTEN WILD-TYPE	151	257	88

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 0.73

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
PTEN MUTATED	6	7	11	11	0
PTEN WILD-TYPE	286	111	256	250	25

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 0.78

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
PTEN MUTATED	4	9	7	6	3
PTEN WILD-TYPE	189	141	115	113	77

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 0.64

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
PTEN MUTATED	4	7	2	9	2	6	0
PTEN WILD-TYPE	148	207	27	190	121	61	10

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.726 (Fisher's exact test), Q value = 0.99

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
PTEN MUTATED	10	12	8
PTEN WILD-TYPE	205	318	241

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.75

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
PTEN MUTATED	6	9	8	6	4	1	1
PTEN WILD-TYPE	227	150	122	199	180	44	17

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 0.92

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
PTEN MUTATED	7	6	5	9	5	3
PTEN WILD-TYPE	256	145	74	252	163	49

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 0.59

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
PTEN MUTATED	4	5	5	12	9	0
PTEN WILD-TYPE	125	238	172	172	175	41

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.153 (Fisher's exact test), Q value = 0.59

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
PTEN MUTATED	1	5	11	2	1	7	5	1	2
PTEN WILD-TYPE	63	114	145	165	68	104	140	53	71

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.84

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
PTEN MUTATED	6	3	1	3	4	8
PTEN WILD-TYPE	108	60	49	117	118	91

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.549 (Fisher's exact test), Q value = 0.91

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
PTEN MUTATED	11	10	4
PTEN WILD-TYPE	270	161	112

'RUNX1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.246 (Fisher's exact test), Q value = 0.7

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
RUNX1 MUTATED	7	7	4
RUNX1 WILD-TYPE	220	110	161

'RUNX1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0413 (Fisher's exact test), Q value = 0.32

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
RUNX1 MUTATED	4	14	0
RUNX1 WILD-TYPE	151	251	89

Figure S66. Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.28

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	292	118	267	261	25
RUNX1 MUTATED	4	8	11	5	0
RUNX1 WILD-TYPE	288	110	256	256	25

Figure S67. Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 0.78

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
RUNX1 MUTATED	4	5	5	1	4
RUNX1 WILD-TYPE	189	145	117	118	76

'RUNX1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.84

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
RUNX1 MUTATED	3	3	2	6	3	3	0
RUNX1 WILD-TYPE	149	211	27	193	120	64	10

'RUNX1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 0.84

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
RUNX1 MUTATED	4	7	9
RUNX1 WILD-TYPE	211	323	240

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.068 (Fisher's exact test), Q value = 0.41

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
RUNX1 MUTATED	4	6	7	9	1	2	0
RUNX1 WILD-TYPE	229	153	123	196	183	43	18

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.13

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
RUNX1 MUTATED	4	9	4	11	1	0
RUNX1 WILD-TYPE	259	142	75	250	167	52

Figure S68. Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00467 (Fisher's exact test), Q value = 0.063

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
RUNX1 MUTATED	4	1	3	10	8	3
RUNX1 WILD-TYPE	125	242	174	174	176	38

Figure S69. Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00362 (Fisher's exact test), Q value = 0.052

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
RUNX1 MUTATED	1	3	13	3	2	6	1	0	0
RUNX1 WILD-TYPE	63	116	143	164	67	105	144	54	73

Figure S70. Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 0.83

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
RUNX1 MUTATED	3	1	4	5	2	4
RUNX1 WILD-TYPE	111	62	46	115	120	95

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.373 (Fisher's exact test), Q value = 0.83

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
RUNX1 MUTATED	7	6	6
RUNX1 WILD-TYPE	274	165	110

'MLL3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.634 (Fisher's exact test), Q value = 0.95

Table S97. Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
MLL3 MUTATED	18	6	13
MLL3 WILD-TYPE	209	111	152

'MLL3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S98. Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
MLL3 MUTATED	13	19	5
MLL3 WILD-TYPE	142	246	84

'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.61

Table S99. Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
MLL3 MUTATED	17	11	24	13	3
MLL3 WILD-TYPE	275	107	243	248	22

'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.69

Table S100. Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
MLL3 MUTATED	20	12	6	5	7
MLL3 WILD-TYPE	173	138	116	114	73

'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 0.97

Table S101. Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
MLL3 MUTATED	9	19	1	9	9	5	0
MLL3 WILD-TYPE	143	195	28	190	114	62	10

'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.53

Table S102. Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
MLL3 MUTATED	10	29	13
MLL3 WILD-TYPE	205	301	236

'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.28

Table S103. Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
MLL3 MUTATED	16	14	8	24	8	0	0
MLL3 WILD-TYPE	217	145	122	181	176	45	18

Figure S71. Get High-res Image Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.415 (Fisher's exact test), Q value = 0.84

Table S104. Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
MLL3 MUTATED	22	15	3	19	8	3
MLL3 WILD-TYPE	241	136	76	242	160	49

'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.32

Table S105. Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
MLL3 MUTATED	9	8	16	11	18	5
MLL3 WILD-TYPE	120	235	161	173	166	36

Figure S72. Get High-res Image Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.121 (Fisher's exact test), Q value = 0.56

Table S106. Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
MLL3 MUTATED	5	7	11	13	11	7	4	3	6
MLL3 WILD-TYPE	59	112	145	154	58	104	141	51	67

'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.79

Table S107. Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
MLL3 MUTATED	12	5	2	8	4	6
MLL3 WILD-TYPE	102	58	48	112	118	93

'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.661 (Fisher's exact test), Q value = 0.97

Table S108. Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
MLL3 MUTATED	16	12	9
MLL3 WILD-TYPE	265	159	107

'CDKN1B MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S109. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
CDKN1B MUTATED	3	1	2
CDKN1B WILD-TYPE	224	116	163

'CDKN1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 0.79

Table S110. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
CDKN1B MUTATED	1	5	0
CDKN1B WILD-TYPE	154	260	89

'CDKN1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.56

Table S111. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
CDKN1B MUTATED	1	3	2	3	1
CDKN1B WILD-TYPE	291	115	265	258	24

'CDKN1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 0.78

Table S112. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
CDKN1B MUTATED	3	0	2	0	1
CDKN1B WILD-TYPE	190	150	120	119	79

'CDKN1B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S113. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
CDKN1B MUTATED	1	5	0	2	1	0	0
CDKN1B WILD-TYPE	151	209	29	197	122	67	10

'CDKN1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.59

Table S114. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
CDKN1B MUTATED	0	6	3
CDKN1B WILD-TYPE	215	324	246

'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0821 (Fisher's exact test), Q value = 0.44

Table S115. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
CDKN1B MUTATED	1	2	1	5	0	0	1
CDKN1B WILD-TYPE	232	157	129	200	184	45	17

'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.464 (Fisher's exact test), Q value = 0.87

Table S116. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
CDKN1B MUTATED	2	2	1	5	0	0
CDKN1B WILD-TYPE	261	149	78	256	168	52

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.53

Table S117. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
CDKN1B MUTATED	1	0	1	3	4	1
CDKN1B WILD-TYPE	128	243	176	181	180	40

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 0.78

Table S118. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
CDKN1B MUTATED	1	0	3	2	2	2	0	0	0
CDKN1B WILD-TYPE	63	119	153	165	67	109	145	54	73

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 0.79

Table S119. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
CDKN1B MUTATED	0	1	1	2	0	1
CDKN1B WILD-TYPE	114	62	49	118	122	98

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.18

Table S120. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
CDKN1B MUTATED	0	2	3
CDKN1B WILD-TYPE	281	169	113

Figure S73. Get High-res Image Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.066 (Fisher's exact test), Q value = 0.41

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
MAP2K4 MUTATED	10	7	2
MAP2K4 WILD-TYPE	217	110	163

'MAP2K4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0692 (Fisher's exact test), Q value = 0.42

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
MAP2K4 MUTATED	8	11	0
MAP2K4 WILD-TYPE	147	254	89

'MAP2K4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0522 (Fisher's exact test), Q value = 0.37

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	292	118	267	261	25
MAP2K4 MUTATED	10	8	8	4	2
MAP2K4 WILD-TYPE	282	110	259	257	23

'MAP2K4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.29

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
MAP2K4 MUTATED	14	6	2	1	2
MAP2K4 WILD-TYPE	179	144	120	118	78

Figure S74. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MAP2K4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.31

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
MAP2K4 MUTATED	0	9	0	8	8	1	0
MAP2K4 WILD-TYPE	152	205	29	191	115	66	10

Figure S75. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MAP2K4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.13

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
MAP2K4 MUTATED	1	14	11
MAP2K4 WILD-TYPE	214	316	238

Figure S76. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00796 (Fisher's exact test), Q value = 0.098

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
MAP2K4 MUTATED	12	5	2	11	0	1	1
MAP2K4 WILD-TYPE	221	154	128	194	184	44	17

Figure S77. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0037 (Fisher's exact test), Q value = 0.052

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
MAP2K4 MUTATED	17	4	2	9	0	0
MAP2K4 WILD-TYPE	246	147	77	252	168	52

Figure S78. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.033

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
MAP2K4 MUTATED	4	1	8	4	13	2
MAP2K4 WILD-TYPE	125	242	169	180	171	39

Figure S79. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0045

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
MAP2K4 MUTATED	4	1	1	12	5	6	0	1	2
MAP2K4 WILD-TYPE	60	118	155	155	64	105	145	53	71

Figure S80. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.29

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
MAP2K4 MUTATED	4	0	3	6	0	4
MAP2K4 WILD-TYPE	110	63	47	114	122	95

Figure S81. 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 = 0.00066 (Fisher's exact test), Q value = 0.012

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
MAP2K4 MUTATED	5	2	10
MAP2K4 WILD-TYPE	276	169	106

Figure S82. Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S133. Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
ARID1A MUTATED	7	3	5
ARID1A WILD-TYPE	220	114	160

'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S134. Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
ARID1A MUTATED	5	8	2
ARID1A WILD-TYPE	150	257	87

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.65

Table S135. Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
ARID1A MUTATED	12	1	8	4	1
ARID1A WILD-TYPE	280	117	259	257	24

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 0.87

Table S136. Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
ARID1A MUTATED	7	5	1	2	3
ARID1A WILD-TYPE	186	145	121	117	77

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.83

Table S137. Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
ARID1A MUTATED	3	5	1	3	7	1	0
ARID1A WILD-TYPE	149	209	28	196	116	66	10

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.485 (Fisher's exact test), Q value = 0.87

Table S138. Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
ARID1A MUTATED	3	10	7
ARID1A WILD-TYPE	212	320	242

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.58

Table S139. Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
ARID1A MUTATED	13	5	3	3	2	1	0
ARID1A WILD-TYPE	220	154	127	202	182	44	18

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 0.96

Table S140. Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
ARID1A MUTATED	8	5	1	10	2	1
ARID1A WILD-TYPE	255	146	78	251	166	51

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.84

Table S141. Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
ARID1A MUTATED	6	5	7	3	6	0
ARID1A WILD-TYPE	123	238	170	181	178	41

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 0.82

Table S142. Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
ARID1A MUTATED	3	4	2	9	1	2	2	1	3
ARID1A WILD-TYPE	61	115	154	158	68	109	143	53	70

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.196 (Fisher's exact test), Q value = 0.64

Table S143. Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
ARID1A MUTATED	1	3	2	1	1	3
ARID1A WILD-TYPE	113	60	48	119	121	96

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 0.77

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
ARID1A MUTATED	3	5	3
ARID1A WILD-TYPE	278	166	113

'FOXA1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0748 (Fisher's exact test), Q value = 0.42

Table S145. Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
FOXA1 MUTATED	6	2	0
FOXA1 WILD-TYPE	221	115	165

'FOXA1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.341 (Fisher's exact test), Q value = 0.79

Table S146. Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
FOXA1 MUTATED	4	4	0
FOXA1 WILD-TYPE	151	261	89

'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.23

Table S147. Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
FOXA1 MUTATED	6	5	10	1	1
FOXA1 WILD-TYPE	286	113	257	260	24

Figure S83. Get High-res Image Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0795 (Fisher's exact test), Q value = 0.44

Table S148. Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
FOXA1 MUTATED	6	8	3	0	1
FOXA1 WILD-TYPE	187	142	119	119	79

'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 0.92

Table S149. Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
FOXA1 MUTATED	1	8	0	4	3	2	0
FOXA1 WILD-TYPE	151	206	29	195	120	65	10

'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0873 (Fisher's exact test), Q value = 0.45

Table S150. Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
FOXA1 MUTATED	1	10	7
FOXA1 WILD-TYPE	214	320	242

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0505 (Fisher's exact test), Q value = 0.37

Table S151. Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
FOXA1 MUTATED	4	4	2	8	1	4	0
FOXA1 WILD-TYPE	229	155	128	197	183	41	18

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.6

Table S152. Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
FOXA1 MUTATED	5	5	1	11	1	0
FOXA1 WILD-TYPE	258	146	78	250	167	52

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 0.71

Table S153. Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
FOXA1 MUTATED	1	3	5	7	5	2
FOXA1 WILD-TYPE	128	240	172	177	179	39

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.6 (Fisher's exact test), Q value = 0.93

Table S154. Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
FOXA1 MUTATED	1	3	4	4	4	2	1	2	2
FOXA1 WILD-TYPE	63	116	152	163	65	109	144	52	71

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.67

Table S155. Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
FOXA1 MUTATED	4	3	1	3	0	3
FOXA1 WILD-TYPE	110	60	49	117	122	96

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.491 (Fisher's exact test), Q value = 0.87

Table S156. Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
FOXA1 MUTATED	5	6	3
FOXA1 WILD-TYPE	276	165	113

'GPS2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00643 (Fisher's exact test), Q value = 0.082

Table S157. Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
GPS2 MUTATED	2	5	0
GPS2 WILD-TYPE	225	112	165

Figure S84. Get High-res Image Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'GPS2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.607 (Fisher's exact test), Q value = 0.94

Table S158. Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
GPS2 MUTATED	2	5	0
GPS2 WILD-TYPE	153	260	89

'GPS2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00725 (Fisher's exact test), Q value = 0.092

Table S159. Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
GPS2 MUTATED	1	1	7	0	1
GPS2 WILD-TYPE	291	117	260	261	24

Figure S85. Get High-res Image Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'GPS2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 0.83

Table S160. Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
GPS2 MUTATED	1	3	0	2	1
GPS2 WILD-TYPE	192	147	122	117	79

'GPS2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.072 (Fisher's exact test), Q value = 0.42

Table S161. Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
GPS2 MUTATED	0	1	0	2	0	3	0
GPS2 WILD-TYPE	152	213	29	197	123	64	10

'GPS2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S162. Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
GPS2 MUTATED	2	2	2
GPS2 WILD-TYPE	213	328	247

'GPS2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 0.87

Table S163. Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
GPS2 MUTATED	3	3	1	2	0	1	0
GPS2 WILD-TYPE	230	156	129	203	184	44	18

'GPS2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0667 (Fisher's exact test), Q value = 0.41

Table S164. Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
GPS2 MUTATED	2	0	1	5	0	2
GPS2 WILD-TYPE	261	151	78	256	168	50

'GPS2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 0.79

Table S165. Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
GPS2 MUTATED	0	2	4	2	1	1
GPS2 WILD-TYPE	129	241	173	182	183	40

'GPS2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.595 (Fisher's exact test), Q value = 0.93

Table S166. Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
GPS2 MUTATED	0	2	2	2	0	3	0	0	1
GPS2 WILD-TYPE	64	117	154	165	69	108	145	54	72

'GPS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 0.79

Table S167. Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
GPS2 MUTATED	0	1	1	2	0	1
GPS2 WILD-TYPE	114	62	49	118	122	98

'GPS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 0.32

Table S168. Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
GPS2 MUTATED	0	3	2
GPS2 WILD-TYPE	281	168	114

Figure S86. Get High-res Image Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TBX3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.63

Table S169. Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
TBX3 MUTATED	10	4	2
TBX3 WILD-TYPE	217	113	163

'TBX3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 0.88

Table S170. Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
TBX3 MUTATED	6	9	1
TBX3 WILD-TYPE	149	256	88

'TBX3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 0.33

Table S171. Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
TBX3 MUTATED	6	6	10	3	2
TBX3 WILD-TYPE	286	112	257	258	23

Figure S87. Get High-res Image Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TBX3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.84

Table S172. Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
TBX3 MUTATED	7	2	3	1	3
TBX3 WILD-TYPE	186	148	119	118	77

'TBX3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.58

Table S173. Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
TBX3 MUTATED	0	6	1	5	6	1	0
TBX3 WILD-TYPE	152	208	28	194	117	66	10

'TBX3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0648 (Fisher's exact test), Q value = 0.41

Table S174. Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
TBX3 MUTATED	3	5	11
TBX3 WILD-TYPE	212	325	238

'TBX3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.081 (Fisher's exact test), Q value = 0.44

Table S175. Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
TBX3 MUTATED	5	1	8	9	3	1	0
TBX3 WILD-TYPE	228	158	122	196	181	44	18

'TBX3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.57

Table S176. Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
TBX3 MUTATED	6	2	5	11	2	1
TBX3 WILD-TYPE	257	149	74	250	166	51

'TBX3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0602 (Fisher's exact test), Q value = 0.4

Table S177. Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
TBX3 MUTATED	2	3	10	7	3	2
TBX3 WILD-TYPE	127	240	167	177	181	39

'TBX3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.57

Table S178. Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
TBX3 MUTATED	0	4	9	8	1	2	1	1	1
TBX3 WILD-TYPE	64	115	147	159	68	109	144	53	72

'TBX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S179. Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
TBX3 MUTATED	2	3	1	3	2	3
TBX3 WILD-TYPE	112	60	49	117	120	96

'TBX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.594 (Fisher's exact test), Q value = 0.93

Table S180. Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
TBX3 MUTATED	6	6	2
TBX3 WILD-TYPE	275	165	114

'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.63

Table S181. Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
RB1 MUTATED	6	0	4
RB1 WILD-TYPE	221	117	161

'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.265 (Fisher's exact test), Q value = 0.71

Table S182. Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
RB1 MUTATED	1	6	3
RB1 WILD-TYPE	154	259	86

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 0.59

Table S183. Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
RB1 MUTATED	3	4	3	9	0
RB1 WILD-TYPE	289	114	264	252	25

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 0.56

Table S184. Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
RB1 MUTATED	2	3	0	5	1
RB1 WILD-TYPE	191	147	122	114	79

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00738 (Fisher's exact test), Q value = 0.092

Table S185. Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
RB1 MUTATED	5	2	0	1	3	3	2
RB1 WILD-TYPE	147	212	29	198	120	64	8

Figure S88. Get High-res Image Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.6

Table S186. Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
RB1 MUTATED	8	5	3
RB1 WILD-TYPE	207	325	246

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 0.65

Table S187. Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
RB1 MUTATED	3	5	0	4	7	0	0
RB1 WILD-TYPE	230	154	130	201	177	45	18

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.71

Table S188. Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
RB1 MUTATED	4	5	0	3	6	1
RB1 WILD-TYPE	259	146	79	258	162	51

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.75

Table S189. Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
RB1 MUTATED	4	6	1	1	3	1
RB1 WILD-TYPE	125	237	176	183	181	40

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.118 (Fisher's exact test), Q value = 0.56

Table S190. Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
RB1 MUTATED	0	5	0	2	1	2	3	0	3
RB1 WILD-TYPE	64	114	156	165	68	109	142	54	70

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.23

Table S191. Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
RB1 MUTATED	1	0	2	2	7	0
RB1 WILD-TYPE	113	63	48	118	115	99

Figure S89. Get High-res Image Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.71

Table S192. Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
RB1 MUTATED	8	1	3
RB1 WILD-TYPE	273	170	113

'CTCF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.36

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
CTCF MUTATED	10	2	1
CTCF WILD-TYPE	217	115	164

Figure S90. Get High-res Image Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CTCF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0596 (Fisher's exact test), Q value = 0.4

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
CTCF MUTATED	8	4	1
CTCF WILD-TYPE	147	261	88

'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.13

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
CTCF MUTATED	2	2	11	1	0
CTCF WILD-TYPE	290	116	256	260	25

Figure S91. Get High-res Image Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0996 (Fisher's exact test), Q value = 0.5

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
CTCF MUTATED	7	1	1	0	1
CTCF WILD-TYPE	186	149	121	119	79

'CTCF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.667 (Fisher's exact test), Q value = 0.97

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
CTCF MUTATED	1	5	1	4	1	1	0
CTCF WILD-TYPE	151	209	28	195	122	66	10

'CTCF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 0.64

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
CTCF MUTATED	1	8	4
CTCF WILD-TYPE	214	322	245

'CTCF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 0.76

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
CTCF MUTATED	3	1	3	7	1	1	0
CTCF WILD-TYPE	230	158	127	198	183	44	18

'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.489 (Fisher's exact test), Q value = 0.87

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
CTCF MUTATED	7	1	1	6	1	0
CTCF WILD-TYPE	256	150	78	255	167	52

'CTCF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.118 (Fisher's exact test), Q value = 0.56

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
CTCF MUTATED	1	1	7	4	3	0
CTCF WILD-TYPE	128	242	170	180	181	41

'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0598 (Fisher's exact test), Q value = 0.4

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
CTCF MUTATED	1	1	1	8	2	1	0	1	1
CTCF WILD-TYPE	63	118	155	159	67	110	145	53	72

'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.972 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
CTCF MUTATED	1	0	0	2	2	1
CTCF WILD-TYPE	113	63	50	118	120	98

'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
CTCF MUTATED	3	1	2
CTCF WILD-TYPE	278	170	114

'RBMX MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
RBMX MUTATED	2	1	3
RBMX WILD-TYPE	225	116	162

'RBMX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.57

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
RBMX MUTATED	1	2	3
RBMX WILD-TYPE	154	263	86

'RBMX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.58

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
RBMX MUTATED	1	1	4	6	1
RBMX WILD-TYPE	291	117	263	255	24

'RBMX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.57

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
RBMX MUTATED	0	3	2	3	2
RBMX WILD-TYPE	193	147	120	116	78

'RBMX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0848 (Fisher's exact test), Q value = 0.45

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
RBMX MUTATED	4	3	2	1	0	1	0
RBMX WILD-TYPE	148	211	27	198	123	66	10

'RBMX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 0.63

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
RBMX MUTATED	5	5	1
RBMX WILD-TYPE	210	325	248

'RBMX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.23

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
RBMX MUTATED	0	1	2	2	6	1	1
RBMX WILD-TYPE	233	158	128	203	178	44	17

Figure S92. Get High-res Image Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'RBMX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.26

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
RBMX MUTATED	0	1	0	6	5	1
RBMX WILD-TYPE	263	150	79	255	163	51

Figure S93. Get High-res Image Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RBMX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 0.97

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
RBMX MUTATED	1	6	1	2	3	0
RBMX WILD-TYPE	128	237	176	182	181	41

'RBMX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.616 (Fisher's exact test), Q value = 0.94

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
RBMX MUTATED	0	2	2	1	1	1	3	0	3
RBMX WILD-TYPE	64	117	154	166	68	110	142	54	70

'RBMX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.68

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
RBMX MUTATED	0	0	0	1	4	2
RBMX WILD-TYPE	114	63	50	119	118	97

'RBMX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
RBMX MUTATED	4	2	1
RBMX WILD-TYPE	277	169	115

'HRNR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.874 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
HRNR MUTATED	8	5	7
HRNR WILD-TYPE	219	112	158

'HRNR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.646 (Fisher's exact test), Q value = 0.96

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
HRNR MUTATED	5	10	5
HRNR WILD-TYPE	150	255	84

'HRNR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.65

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
HRNR MUTATED	5	5	10	9	2
HRNR WILD-TYPE	287	113	257	252	23

'HRNR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.516 (Fisher's exact test), Q value = 0.88

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
HRNR MUTATED	6	3	3	3	5
HRNR WILD-TYPE	187	147	119	116	75

'HRNR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 0.95

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
HRNR MUTATED	7	6	0	6	4	1	1
HRNR WILD-TYPE	145	208	29	193	119	66	9

'HRNR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.393 (Fisher's exact test), Q value = 0.83

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
HRNR MUTATED	9	11	5
HRNR WILD-TYPE	206	319	244

'HRNR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.99 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
HRNR MUTATED	6	6	4	7	7	1	0
HRNR WILD-TYPE	227	153	126	198	177	44	18

'HRNR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.677 (Fisher's exact test), Q value = 0.97

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
HRNR MUTATED	8	3	3	7	7	3
HRNR WILD-TYPE	255	148	76	254	161	49

'HRNR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.643 (Fisher's exact test), Q value = 0.96

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
HRNR MUTATED	2	8	6	4	9	1
HRNR WILD-TYPE	127	235	171	180	175	40

'HRNR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
HRNR MUTATED	2	5	5	7	3	1	5	1	1
HRNR WILD-TYPE	62	114	151	160	66	110	140	53	72

'HRNR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 0.95

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
HRNR MUTATED	2	0	2	3	4	4
HRNR WILD-TYPE	112	63	48	117	118	95

'HRNR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.743 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
HRNR MUTATED	9	3	3
HRNR WILD-TYPE	272	168	113

'ZMYM3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 0.78

Table S229. Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
ZMYM3 MUTATED	3	2	6
ZMYM3 WILD-TYPE	224	115	159

'ZMYM3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.71

Table S230. Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
ZMYM3 MUTATED	2	5	4
ZMYM3 WILD-TYPE	153	260	85

'ZMYM3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.84

Table S231. Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
ZMYM3 MUTATED	2	1	7	5	0
ZMYM3 WILD-TYPE	290	117	260	256	25

'ZMYM3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.679 (Fisher's exact test), Q value = 0.97

Table S232. Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
ZMYM3 MUTATED	2	2	1	3	0
ZMYM3 WILD-TYPE	191	148	121	116	80

'ZMYM3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 0.87

Table S233. Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
ZMYM3 MUTATED	4	3	0	1	1	2	0
ZMYM3 WILD-TYPE	148	211	29	198	122	65	10

'ZMYM3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 0.36

Table S234. Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
ZMYM3 MUTATED	4	7	0
ZMYM3 WILD-TYPE	211	323	249

Figure S94. Get High-res Image Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.398 (Fisher's exact test), Q value = 0.84

Table S235. Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
ZMYM3 MUTATED	4	1	0	6	4	0	0
ZMYM3 WILD-TYPE	229	158	130	199	180	45	18

'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.487 (Fisher's exact test), Q value = 0.87

Table S236. Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
ZMYM3 MUTATED	2	3	0	6	4	0
ZMYM3 WILD-TYPE	261	148	79	255	164	52

'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.87

Table S237. Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
ZMYM3 MUTATED	1	6	4	1	2	1
ZMYM3 WILD-TYPE	128	237	173	183	182	40

'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 0.84

Table S238. Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
ZMYM3 MUTATED	0	3	1	2	1	1	3	3	1
ZMYM3 WILD-TYPE	64	116	155	165	68	110	142	51	72

'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 0.98

Table S239. Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
ZMYM3 MUTATED	2	1	0	1	0	1
ZMYM3 WILD-TYPE	112	62	50	119	122	98

'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S240. Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
ZMYM3 MUTATED	2	2	1
ZMYM3 WILD-TYPE	279	169	115

'NCOR1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S241. Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
NCOR1 MUTATED	9	3	6
NCOR1 WILD-TYPE	218	114	159

'NCOR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.947 (Fisher's exact test), Q value = 1

Table S242. Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
NCOR1 MUTATED	6	9	3
NCOR1 WILD-TYPE	149	256	86

'NCOR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S243. Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
NCOR1 MUTATED	12	6	11	8	1
NCOR1 WILD-TYPE	280	112	256	253	24

'NCOR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 0.77

Table S244. Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
NCOR1 MUTATED	6	10	4	4	6
NCOR1 WILD-TYPE	187	140	118	115	74

'NCOR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 0.81

Table S245. Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
NCOR1 MUTATED	4	6	1	6	8	5	0
NCOR1 WILD-TYPE	148	208	28	193	115	62	10

'NCOR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.944 (Fisher's exact test), Q value = 1

Table S246. Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
NCOR1 MUTATED	9	12	9
NCOR1 WILD-TYPE	206	318	240

'NCOR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.313 (Fisher's exact test), Q value = 0.77

Table S247. Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
NCOR1 MUTATED	6	12	6	8	6	1	1
NCOR1 WILD-TYPE	227	147	124	197	178	44	17

'NCOR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 0.9

Table S248. Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
NCOR1 MUTATED	7	10	3	12	6	2
NCOR1 WILD-TYPE	256	141	76	249	162	50

'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.896 (Fisher's exact test), Q value = 1

Table S249. Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
NCOR1 MUTATED	4	12	6	7	10	1
NCOR1 WILD-TYPE	125	231	171	177	174	40

'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.21

Table S250. Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
NCOR1 MUTATED	4	8	8	0	3	4	5	4	4
NCOR1 WILD-TYPE	60	111	148	167	66	107	140	50	69

Figure S95. Get High-res Image Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.84

Table S251. Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
NCOR1 MUTATED	1	2	1	7	4	4
NCOR1 WILD-TYPE	113	61	49	113	118	95

'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 0.98

Table S252. Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
NCOR1 MUTATED	8	6	5
NCOR1 WILD-TYPE	273	165	111

'GPRIN2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S253. Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
GPRIN2 MUTATED	3	1	3
GPRIN2 WILD-TYPE	224	116	162

'GPRIN2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.69 (Fisher's exact test), Q value = 0.97

Table S254. Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
GPRIN2 MUTATED	2	3	2
GPRIN2 WILD-TYPE	153	262	87

'GPRIN2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S255. Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
GPRIN2 MUTATED	3	1	3	4	0
GPRIN2 WILD-TYPE	289	117	264	257	25

'GPRIN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.61 (Fisher's exact test), Q value = 0.94

Table S256. Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
GPRIN2 MUTATED	3	2	0	2	0
GPRIN2 WILD-TYPE	190	148	122	117	80

'GPRIN2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S257. Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
GPRIN2 MUTATED	3	2	0	3	1	1	0
GPRIN2 WILD-TYPE	149	212	29	196	122	66	10

'GPRIN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.71

Table S258. Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
GPRIN2 MUTATED	5	3	2
GPRIN2 WILD-TYPE	210	327	247

'GPRIN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S259. Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
GPRIN2 MUTATED	1	2	1	4	3	0	0
GPRIN2 WILD-TYPE	232	157	129	201	181	45	18

'GPRIN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 0.84

Table S260. Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
GPRIN2 MUTATED	1	2	0	4	4	0
GPRIN2 WILD-TYPE	262	149	79	257	164	52

'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.67 (Fisher's exact test), Q value = 0.97

Table S261. Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
GPRIN2 MUTATED	0	4	3	2	1	0
GPRIN2 WILD-TYPE	129	239	174	182	183	41

'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 0.7

Table S262. Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
GPRIN2 MUTATED	0	1	0	3	1	0	4	1	0
GPRIN2 WILD-TYPE	64	118	156	164	68	111	141	53	73

'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 0.92

Table S263. Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
GPRIN2 MUTATED	0	1	0	1	3	1
GPRIN2 WILD-TYPE	114	62	50	119	119	98

'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S264. Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
GPRIN2 MUTATED	3	2	1
GPRIN2 WILD-TYPE	278	169	115

'SPEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S265. Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
SPEN MUTATED	8	5	7
SPEN WILD-TYPE	219	112	158

'SPEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.53 (Fisher's exact test), Q value = 0.9

Table S266. Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
SPEN MUTATED	5	13	2
SPEN WILD-TYPE	150	252	87

'SPEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.507 (Fisher's exact test), Q value = 0.88

Table S267. Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
SPEN MUTATED	9	4	12	5	0
SPEN WILD-TYPE	283	114	255	256	25

'SPEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.84

Table S268. Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
SPEN MUTATED	9	6	5	1	3
SPEN WILD-TYPE	184	144	117	118	77

'SPEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.945 (Fisher's exact test), Q value = 1

Table S269. Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
SPEN MUTATED	4	7	0	8	3	1	0
SPEN WILD-TYPE	148	207	29	191	120	66	10

'SPEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S270. Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
SPEN MUTATED	6	10	7
SPEN WILD-TYPE	209	320	242

'SPEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 0.65

Table S271. Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
SPEN MUTATED	8	5	4	9	2	2	2
SPEN WILD-TYPE	225	154	126	196	182	43	16

'SPEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 0.56

Table S272. Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
SPEN MUTATED	6	7	1	14	2	2
SPEN WILD-TYPE	257	144	78	247	166	50

'SPEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0666 (Fisher's exact test), Q value = 0.41

Table S273. Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
SPEN MUTATED	5	4	6	3	12	2
SPEN WILD-TYPE	124	239	171	181	172	39

'SPEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 0.64

Table S274. Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
SPEN MUTATED	3	6	5	4	5	5	2	2	0
SPEN WILD-TYPE	61	113	151	163	64	106	143	52	73

'SPEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 0.89

Table S275. Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
SPEN MUTATED	4	3	1	2	1	2
SPEN WILD-TYPE	110	60	49	118	121	97

'SPEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 0.91

Table S276. Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
SPEN MUTATED	7	5	1
SPEN WILD-TYPE	274	166	115

'NF1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S277. Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
NF1 MUTATED	7	3	5
NF1 WILD-TYPE	220	114	160

'NF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.94 (Fisher's exact test), Q value = 1

Table S278. Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
NF1 MUTATED	4	8	3
NF1 WILD-TYPE	151	257	86

'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.58

Table S279. Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
NF1 MUTATED	4	6	11	6	0
NF1 WILD-TYPE	288	112	256	255	25

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.65

Table S280. Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
NF1 MUTATED	3	7	6	2	1
NF1 WILD-TYPE	190	143	116	117	79

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.84

Table S281. Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
NF1 MUTATED	3	6	0	5	5	5	0
NF1 WILD-TYPE	149	208	29	194	118	62	10

'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S282. Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
NF1 MUTATED	6	9	9
NF1 WILD-TYPE	209	321	240

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.57

Table S283. Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
NF1 MUTATED	4	9	2	3	6	2	1
NF1 WILD-TYPE	229	150	128	202	178	43	17

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.418 (Fisher's exact test), Q value = 0.84

Table S284. Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
NF1 MUTATED	4	7	3	6	6	1
NF1 WILD-TYPE	259	144	76	255	162	51

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.29 (Fisher's exact test), Q value = 0.75

Table S285. Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
NF1 MUTATED	1	6	3	8	8	1
NF1 WILD-TYPE	128	237	174	176	176	40

'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.556 (Fisher's exact test), Q value = 0.92

Table S286. Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
NF1 MUTATED	0	6	4	5	1	4	6	0	1
NF1 WILD-TYPE	64	113	152	162	68	107	139	54	72

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S287. Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
NF1 MUTATED	3	1	2	4	2	3
NF1 WILD-TYPE	111	62	48	116	120	96

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S288. Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
NF1 MUTATED	9	4	2
NF1 WILD-TYPE	272	167	114

'TCP11 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S289. Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
TCP11 MUTATED	2	2	2
TCP11 WILD-TYPE	225	115	163

'TCP11 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S290. Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
TCP11 MUTATED	2	3	1
TCP11 WILD-TYPE	153	262	88

'TCP11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 0.87

Table S291. Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
TCP11 MUTATED	1	0	4	1	0
TCP11 WILD-TYPE	291	118	263	260	25

'TCP11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 1

Table S292. Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
TCP11 MUTATED	2	1	0	2	0	0	0
TCP11 WILD-TYPE	150	213	29	197	123	67	10

'TCP11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S293. Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
TCP11 MUTATED	1	2	2
TCP11 WILD-TYPE	214	328	247

'TCP11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S294. Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
TCP11 MUTATED	2	0	2	1	1	0	0
TCP11 WILD-TYPE	231	159	128	204	183	45	18

'TCP11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.376 (Fisher's exact test), Q value = 0.83

Table S295. Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
TCP11 MUTATED	1	1	2	1	1	0
TCP11 WILD-TYPE	262	150	77	260	167	52

'TCP11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.647 (Fisher's exact test), Q value = 0.96

Table S296. Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
TCP11 MUTATED	1	1	1	1	1	1
TCP11 WILD-TYPE	128	242	176	183	183	40

'TCP11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.399 (Fisher's exact test), Q value = 0.84

Table S297. Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
TCP11 MUTATED	2	0	2	1	0	0	1	0	0
TCP11 WILD-TYPE	62	119	154	166	69	111	144	54	73

'SF3B1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.73 (Fisher's exact test), Q value = 0.99

Table S298. Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
SF3B1 MUTATED	5	1	2
SF3B1 WILD-TYPE	222	116	163

'SF3B1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.453 (Fisher's exact test), Q value = 0.86

Table S299. Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
SF3B1 MUTATED	1	6	1
SF3B1 WILD-TYPE	154	259	88

'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 0.88

Table S300. Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
SF3B1 MUTATED	7	3	4	2	0
SF3B1 WILD-TYPE	285	115	263	259	25

'SF3B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.172 (Fisher's exact test), Q value = 0.61

Table S301. Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
SF3B1 MUTATED	6	5	1	0	2
SF3B1 WILD-TYPE	187	145	121	119	78

'SF3B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.62

Table S302. Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
SF3B1 MUTATED	1	1	1	6	1	2	0
SF3B1 WILD-TYPE	151	213	28	193	122	65	10

'SF3B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 0.71

Table S303. Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
SF3B1 MUTATED	1	5	6
SF3B1 WILD-TYPE	214	325	243

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.646 (Fisher's exact test), Q value = 0.96

Table S304. Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
SF3B1 MUTATED	3	4	3	5	1	0	0
SF3B1 WILD-TYPE	230	155	127	200	183	45	18

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.81

Table S305. Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
SF3B1 MUTATED	5	4	3	3	1	0
SF3B1 WILD-TYPE	258	147	76	258	167	52

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 0.79

Table S306. Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
SF3B1 MUTATED	3	2	4	5	1	1
SF3B1 WILD-TYPE	126	241	173	179	183	40

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 0.63

Table S307. Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
SF3B1 MUTATED	0	1	4	4	1	0	1	3	2
SF3B1 WILD-TYPE	64	118	152	163	68	111	144	51	71

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 0.95

Table S308. Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
SF3B1 MUTATED	2	1	1	1	0	1
SF3B1 WILD-TYPE	112	62	49	119	122	98

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.183 (Fisher's exact test), Q value = 0.63

Table S309. Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
SF3B1 MUTATED	1	3	2
SF3B1 WILD-TYPE	280	168	114

'ERBB2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.64

Table S310. Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
ERBB2 MUTATED	6	4	1
ERBB2 WILD-TYPE	221	113	164

'ERBB2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 0.61

Table S311. Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
ERBB2 MUTATED	1	9	1
ERBB2 WILD-TYPE	154	256	88

'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.83

Table S312. Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
ERBB2 MUTATED	5	5	6	3	0
ERBB2 WILD-TYPE	287	113	261	258	25

'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 0.59

Table S313. Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
ERBB2 MUTATED	1	4	4	1	3
ERBB2 WILD-TYPE	192	146	118	118	77

'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.2

Table S314. Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
ERBB2 MUTATED	0	2	1	6	1	3	1
ERBB2 WILD-TYPE	152	212	28	193	122	64	9

Figure S96. Get High-res Image Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.359 (Fisher's exact test), Q value = 0.81

Table S315. Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
ERBB2 MUTATED	3	4	7
ERBB2 WILD-TYPE	212	326	242

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0689 (Fisher's exact test), Q value = 0.42

Table S316. Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
ERBB2 MUTATED	2	8	4	5	1	0	0
ERBB2 WILD-TYPE	231	151	126	200	183	45	18

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.57

Table S317. Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
ERBB2 MUTATED	3	3	2	8	1	3
ERBB2 WILD-TYPE	260	148	77	253	167	49

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0551 (Fisher's exact test), Q value = 0.39

Table S318. Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
ERBB2 MUTATED	0	2	6	4	6	2
ERBB2 WILD-TYPE	129	241	171	180	178	39

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0569 (Fisher's exact test), Q value = 0.4

Table S319. Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
ERBB2 MUTATED	1	3	8	3	3	1	0	1	0
ERBB2 WILD-TYPE	63	116	148	164	66	110	145	53	73

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S320. Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
ERBB2 MUTATED	2	1	0	3	1	2
ERBB2 WILD-TYPE	112	62	50	117	121	97

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.497 (Fisher's exact test), Q value = 0.87

Table S321. Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
ERBB2 MUTATED	3	3	3
ERBB2 WILD-TYPE	278	168	113

'RAB42 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S322. Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
RAB42 MUTATED	1	1	2
RAB42 WILD-TYPE	226	116	163

'RAB42 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.25

Table S323. Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
RAB42 MUTATED	0	1	3
RAB42 WILD-TYPE	155	264	86

Figure S97. Get High-res Image Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'RAB42 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.76

Table S324. Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
RAB42 MUTATED	1	0	0	3	0
RAB42 WILD-TYPE	291	118	267	258	25

'RAB42 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.402 (Fisher's exact test), Q value = 0.84

Table S325. Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
RAB42 MUTATED	1	0	0	1	0	1	0
RAB42 WILD-TYPE	151	214	29	198	123	66	10

'RAB42 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.56

Table S326. Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
RAB42 MUTATED	2	0	1
RAB42 WILD-TYPE	213	330	248

'RAB42 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.65

Table S327. Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
RAB42 MUTATED	0	0	0	1	3	0	0
RAB42 WILD-TYPE	233	159	130	204	181	45	18

'RAB42 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 0.59

Table S328. Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
RAB42 MUTATED	0	0	0	1	3	0
RAB42 WILD-TYPE	263	151	79	260	165	52

'RAB42 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 0.85

Table S329. Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
RAB42 MUTATED	0	3	0	0	1	0
RAB42 WILD-TYPE	129	240	177	184	183	41

'RAB42 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.8

Table S330. Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
RAB42 MUTATED	0	0	0	1	0	0	3	0	0
RAB42 WILD-TYPE	64	119	156	166	69	111	142	54	73

'CDC42EP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S331. Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
CDC42EP1 MUTATED	1	1	2
CDC42EP1 WILD-TYPE	226	116	163

'CDC42EP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 0.61

Table S332. Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
CDC42EP1 MUTATED	1	1	2
CDC42EP1 WILD-TYPE	154	264	87

'CDC42EP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.62

Table S333. Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
CDC42EP1 MUTATED	0	2	1	2	0
CDC42EP1 WILD-TYPE	292	116	266	259	25

'CDC42EP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.8

Table S334. Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
CDC42EP1 MUTATED	1	0	2	0	0
CDC42EP1 WILD-TYPE	192	150	120	119	80

'CDC42EP1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S335. Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
CDC42EP1 MUTATED	1	2	0	1	0	1	0
CDC42EP1 WILD-TYPE	151	212	29	198	123	66	10

'CDC42EP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.739 (Fisher's exact test), Q value = 0.99

Table S336. Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
CDC42EP1 MUTATED	2	2	1
CDC42EP1 WILD-TYPE	213	328	248

'CDC42EP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.71

Table S337. Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
CDC42EP1 MUTATED	1	0	1	0	2	1	0
CDC42EP1 WILD-TYPE	232	159	129	205	182	44	18

'CDC42EP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.559 (Fisher's exact test), Q value = 0.92

Table S338. Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
CDC42EP1 MUTATED	1	0	1	1	2	0
CDC42EP1 WILD-TYPE	262	151	78	260	166	52

'CDC42EP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 0.97

Table S339. Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
CDC42EP1 MUTATED	0	2	2	0	1	0
CDC42EP1 WILD-TYPE	129	241	175	184	183	41

'CDC42EP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.218 (Fisher's exact test), Q value = 0.66

Table S340. Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
CDC42EP1 MUTATED	0	0	2	0	0	0	1	0	2
CDC42EP1 WILD-TYPE	64	119	154	167	69	111	144	54	71

'KDM6A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0841 (Fisher's exact test), Q value = 0.45

Table S341. Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
KDM6A MUTATED	1	4	3
KDM6A WILD-TYPE	226	113	162

'KDM6A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 0.92

Table S342. Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
KDM6A MUTATED	1	5	2
KDM6A WILD-TYPE	154	260	87

'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.83

Table S343. Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
KDM6A MUTATED	5	3	4	2	1
KDM6A WILD-TYPE	287	115	263	259	24

'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.8

Table S344. Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
KDM6A MUTATED	2	3	0	3	2
KDM6A WILD-TYPE	191	147	122	116	78

'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 0.71

Table S345. Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
KDM6A MUTATED	4	2	1	2	1	3	0
KDM6A WILD-TYPE	148	212	28	197	122	64	10

'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.153 (Fisher's exact test), Q value = 0.59

Table S346. Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
KDM6A MUTATED	5	7	1
KDM6A WILD-TYPE	210	323	248

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.9

Table S347. Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
KDM6A MUTATED	3	2	3	1	5	1	0
KDM6A WILD-TYPE	230	157	127	204	179	44	18

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 0.84

Table S348. Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
KDM6A MUTATED	2	3	0	5	5	0
KDM6A WILD-TYPE	261	148	79	256	163	52

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S349. Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
KDM6A MUTATED	3	5	2	2	3	0
KDM6A WILD-TYPE	126	238	175	182	181	41

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.987 (Fisher's exact test), Q value = 1

Table S350. Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
KDM6A MUTATED	1	2	2	3	1	1	4	0	1
KDM6A WILD-TYPE	63	117	154	164	68	110	141	54	72

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S351. Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
KDM6A MUTATED	2	0	0	3	3	1
KDM6A WILD-TYPE	112	63	50	117	119	98

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 0.84

Table S352. Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
KDM6A MUTATED	5	1	3
KDM6A WILD-TYPE	276	170	113

'AQP12A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.87

Table S353. Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
AQP12A MUTATED	2	1	0
AQP12A WILD-TYPE	225	116	165

'AQP12A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S354. Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
AQP12A MUTATED	1	2	0
AQP12A WILD-TYPE	154	263	89

'AQP12A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 0.92

Table S355. Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
AQP12A MUTATED	4	0	1	1	0
AQP12A WILD-TYPE	288	118	266	260	25

'AQP12A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S356. Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
AQP12A MUTATED	2	2	0	1	0
AQP12A WILD-TYPE	191	148	122	118	80

'AQP12A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S357. Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
AQP12A MUTATED	1	2	0	2	0	0	0
AQP12A WILD-TYPE	151	212	29	197	123	67	10

'AQP12A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.63

Table S358. Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
AQP12A MUTATED	1	4	0
AQP12A WILD-TYPE	214	326	249

'AQP12A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S359. Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
AQP12A MUTATED	2	2	1	1	0	0	0
AQP12A WILD-TYPE	231	157	129	204	184	45	18

'AQP12A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S360. Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
AQP12A MUTATED	2	1	0	2	1	0
AQP12A WILD-TYPE	261	150	79	259	167	52

'AQP12A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S361. Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
AQP12A MUTATED	0	2	1	1	2	0
AQP12A WILD-TYPE	129	241	176	183	182	41

'AQP12A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.559 (Fisher's exact test), Q value = 0.92

Table S362. Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
AQP12A MUTATED	0	0	0	3	1	1	1	0	0
AQP12A WILD-TYPE	64	119	156	164	68	110	144	54	73

'AQP12A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.64

Table S363. Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
AQP12A MUTATED	2	1	0	0	0	0
AQP12A WILD-TYPE	112	62	50	120	122	99

'AQP12A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S364. Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
AQP12A MUTATED	2	1	0
AQP12A WILD-TYPE	279	170	116

'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 0.92

Table S365. Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
KRAS MUTATED	3	0	1
KRAS WILD-TYPE	224	117	164

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S366. Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
KRAS MUTATED	1	3	0
KRAS WILD-TYPE	154	262	89

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.62

Table S367. Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
KRAS MUTATED	0	1	4	1	0
KRAS WILD-TYPE	292	117	263	260	25

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 0.81

Table S368. Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
KRAS MUTATED	2	0	2	0	0
KRAS WILD-TYPE	191	150	120	119	80

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 0.95

Table S369. Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
KRAS MUTATED	0	1	0	1	2	0	0
KRAS WILD-TYPE	152	213	29	198	121	67	10

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S370. Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
KRAS MUTATED	1	2	1
KRAS WILD-TYPE	214	328	248

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 0.92

Table S371. Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
KRAS MUTATED	0	1	1	3	1	0	0
KRAS WILD-TYPE	233	158	129	202	183	45	18

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0851 (Fisher's exact test), Q value = 0.45

Table S372. Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
KRAS MUTATED	2	0	2	1	0	1
KRAS WILD-TYPE	261	151	77	260	168	51

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.693 (Fisher's exact test), Q value = 0.97

Table S373. Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
KRAS MUTATED	0	1	1	1	3	0
KRAS WILD-TYPE	129	242	176	183	181	41

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0391 (Fisher's exact test), Q value = 0.32

Table S374. Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
KRAS MUTATED	0	4	2	0	0	0	0	0	0
KRAS WILD-TYPE	64	115	154	167	69	111	145	54	73

Figure S98. Get High-res Image Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 0.99

Table S375. Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
KRAS MUTATED	0	0	0	2	1	0
KRAS WILD-TYPE	114	63	50	118	121	99

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 0.63

Table S376. Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
KRAS MUTATED	1	0	2
KRAS WILD-TYPE	280	171	114

'NBPF9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 0.78

Table S377. Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
NBPF9 MUTATED	4	0	1
NBPF9 WILD-TYPE	223	117	164

'NBPF9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S378. Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
NBPF9 MUTATED	2	2	1
NBPF9 WILD-TYPE	153	263	88

'NBPF9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00409 (Fisher's exact test), Q value = 0.057

Table S379. Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
NBPF9 MUTATED	1	1	0	1	2
NBPF9 WILD-TYPE	291	117	267	260	23

Figure S99. Get High-res Image Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NBPF9 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S380. Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
NBPF9 MUTATED	1	2	0	2	0	0	0
NBPF9 WILD-TYPE	151	212	29	197	123	67	10

'NBPF9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S381. Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
NBPF9 MUTATED	1	2	2
NBPF9 WILD-TYPE	214	328	247

'NBPF9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S382. Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
NBPF9 MUTATED	1	1	0	2	1	0	0
NBPF9 WILD-TYPE	232	158	130	203	183	45	18

'NBPF9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.155 (Fisher's exact test), Q value = 0.59

Table S383. Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
NBPF9 MUTATED	1	3	0	0	1	0
NBPF9 WILD-TYPE	262	148	79	261	167	52

'NBPF9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 0.81

Table S384. Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
NBPF9 MUTATED	0	2	1	0	1	1
NBPF9 WILD-TYPE	129	241	176	184	183	40

'NBPF9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.561 (Fisher's exact test), Q value = 0.92

Table S385. Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
NBPF9 MUTATED	0	0	0	1	0	2	1	0	1
NBPF9 WILD-TYPE	64	119	156	166	69	109	144	54	72

'MYB MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 0.83

Table S386. Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
MYB MUTATED	6	2	1
MYB WILD-TYPE	221	115	164

'MYB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 0.93

Table S387. Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
MYB MUTATED	4	3	2
MYB WILD-TYPE	151	262	87

'MYB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.59

Table S388. Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
MYB MUTATED	1	3	6	2	0
MYB WILD-TYPE	291	115	261	259	25

'MYB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.555 (Fisher's exact test), Q value = 0.92

Table S389. Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
MYB MUTATED	1	1	0	2	1
MYB WILD-TYPE	192	149	122	117	79

'MYB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.59

Table S390. Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
MYB MUTATED	0	2	0	0	3	1	0
MYB WILD-TYPE	152	212	29	199	120	66	10

'MYB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S391. Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
MYB MUTATED	1	3	2
MYB WILD-TYPE	214	327	247

'MYB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.895 (Fisher's exact test), Q value = 1

Table S392. Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
MYB MUTATED	3	1	1	3	3	1	0
MYB WILD-TYPE	230	158	129	202	181	44	18

'MYB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S393. Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
MYB MUTATED	4	1	0	4	3	0
MYB WILD-TYPE	259	150	79	257	165	52

'MYB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 0.7

Table S394. Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
MYB MUTATED	0	2	4	1	4	1
MYB WILD-TYPE	129	241	173	183	180	40

'MYB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 0.77

Table S395. Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
MYB MUTATED	1	0	0	4	1	3	2	0	1
MYB WILD-TYPE	63	119	156	163	68	108	143	54	72

'MYB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0866 (Fisher's exact test), Q value = 0.45

Table S396. Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
MYB MUTATED	1	0	2	1	0	0
MYB WILD-TYPE	113	63	48	119	122	99

'MYB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00177 (Fisher's exact test), Q value = 0.028

Table S397. Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
MYB MUTATED	0	0	4
MYB WILD-TYPE	281	171	112

Figure S100. Get High-res Image Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ZNF362 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0996 (Fisher's exact test), Q value = 0.5

Table S398. Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
ZNF362 MUTATED	2	3	0
ZNF362 WILD-TYPE	225	114	165

'ZNF362 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 0.98

Table S399. Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
ZNF362 MUTATED	2	3	0
ZNF362 WILD-TYPE	153	262	89

'ZNF362 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 0.63

Table S400. Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
ZNF362 MUTATED	3	1	0	0	0
ZNF362 WILD-TYPE	289	117	267	261	25

'ZNF362 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S401. Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
ZNF362 MUTATED	0	2	0	2	0	0	0
ZNF362 WILD-TYPE	152	212	29	197	123	67	10

'ZNF362 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 0.87

Table S402. Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
ZNF362 MUTATED	0	3	1
ZNF362 WILD-TYPE	215	327	248

'ZNF362 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.87

Table S403. Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
ZNF362 MUTATED	3	1	1	0	0	0	0
ZNF362 WILD-TYPE	230	158	129	205	184	45	18

'ZNF362 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.909 (Fisher's exact test), Q value = 1

Table S404. Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
ZNF362 MUTATED	2	1	0	2	0	0
ZNF362 WILD-TYPE	261	150	79	259	168	52

'ZNF362 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.62

Table S405. Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
ZNF362 MUTATED	1	0	1	0	3	0
ZNF362 WILD-TYPE	128	243	176	184	181	41

'ZNF362 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0701 (Fisher's exact test), Q value = 0.42

Table S406. Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
ZNF362 MUTATED	0	0	0	4	1	0	0	0	0
ZNF362 WILD-TYPE	64	119	156	163	68	111	145	54	73

'TBL1XR1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0631 (Fisher's exact test), Q value = 0.41

Table S407. Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
TBL1XR1 MUTATED	7	0	1
TBL1XR1 WILD-TYPE	220	117	164

'TBL1XR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.34 (Fisher's exact test), Q value = 0.79

Table S408. Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
TBL1XR1 MUTATED	4	4	0
TBL1XR1 WILD-TYPE	151	261	89

'TBL1XR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0983 (Fisher's exact test), Q value = 0.5

Table S409. Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
TBL1XR1 MUTATED	2	3	4	0	0
TBL1XR1 WILD-TYPE	290	115	263	261	25

'TBL1XR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.474 (Fisher's exact test), Q value = 0.87

Table S410. Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
TBL1XR1 MUTATED	1	2	1	3	0	1	0
TBL1XR1 WILD-TYPE	151	212	28	196	123	66	10

'TBL1XR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S411. Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
TBL1XR1 MUTATED	2	3	3
TBL1XR1 WILD-TYPE	213	327	246

'TBL1XR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.32

Table S412. Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
TBL1XR1 MUTATED	0	2	1	6	0	0	0
TBL1XR1 WILD-TYPE	233	157	129	199	184	45	18

Figure S101. Get High-res Image Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TBL1XR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 0.92

Table S413. Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
TBL1XR1 MUTATED	4	1	0	4	0	0
TBL1XR1 WILD-TYPE	259	150	79	257	168	52

'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 0.84

Table S414. Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
TBL1XR1 MUTATED	0	1	2	2	3	1
TBL1XR1 WILD-TYPE	129	242	175	182	181	40

'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.2 (Fisher's exact test), Q value = 0.64

Table S415. Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
TBL1XR1 MUTATED	0	1	1	2	3	2	0	0	0
TBL1XR1 WILD-TYPE	64	118	155	165	66	109	145	54	73

'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S416. Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
TBL1XR1 MUTATED	1	0	0	1	1	2
TBL1XR1 WILD-TYPE	113	63	50	119	121	97

'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.51

Table S417. Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
TBL1XR1 MUTATED	1	1	3
TBL1XR1 WILD-TYPE	280	170	113

'SP3 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S418. Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
SP3 MUTATED	2	1	1
SP3 WILD-TYPE	225	116	164

'SP3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.3 (Fisher's exact test), Q value = 0.77

Table S419. Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
SP3 MUTATED	0	4	0
SP3 WILD-TYPE	155	261	89

'SP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 0.87

Table S420. Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
SP3 MUTATED	3	1	2	0	0
SP3 WILD-TYPE	289	117	265	261	25

'SP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.947 (Fisher's exact test), Q value = 1

Table S421. Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
SP3 MUTATED	2	1	1	0	0
SP3 WILD-TYPE	191	149	121	119	80

'SP3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S422. Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
SP3 MUTATED	0	1	0	2	1	0	0
SP3 WILD-TYPE	152	213	29	197	122	67	10

'SP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S423. Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
SP3 MUTATED	1	1	2
SP3 WILD-TYPE	214	329	247

'SP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 0.64

Table S424. Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
SP3 MUTATED	2	2	2	0	0	1	0
SP3 WILD-TYPE	231	157	128	205	184	44	18

'SP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.84

Table S425. Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
SP3 MUTATED	1	2	0	4	0	0
SP3 WILD-TYPE	262	149	79	257	168	52

'SP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 0.88

Table S426. Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
SP3 MUTATED	3	1	1	1	1	0
SP3 WILD-TYPE	126	242	176	183	183	41

'SP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0652 (Fisher's exact test), Q value = 0.41

Table S427. Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
SP3 MUTATED	2	1	0	2	0	0	0	0	2
SP3 WILD-TYPE	62	118	156	165	69	111	145	54	71

'SP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.83

Table S428. Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
SP3 MUTATED	2	1	0	0	0	1
SP3 WILD-TYPE	112	62	50	120	122	98

'SP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S429. Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
SP3 MUTATED	2	1	1
SP3 WILD-TYPE	279	170	115

'FGFR2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.498 (Fisher's exact test), Q value = 0.87

Table S430. Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
FGFR2 MUTATED	4	0	2
FGFR2 WILD-TYPE	223	117	163

'FGFR2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S431. Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
FGFR2 MUTATED	2	3	1
FGFR2 WILD-TYPE	153	262	88

'FGFR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 0.95

Table S432. Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
FGFR2 MUTATED	3	3	2	3	0
FGFR2 WILD-TYPE	289	115	265	258	25

'FGFR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.559 (Fisher's exact test), Q value = 0.92

Table S433. Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
FGFR2 MUTATED	2	3	1	0	0
FGFR2 WILD-TYPE	191	147	121	119	80

'FGFR2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.32

Table S434. Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
FGFR2 MUTATED	2	3	1	0	3	0	1
FGFR2 WILD-TYPE	150	211	28	199	120	67	9

Figure S102. Get High-res Image Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'FGFR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 0.77

Table S435. Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
FGFR2 MUTATED	4	5	1
FGFR2 WILD-TYPE	211	325	248

'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 0.64

Table S436. Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
FGFR2 MUTATED	2	4	0	3	1	0	1
FGFR2 WILD-TYPE	231	155	130	202	183	45	17

'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.428 (Fisher's exact test), Q value = 0.84

Table S437. Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
FGFR2 MUTATED	2	4	0	3	1	1
FGFR2 WILD-TYPE	261	147	79	258	167	51

'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.66

Table S438. Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
FGFR2 MUTATED	1	5	3	0	1	1
FGFR2 WILD-TYPE	128	238	174	184	183	40

'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0721 (Fisher's exact test), Q value = 0.42

Table S439. Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
FGFR2 MUTATED	1	5	0	3	0	0	1	0	1
FGFR2 WILD-TYPE	63	114	156	164	69	111	144	54	72

'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S440. Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
FGFR2 MUTATED	1	1	0	0	1	1
FGFR2 WILD-TYPE	113	62	50	120	121	98

'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.673 (Fisher's exact test), Q value = 0.97

Table S441. Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
FGFR2 MUTATED	2	2	0
FGFR2 WILD-TYPE	279	169	116

'ZBTB7C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.126 (Fisher's exact test), Q value = 0.56

Table S442. Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
ZBTB7C MUTATED	2	2	0	0	0
ZBTB7C WILD-TYPE	290	116	267	261	25

'ZBTB7C MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S443. Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
ZBTB7C MUTATED	1	1	1	0	0
ZBTB7C WILD-TYPE	192	149	121	119	80

'ZBTB7C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.704 (Fisher's exact test), Q value = 0.98

Table S444. Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
ZBTB7C MUTATED	0	2	0	1	1	1	0
ZBTB7C WILD-TYPE	152	212	29	198	122	66	10

'ZBTB7C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S445. Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
ZBTB7C MUTATED	1	2	2
ZBTB7C WILD-TYPE	214	328	247

'ZBTB7C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.881 (Fisher's exact test), Q value = 1

Table S446. Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
ZBTB7C MUTATED	2	1	1	1	0	0	0
ZBTB7C WILD-TYPE	231	158	129	204	184	45	18

'ZBTB7C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.677 (Fisher's exact test), Q value = 0.97

Table S447. Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
ZBTB7C MUTATED	1	1	1	2	0	0
ZBTB7C WILD-TYPE	262	150	78	259	168	52

'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S448. Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
ZBTB7C MUTATED	1	1	0	2	1	0
ZBTB7C WILD-TYPE	128	242	177	182	183	41

'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.597 (Fisher's exact test), Q value = 0.93

Table S449. Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
ZBTB7C MUTATED	0	1	2	0	0	1	0	0	1
ZBTB7C WILD-TYPE	64	118	154	167	69	110	145	54	72

'NCDN MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S450. Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
NCDN MUTATED	2	0	1
NCDN WILD-TYPE	225	117	164

'NCDN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 0.59

Table S451. Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
NCDN MUTATED	2	0	1
NCDN WILD-TYPE	153	265	88

'NCDN MUTATION STATUS' versus 'CN_CNMF'

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

Table S452. Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
NCDN MUTATED	1	0	2	1	0
NCDN WILD-TYPE	291	118	265	260	25

'NCDN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S453. Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
NCDN MUTATED	1	2	0	1	0	0	0
NCDN WILD-TYPE	151	212	29	198	123	67	10

'NCDN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S454. Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
NCDN MUTATED	1	2	1
NCDN WILD-TYPE	214	328	248

'NCDN MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S455. Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
NCDN MUTATED	1	0	0	2	1	0	0
NCDN WILD-TYPE	232	159	130	203	183	45	18

'NCDN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S456. Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
NCDN MUTATED	1	0	0	2	1	0
NCDN WILD-TYPE	262	151	79	259	167	52

'NCDN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.501 (Fisher's exact test), Q value = 0.87

Table S457. Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
NCDN MUTATED	0	2	0	0	2	0
NCDN WILD-TYPE	129	241	177	184	182	41

'NCDN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.468 (Fisher's exact test), Q value = 0.87

Table S458. Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
NCDN MUTATED	1	0	0	1	1	0	1	0	0
NCDN WILD-TYPE	63	119	156	166	68	111	144	54	73

'MUC6 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 0.95

Table S459. Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
MUC6 MUTATED	4	1	4
MUC6 WILD-TYPE	223	116	161

'MUC6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S460. Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
MUC6 MUTATED	2	5	2
MUC6 WILD-TYPE	153	260	87

'MUC6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.56

Table S461. Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
MUC6 MUTATED	4	0	2	7	1
MUC6 WILD-TYPE	288	118	265	254	24

'MUC6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.57

Table S462. Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
MUC6 MUTATED	0	3	2	3	2
MUC6 WILD-TYPE	193	147	120	116	78

'MUC6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 0.87

Table S463. Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
MUC6 MUTATED	2	1	1	5	2	1	0
MUC6 WILD-TYPE	150	213	28	194	121	66	10

'MUC6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 0.61

Table S464. Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
MUC6 MUTATED	5	2	5
MUC6 WILD-TYPE	210	328	244

'MUC6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0623 (Fisher's exact test), Q value = 0.4

Table S465. Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
MUC6 MUTATED	0	4	1	2	6	1	0
MUC6 WILD-TYPE	233	155	129	203	178	44	18

'MUC6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.205 (Fisher's exact test), Q value = 0.64

Table S466. Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
MUC6 MUTATED	1	3	0	4	5	1
MUC6 WILD-TYPE	262	148	79	257	163	51

'MUC6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 0.87

Table S467. Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
MUC6 MUTATED	1	7	2	1	3	0
MUC6 WILD-TYPE	128	236	175	183	181	41

'MUC6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 0.29

Table S468. Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
MUC6 MUTATED	0	4	0	3	1	0	6	0	0
MUC6 WILD-TYPE	64	115	156	164	68	111	139	54	73

Figure S103. Get High-res Image Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.587 (Fisher's exact test), Q value = 0.93

Table S469. Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
MUC6 MUTATED	2	0	0	1	3	0
MUC6 WILD-TYPE	112	63	50	119	119	99

'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.052 (Fisher's exact test), Q value = 0.37

Table S470. Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
MUC6 MUTATED	6	0	0
MUC6 WILD-TYPE	275	171	116

'TGS1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.65

Table S471. Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
TGS1 MUTATED	1	1	4
TGS1 WILD-TYPE	226	116	161

'TGS1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 0.71

Table S472. Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
TGS1 MUTATED	0	5	1
TGS1 WILD-TYPE	155	260	88

'TGS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.625 (Fisher's exact test), Q value = 0.95

Table S473. Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
TGS1 MUTATED	3	1	6	2	0
TGS1 WILD-TYPE	289	117	261	259	25

'TGS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.285 (Fisher's exact test), Q value = 0.75

Table S474. Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
TGS1 MUTATED	4	4	3	0	0
TGS1 WILD-TYPE	189	146	119	119	80

'TGS1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S475. Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
TGS1 MUTATED	2	4	0	1	2	1	0
TGS1 WILD-TYPE	150	210	29	198	121	66	10

'TGS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 0.92

Table S476. Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
TGS1 MUTATED	2	6	2
TGS1 WILD-TYPE	213	324	247

'TGS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S477. Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
TGS1 MUTATED	2	4	1	3	2	1	0
TGS1 WILD-TYPE	231	155	129	202	182	44	18

'TGS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 0.7

Table S478. Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
TGS1 MUTATED	2	5	0	4	1	1
TGS1 WILD-TYPE	261	146	79	257	167	51

'TGS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.689 (Fisher's exact test), Q value = 0.97

Table S479. Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
TGS1 MUTATED	2	2	2	2	5	0
TGS1 WILD-TYPE	127	241	175	182	179	41

'TGS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.23

Table S480. Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
TGS1 MUTATED	1	3	1	1	1	1	0	4	1
TGS1 WILD-TYPE	63	116	155	166	68	110	145	50	72

Figure S104. Get High-res Image Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TGS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0869 (Fisher's exact test), Q value = 0.45

Table S481. Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
TGS1 MUTATED	3	2	0	0	0	2
TGS1 WILD-TYPE	111	61	50	120	122	97

'TGS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 0.78

Table S482. Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
TGS1 MUTATED	2	4	1
TGS1 WILD-TYPE	279	167	115

'TFE3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.63

Table S483. Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
TFE3 MUTATED	1	3	3
TFE3 WILD-TYPE	226	114	162

'TFE3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 0.59

Table S484. Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
TFE3 MUTATED	0	5	2
TFE3 WILD-TYPE	155	260	87

'TFE3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.407 (Fisher's exact test), Q value = 0.84

Table S485. Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
TFE3 MUTATED	3	1	0	3	0
TFE3 WILD-TYPE	289	117	267	258	25

'TFE3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.694 (Fisher's exact test), Q value = 0.97

Table S486. Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
TFE3 MUTATED	1	0	1	1	1
TFE3 WILD-TYPE	192	150	121	118	79

'TFE3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 0.81

Table S487. Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
TFE3 MUTATED	0	0	0	1	1	1	0
TFE3 WILD-TYPE	152	214	29	198	122	66	10

'TFE3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S488. Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
TFE3 MUTATED	1	1	1
TFE3 WILD-TYPE	214	329	248

'TFE3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 0.99

Table S489. Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
TFE3 MUTATED	2	2	1	0	2	0	0
TFE3 WILD-TYPE	231	157	129	205	182	45	18

'TFE3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 0.96

Table S490. Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
TFE3 MUTATED	2	1	0	1	2	1
TFE3 WILD-TYPE	261	150	79	260	166	51

'TFE3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.958 (Fisher's exact test), Q value = 1

Table S491. Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
TFE3 MUTATED	1	3	1	1	1	0
TFE3 WILD-TYPE	128	240	176	183	183	41

'TFE3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.165 (Fisher's exact test), Q value = 0.6

Table S492. Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
TFE3 MUTATED	0	0	2	1	0	0	1	0	3
TFE3 WILD-TYPE	64	119	154	166	69	111	144	54	70

'TFE3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S493. Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
TFE3 MUTATED	1	0	0	1	1	0
TFE3 WILD-TYPE	113	63	50	119	121	99

'TFE3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 0.77

Table S494. Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
TFE3 MUTATED	3	0	0
TFE3 WILD-TYPE	278	171	116

'IRS4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 0.63

Table S495. Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
IRS4 MUTATED	1	3	3
IRS4 WILD-TYPE	226	114	162

'IRS4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.56

Table S496. Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
IRS4 MUTATED	0	6	1
IRS4 WILD-TYPE	155	259	88

'IRS4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.68

Table S497. Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
IRS4 MUTATED	4	0	1	6	0
IRS4 WILD-TYPE	288	118	266	255	25

'IRS4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.638 (Fisher's exact test), Q value = 0.95

Table S498. Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
IRS4 MUTATED	1	2	3	2	1
IRS4 WILD-TYPE	192	148	119	117	79

'IRS4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.166 (Fisher's exact test), Q value = 0.61

Table S499. Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
IRS4 MUTATED	1	3	1	0	3	0	0
IRS4 WILD-TYPE	151	211	28	199	120	67	10

'IRS4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0652 (Fisher's exact test), Q value = 0.41

Table S500. Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
IRS4 MUTATED	2	6	0
IRS4 WILD-TYPE	213	324	249

'IRS4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.59

Table S501. Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
IRS4 MUTATED	3	1	2	0	3	1	1
IRS4 WILD-TYPE	230	158	128	205	181	44	17

'IRS4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.47 (Fisher's exact test), Q value = 0.87

Table S502. Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
IRS4 MUTATED	2	0	1	4	3	1
IRS4 WILD-TYPE	261	151	78	257	165	51

'IRS4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0614 (Fisher's exact test), Q value = 0.4

Table S503. Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
IRS4 MUTATED	4	3	0	0	3	0
IRS4 WILD-TYPE	125	240	177	184	181	41

'IRS4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S504. Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
IRS4 MUTATED	2	1	1	1	1	1	2	0	1
IRS4 WILD-TYPE	62	118	155	166	68	110	143	54	72

'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.709 (Fisher's exact test), Q value = 0.98

Table S505. Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
IRS4 MUTATED	2	0	0	0	1	1
IRS4 WILD-TYPE	112	63	50	120	121	98

'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S506. Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
IRS4 MUTATED	3	1	0
IRS4 WILD-TYPE	278	170	116

'NLGN3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.69

Table S507. Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
NLGN3 MUTATED	2	1	5
NLGN3 WILD-TYPE	225	116	160

'NLGN3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S508. Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
NLGN3 MUTATED	2	5	1
NLGN3 WILD-TYPE	153	260	88

'NLGN3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S509. Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
NLGN3 MUTATED	3	1	5	2	0
NLGN3 WILD-TYPE	289	117	262	259	25

'NLGN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S510. Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
NLGN3 MUTATED	2	1	0	1	1
NLGN3 WILD-TYPE	191	149	122	118	79

'NLGN3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.56

Table S511. Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
NLGN3 MUTATED	2	0	0	1	3	2	0
NLGN3 WILD-TYPE	150	214	29	198	120	65	10

'NLGN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.396 (Fisher's exact test), Q value = 0.84

Table S512. Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
NLGN3 MUTATED	2	5	1
NLGN3 WILD-TYPE	213	325	248

'NLGN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.928 (Fisher's exact test), Q value = 1

Table S513. Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
NLGN3 MUTATED	4	2	1	3	1	0	0
NLGN3 WILD-TYPE	229	157	129	202	183	45	18

'NLGN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0819 (Fisher's exact test), Q value = 0.44

Table S514. Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
NLGN3 MUTATED	4	4	1	0	1	1
NLGN3 WILD-TYPE	259	147	78	261	167	51

'NLGN3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.994 (Fisher's exact test), Q value = 1

Table S515. Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
NLGN3 MUTATED	1	3	2	3	2	0
NLGN3 WILD-TYPE	128	240	175	181	182	41

'NLGN3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.996 (Fisher's exact test), Q value = 1

Table S516. Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
NLGN3 MUTATED	1	1	2	2	0	2	2	0	1
NLGN3 WILD-TYPE	63	118	154	165	69	109	143	54	72

'NLGN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 0.83

Table S517. Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
NLGN3 MUTATED	2	1	0	0	0	1
NLGN3 WILD-TYPE	112	62	50	120	122	98

'NLGN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.673 (Fisher's exact test), Q value = 0.97

Table S518. Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
NLGN3 MUTATED	2	2	0
NLGN3 WILD-TYPE	279	169	116

'IL1RAP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 0.84

Table S519. Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
IL1RAP MUTATED	2	1	1	5	0
IL1RAP WILD-TYPE	290	117	266	256	25

'IL1RAP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 0.77

Table S520. Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
IL1RAP MUTATED	1	2	0	3	1
IL1RAP WILD-TYPE	192	148	122	116	79

'IL1RAP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 0.79

Table S521. Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
IL1RAP MUTATED	0	3	0	1	2	2	0
IL1RAP WILD-TYPE	152	211	29	198	121	65	10

'IL1RAP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.312 (Fisher's exact test), Q value = 0.77

Table S522. Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
IL1RAP MUTATED	4	3	1
IL1RAP WILD-TYPE	211	327	248

'IL1RAP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.873 (Fisher's exact test), Q value = 1

Table S523. Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
IL1RAP MUTATED	2	2	0	3	2	0	0
IL1RAP WILD-TYPE	231	157	130	202	182	45	18

'IL1RAP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.643 (Fisher's exact test), Q value = 0.96

Table S524. Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
IL1RAP MUTATED	1	2	0	3	2	1
IL1RAP WILD-TYPE	262	149	79	258	166	51

'IL1RAP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 0.92

Table S525. Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
IL1RAP MUTATED	0	3	1	1	2	1
IL1RAP WILD-TYPE	129	240	176	183	182	40

'IL1RAP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 0.77

Table S526. Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
IL1RAP MUTATED	0	1	0	0	1	2	2	1	1
IL1RAP WILD-TYPE	64	118	156	167	68	109	143	53	72

'IL1RAP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S527. Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
IL1RAP MUTATED	1	0	0	2	3	1
IL1RAP WILD-TYPE	113	63	50	118	119	98

'IL1RAP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.611 (Fisher's exact test), Q value = 0.94

Table S528. Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
IL1RAP MUTATED	5	1	1
IL1RAP WILD-TYPE	276	170	115

'USP36 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.79

Table S529. Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
USP36 MUTATED	4	0	3
USP36 WILD-TYPE	223	117	162

'USP36 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.006 (Fisher's exact test), Q value = 0.078

Table S530. Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
USP36 MUTATED	4	0	3
USP36 WILD-TYPE	151	265	86

Figure S105. Get High-res Image Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'USP36 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S531. Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
USP36 MUTATED	3	0	2	3	0
USP36 WILD-TYPE	289	118	265	258	25

'USP36 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S532. Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
USP36 MUTATED	1	1	0	1	0
USP36 WILD-TYPE	192	149	122	118	80

'USP36 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 0.86

Table S533. Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
USP36 MUTATED	2	4	0	0	1	1	0
USP36 WILD-TYPE	150	210	29	199	122	66	10

'USP36 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.499 (Fisher's exact test), Q value = 0.87

Table S534. Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
USP36 MUTATED	3	4	1
USP36 WILD-TYPE	212	326	248

'USP36 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.409 (Fisher's exact test), Q value = 0.84

Table S535. Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
USP36 MUTATED	4	0	0	1	3	0	0
USP36 WILD-TYPE	229	159	130	204	181	45	18

'USP36 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0759 (Fisher's exact test), Q value = 0.43

Table S536. Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
USP36 MUTATED	5	0	0	0	3	0
USP36 WILD-TYPE	258	151	79	261	165	52

'USP36 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.596 (Fisher's exact test), Q value = 0.93

Table S537. Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
USP36 MUTATED	2	3	2	0	1	0
USP36 WILD-TYPE	127	240	175	184	183	41

'USP36 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.749 (Fisher's exact test), Q value = 1

Table S538. Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
USP36 MUTATED	1	0	2	1	0	1	3	0	0
USP36 WILD-TYPE	63	119	154	166	69	110	142	54	73

'CASZ1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.896 (Fisher's exact test), Q value = 1

Table S539. Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
CASZ1 MUTATED	4	1	2
CASZ1 WILD-TYPE	223	116	163

'CASZ1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.86

Table S540. Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
CASZ1 MUTATED	1	4	2
CASZ1 WILD-TYPE	154	261	87

'CASZ1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.972 (Fisher's exact test), Q value = 1

Table S541. Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
CASZ1 MUTATED	5	1	4	3	0
CASZ1 WILD-TYPE	287	117	263	258	25

'CASZ1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.87

Table S542. Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
CASZ1 MUTATED	2	4	1	3	0
CASZ1 WILD-TYPE	191	146	121	116	80

'CASZ1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 0.87

Table S543. Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
CASZ1 MUTATED	1	1	0	5	2	0	0
CASZ1 WILD-TYPE	151	213	29	194	121	67	10

'CASZ1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.098 (Fisher's exact test), Q value = 0.5

Table S544. Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
CASZ1 MUTATED	1	2	6
CASZ1 WILD-TYPE	214	328	243

'CASZ1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.986 (Fisher's exact test), Q value = 1

Table S545. Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
CASZ1 MUTATED	3	2	2	3	4	0	0
CASZ1 WILD-TYPE	230	157	128	202	180	45	18

'CASZ1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.733 (Fisher's exact test), Q value = 0.99

Table S546. Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
CASZ1 MUTATED	2	2	1	5	4	0
CASZ1 WILD-TYPE	261	149	78	256	164	52

'CASZ1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 0.87

Table S547. Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
CASZ1 MUTATED	3	2	2	4	1	1
CASZ1 WILD-TYPE	126	241	175	180	183	40

'CASZ1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.986 (Fisher's exact test), Q value = 1

Table S548. Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
CASZ1 MUTATED	1	2	2	2	0	1	3	1	1
CASZ1 WILD-TYPE	63	117	154	165	69	110	142	53	72

'CASZ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.707 (Fisher's exact test), Q value = 0.98

Table S549. Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
CASZ1 MUTATED	2	0	0	2	1	3
CASZ1 WILD-TYPE	112	63	50	118	121	96

'CASZ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.809 (Fisher's exact test), Q value = 1

Table S550. Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
CASZ1 MUTATED	5	2	1
CASZ1 WILD-TYPE	276	169	115

'EYS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 0.63

Table S551. Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
EYS MUTATED	4	1	7
EYS WILD-TYPE	223	116	158

'EYS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.178 (Fisher's exact test), Q value = 0.62

Table S552. Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
EYS MUTATED	1	9	2
EYS WILD-TYPE	154	256	87

'EYS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.59

Table S553. Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
EYS MUTATED	7	0	4	10	0
EYS WILD-TYPE	285	118	263	251	25

'EYS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 0.87

Table S554. Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
EYS MUTATED	2	4	1	4	1
EYS WILD-TYPE	191	146	121	115	79

'EYS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.32

Table S555. Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
EYS MUTATED	6	3	2	1	5	0	0
EYS WILD-TYPE	146	211	27	198	118	67	10

Figure S106. Get High-res Image Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'EYS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0785 (Fisher's exact test), Q value = 0.44

Table S556. Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
EYS MUTATED	9	5	3
EYS WILD-TYPE	206	325	246

'EYS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.13

Table S557. Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
EYS MUTATED	3	7	1	3	4	0	3
EYS WILD-TYPE	230	152	129	202	180	45	15

Figure S107. Get High-res Image Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EYS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 0.64

Table S558. Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
EYS MUTATED	2	4	1	7	4	3
EYS WILD-TYPE	261	147	78	254	164	49

'EYS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.31

Table S559. Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
EYS MUTATED	6	9	3	1	1	1
EYS WILD-TYPE	123	234	174	183	183	40

Figure S108. Get High-res Image Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'EYS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.16

Table S560. Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
EYS MUTATED	1	7	1	0	1	3	3	1	4
EYS WILD-TYPE	63	112	155	167	68	108	142	53	69

Figure S109. Get High-res Image Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'EYS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.64

Table S561. Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
EYS MUTATED	2	1	0	1	7	3
EYS WILD-TYPE	112	62	50	119	115	96

'EYS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0885 (Fisher's exact test), Q value = 0.46

Table S562. Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
EYS MUTATED	10	4	0
EYS WILD-TYPE	271	167	116

'KCNN3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 0.83

Table S563. Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
KCNN3 MUTATED	2	0	3
KCNN3 WILD-TYPE	225	117	162

'KCNN3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 0.6

Table S564. Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
KCNN3 MUTATED	0	3	2
KCNN3 WILD-TYPE	155	262	87

'KCNN3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 0.83

Table S565. Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
KCNN3 MUTATED	3	0	1	5	0
KCNN3 WILD-TYPE	289	118	266	256	25

'KCNN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.56

Table S566. Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
KCNN3 MUTATED	2	0	0	3	0
KCNN3 WILD-TYPE	191	150	122	116	80

'KCNN3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.32

Table S567. Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
KCNN3 MUTATED	5	0	0	1	0	1	0
KCNN3 WILD-TYPE	147	214	29	198	123	66	10

Figure S110. Get High-res Image Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'KCNN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.495 (Fisher's exact test), Q value = 0.87

Table S568. Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
KCNN3 MUTATED	3	3	1
KCNN3 WILD-TYPE	212	327	248

'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0729 (Fisher's exact test), Q value = 0.42

Table S569. Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
KCNN3 MUTATED	1	3	1	0	2	1	1
KCNN3 WILD-TYPE	232	156	129	205	182	44	17

'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.398 (Fisher's exact test), Q value = 0.84

Table S570. Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
KCNN3 MUTATED	1	3	0	2	2	1
KCNN3 WILD-TYPE	262	148	79	259	166	51

'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.58

Table S571. Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
KCNN3 MUTATED	3	4	0	0	2	0
KCNN3 WILD-TYPE	126	239	177	184	182	41

'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.487 (Fisher's exact test), Q value = 0.87

Table S572. Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
KCNN3 MUTATED	0	1	0	1	1	3	2	0	1
KCNN3 WILD-TYPE	64	118	156	166	68	108	143	54	72

'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.491 (Fisher's exact test), Q value = 0.87

Table S573. Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
KCNN3 MUTATED	2	0	0	0	2	0
KCNN3 WILD-TYPE	112	63	50	120	120	99

'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.428 (Fisher's exact test), Q value = 0.84

Table S574. Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
KCNN3 MUTATED	3	0	1
KCNN3 WILD-TYPE	278	171	115

'ZFP36L1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 0.64

Table S575. Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
ZFP36L1 MUTATED	4	1	0
ZFP36L1 WILD-TYPE	223	116	165

'ZFP36L1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 0.93

Table S576. Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
ZFP36L1 MUTATED	1	4	0
ZFP36L1 WILD-TYPE	154	261	89

'ZFP36L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.017

Table S577. Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
ZFP36L1 MUTATED	3	4	0	0	1
ZFP36L1 WILD-TYPE	289	114	267	261	24

Figure S111. Get High-res Image Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZFP36L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.418 (Fisher's exact test), Q value = 0.84

Table S578. Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
ZFP36L1 MUTATED	1	3	0	1	0
ZFP36L1 WILD-TYPE	192	147	122	118	80

'ZFP36L1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S579. Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
ZFP36L1 MUTATED	1	2	0	3	1	0	0
ZFP36L1 WILD-TYPE	151	212	29	196	122	67	10

'ZFP36L1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.434 (Fisher's exact test), Q value = 0.84

Table S580. Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
ZFP36L1 MUTATED	1	2	4
ZFP36L1 WILD-TYPE	214	328	245

'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.69

Table S581. Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
ZFP36L1 MUTATED	5	2	0	0	1	0	0
ZFP36L1 WILD-TYPE	228	157	130	205	183	45	18

'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.732 (Fisher's exact test), Q value = 0.99

Table S582. Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
ZFP36L1 MUTATED	4	2	0	1	1	0
ZFP36L1 WILD-TYPE	259	149	79	260	167	52

'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.21

Table S583. Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
ZFP36L1 MUTATED	3	1	1	0	1	2
ZFP36L1 WILD-TYPE	126	242	176	184	183	39

Figure S112. Get High-res Image Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.538 (Fisher's exact test), Q value = 0.9

Table S584. Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
ZFP36L1 MUTATED	0	2	0	1	0	2	1	1	1
ZFP36L1 WILD-TYPE	64	117	156	166	69	109	144	53	72

'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.71 (Fisher's exact test), Q value = 0.98

Table S585. Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
ZFP36L1 MUTATED	2	0	0	0	1	1
ZFP36L1 WILD-TYPE	112	63	50	120	121	98

'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S586. Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
ZFP36L1 MUTATED	3	1	0
ZFP36L1 WILD-TYPE	278	170	116

'ICOSLG MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.799 (Fisher's exact test), Q value = 1

Table S587. Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
ICOSLG MUTATED	2	0	1
ICOSLG WILD-TYPE	225	117	164

'ICOSLG MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 0.59

Table S588. Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
ICOSLG MUTATED	2	0	1
ICOSLG WILD-TYPE	153	265	88

'ICOSLG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 0.87

Table S589. Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
ICOSLG MUTATED	3	0	0	2	0
ICOSLG WILD-TYPE	289	118	267	259	25

'ICOSLG MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S590. Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
ICOSLG MUTATED	1	1	1	1	0
ICOSLG WILD-TYPE	192	149	121	118	80

'ICOSLG MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.51

Table S591. Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
ICOSLG MUTATED	0	2	0	0	0	2	0
ICOSLG WILD-TYPE	152	212	29	199	123	65	10

'ICOSLG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 0.83

Table S592. Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
ICOSLG MUTATED	1	3	0
ICOSLG WILD-TYPE	214	327	249

'ICOSLG MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S593. Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
ICOSLG MUTATED	2	0	0	2	1	0	0
ICOSLG WILD-TYPE	231	159	130	203	183	45	18

'ICOSLG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.968 (Fisher's exact test), Q value = 1

Table S594. Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
ICOSLG MUTATED	1	1	0	2	1	0
ICOSLG WILD-TYPE	262	150	79	259	167	52

'ICOSLG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.58

Table S595. Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
ICOSLG MUTATED	1	1	2	0	0	1
ICOSLG WILD-TYPE	128	242	175	184	184	40

'ICOSLG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.682 (Fisher's exact test), Q value = 0.97

Table S596. Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
ICOSLG MUTATED	0	0	0	1	1	1	1	0	1
ICOSLG WILD-TYPE	64	119	156	166	68	110	144	54	72

'ACTL6B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 0.97

Table S597. Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
ACTL6B MUTATED	3	2	1
ACTL6B WILD-TYPE	224	115	164

'ACTL6B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 0.84

Table S598. Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
ACTL6B MUTATED	2	2	2
ACTL6B WILD-TYPE	153	263	87

'ACTL6B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00576 (Fisher's exact test), Q value = 0.076

Table S599. Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
ACTL6B MUTATED	3	0	0	5	2
ACTL6B WILD-TYPE	289	118	267	256	23

Figure S113. Get High-res Image Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ACTL6B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 0.77

Table S600. Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
ACTL6B MUTATED	3	1	0	3	0
ACTL6B WILD-TYPE	190	149	122	116	80

'ACTL6B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.6

Table S601. Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
ACTL6B MUTATED	2	1	0	2	0	1	1
ACTL6B WILD-TYPE	150	213	29	197	123	66	9

'ACTL6B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 0.92

Table S602. Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
ACTL6B MUTATED	3	2	2
ACTL6B WILD-TYPE	212	328	247

'ACTL6B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.97

Table S603. Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
ACTL6B MUTATED	2	2	0	2	3	1	0
ACTL6B WILD-TYPE	231	157	130	203	181	44	18

'ACTL6B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.64

Table S604. Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
ACTL6B MUTATED	3	3	1	0	3	0
ACTL6B WILD-TYPE	260	148	78	261	165	52

'ACTL6B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S605. Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
ACTL6B MUTATED	2	2	1	2	2	1
ACTL6B WILD-TYPE	127	241	176	182	182	40

'ACTL6B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S606. Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
ACTL6B MUTATED	0	1	1	3	1	1	3	0	0
ACTL6B WILD-TYPE	64	118	155	164	68	110	142	54	73

'ACTL6B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 0.88

Table S607. Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
ACTL6B MUTATED	2	0	0	1	0	2
ACTL6B WILD-TYPE	112	63	50	119	122	97

'ACTL6B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S608. Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
ACTL6B MUTATED	2	2	1
ACTL6B WILD-TYPE	279	169	115

'MYH9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 0.87

Table S609. Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
MYH9 MUTATED	2	2	4
MYH9 WILD-TYPE	225	115	161

'MYH9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S610. Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
MYH9 MUTATED	2	5	1
MYH9 WILD-TYPE	153	260	88

'MYH9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.58

Table S611. Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
MYH9 MUTATED	4	0	8	3	1
MYH9 WILD-TYPE	288	118	259	258	24

'MYH9 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S612. Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
MYH9 MUTATED	5	4	1	2	2
MYH9 WILD-TYPE	188	146	121	117	78

'MYH9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 0.83

Table S613. Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
MYH9 MUTATED	2	4	0	3	4	4	0
MYH9 WILD-TYPE	150	210	29	196	119	63	10

'MYH9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 0.84

Table S614. Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
MYH9 MUTATED	7	5	5
MYH9 WILD-TYPE	208	325	244

'MYH9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 0.79

Table S615. Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
MYH9 MUTATED	1	5	2	6	3	1	0
MYH9 WILD-TYPE	232	154	128	199	181	44	18

'MYH9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 0.58

Table S616. Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
MYH9 MUTATED	1	3	1	8	3	2
MYH9 WILD-TYPE	262	148	78	253	165	50

'MYH9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.633 (Fisher's exact test), Q value = 0.95

Table S617. Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
MYH9 MUTATED	3	4	3	2	4	2
MYH9 WILD-TYPE	126	239	174	182	180	39

'MYH9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.504 (Fisher's exact test), Q value = 0.87

Table S618. Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
MYH9 MUTATED	0	3	3	2	2	2	3	3	0
MYH9 WILD-TYPE	64	116	153	165	67	109	142	51	73

'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S619. Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
MYH9 MUTATED	3	2	0	2	2	2
MYH9 WILD-TYPE	111	61	50	118	120	97

'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.171 (Fisher's exact test), Q value = 0.61

Table S620. Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
MYH9 MUTATED	6	5	0
MYH9 WILD-TYPE	275	166	116

'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S621. Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
FBXW7 MUTATED	2	1	3
FBXW7 WILD-TYPE	225	116	162

'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.479 (Fisher's exact test), Q value = 0.87

Table S622. Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
FBXW7 MUTATED	1	3	2
FBXW7 WILD-TYPE	154	262	87

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.57

Table S623. Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
FBXW7 MUTATED	2	0	5	8	0
FBXW7 WILD-TYPE	290	118	262	253	25

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.26

Table S624. Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
FBXW7 MUTATED	3	0	1	6	1
FBXW7 WILD-TYPE	190	150	121	113	79

Figure S114. Get High-res Image Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.263 (Fisher's exact test), Q value = 0.71

Table S625. Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
FBXW7 MUTATED	6	2	0	1	2	1	0
FBXW7 WILD-TYPE	146	212	29	198	121	66	10

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 0.51

Table S626. Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
FBXW7 MUTATED	6	5	1
FBXW7 WILD-TYPE	209	325	248

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.56

Table S627. Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
FBXW7 MUTATED	1	1	1	5	7	0	0
FBXW7 WILD-TYPE	232	158	129	200	177	45	18

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.59

Table S628. Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
FBXW7 MUTATED	3	1	0	4	7	0
FBXW7 WILD-TYPE	260	150	79	257	161	52

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 0.88

Table S629. Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
FBXW7 MUTATED	1	7	3	1	3	0
FBXW7 WILD-TYPE	128	236	174	183	181	41

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.403 (Fisher's exact test), Q value = 0.84

Table S630. Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
FBXW7 MUTATED	0	2	3	1	0	1	6	1	1
FBXW7 WILD-TYPE	64	117	153	166	69	110	139	53	72

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.3

Table S631. Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
FBXW7 MUTATED	0	0	1	0	5	2
FBXW7 WILD-TYPE	114	63	49	120	117	97

Figure S115. Get High-res Image Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S632. Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
FBXW7 MUTATED	5	2	1
FBXW7 WILD-TYPE	276	169	115

'FRMPD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.84

Table S633. Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
FRMPD2 MUTATED	2	1	4
FRMPD2 WILD-TYPE	225	116	161

'FRMPD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 0.56

Table S634. Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
FRMPD2 MUTATED	0	6	1
FRMPD2 WILD-TYPE	155	259	88

'FRMPD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.68

Table S635. Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
FRMPD2 MUTATED	3	0	3	6	1
FRMPD2 WILD-TYPE	289	118	264	255	24

'FRMPD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.57

Table S636. Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
FRMPD2 MUTATED	0	3	2	3	2
FRMPD2 WILD-TYPE	193	147	120	116	78

'FRMPD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.57

Table S637. Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
FRMPD2 MUTATED	3	1	1	2	1	1	1
FRMPD2 WILD-TYPE	149	213	28	197	122	66	9

'FRMPD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 0.71

Table S638. Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
FRMPD2 MUTATED	5	3	2
FRMPD2 WILD-TYPE	210	327	247

'FRMPD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 0.92

Table S639. Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
FRMPD2 MUTATED	1	3	2	2	4	1	0
FRMPD2 WILD-TYPE	232	156	128	203	180	44	18

'FRMPD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0541 (Fisher's exact test), Q value = 0.39

Table S640. Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
FRMPD2 MUTATED	0	4	0	5	4	0
FRMPD2 WILD-TYPE	263	147	79	256	164	52

'FRMPD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 0.84

Table S641. Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
FRMPD2 MUTATED	0	4	1	4	3	1
FRMPD2 WILD-TYPE	129	239	176	180	181	40

'FRMPD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 0.75

Table S642. Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
FRMPD2 MUTATED	0	5	3	1	0	1	3	0	0
FRMPD2 WILD-TYPE	64	114	153	166	69	110	142	54	73

'FRMPD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 0.92

Table S643. Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
FRMPD2 MUTATED	0	0	1	1	2	2
FRMPD2 WILD-TYPE	114	63	49	119	120	97

'FRMPD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.579 (Fisher's exact test), Q value = 0.93

Table S644. Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
FRMPD2 MUTATED	2	3	1
FRMPD2 WILD-TYPE	279	168	115

'ZFP36L2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S645. Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
ZFP36L2 MUTATED	1	1	2
ZFP36L2 WILD-TYPE	226	116	163

'ZFP36L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S646. Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
ZFP36L2 MUTATED	1	2	1
ZFP36L2 WILD-TYPE	154	263	88

'ZFP36L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.13

Table S647. Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
ZFP36L2 MUTATED	2	1	0	2	2
ZFP36L2 WILD-TYPE	290	117	267	259	23

Figure S116. Get High-res Image Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZFP36L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.42 (Fisher's exact test), Q value = 0.84

Table S648. Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
ZFP36L2 MUTATED	1	3	0	1	0
ZFP36L2 WILD-TYPE	192	147	122	118	80

'ZFP36L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.654 (Fisher's exact test), Q value = 0.96

Table S649. Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
ZFP36L2 MUTATED	1	1	0	3	0	1	0
ZFP36L2 WILD-TYPE	151	213	29	196	123	66	10

'ZFP36L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.84

Table S650. Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
ZFP36L2 MUTATED	2	1	3
ZFP36L2 WILD-TYPE	213	329	246

'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.97

Table S651. Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
ZFP36L2 MUTATED	2	3	0	1	1	0	0
ZFP36L2 WILD-TYPE	231	156	130	204	183	45	18

'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 0.92

Table S652. Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
ZFP36L2 MUTATED	2	3	0	1	1	0
ZFP36L2 WILD-TYPE	261	148	79	260	167	52

'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.614 (Fisher's exact test), Q value = 0.94

Table S653. Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
ZFP36L2 MUTATED	1	1	2	1	1	1
ZFP36L2 WILD-TYPE	128	242	175	183	183	40

'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.737 (Fisher's exact test), Q value = 0.99

Table S654. Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
ZFP36L2 MUTATED	0	2	1	1	1	0	1	1	0
ZFP36L2 WILD-TYPE	64	117	155	166	68	111	144	53	73

'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.316 (Fisher's exact test), Q value = 0.78

Table S655. Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
ZFP36L2 MUTATED	1	0	0	0	1	3
ZFP36L2 WILD-TYPE	113	63	50	120	121	96

'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S656. Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
ZFP36L2 MUTATED	2	2	1
ZFP36L2 WILD-TYPE	279	169	115

'TPP2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.358 (Fisher's exact test), Q value = 0.81

Table S657. Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
TPP2 MUTATED	3	1	0
TPP2 WILD-TYPE	224	116	165

'TPP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S658. Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
TPP2 MUTATED	1	3	0
TPP2 WILD-TYPE	154	262	89

'TPP2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S659. Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
TPP2 MUTATED	3	0	3	2	0
TPP2 WILD-TYPE	289	118	264	259	25

'TPP2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.635 (Fisher's exact test), Q value = 0.95

Table S660. Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
TPP2 MUTATED	2	1	0	2	0
TPP2 WILD-TYPE	191	149	122	117	80

'TPP2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S661. Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
TPP2 MUTATED	1	2	0	2	0	0	0
TPP2 WILD-TYPE	151	212	29	197	123	67	10

'TPP2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S662. Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
TPP2 MUTATED	1	2	2
TPP2 WILD-TYPE	214	328	247

'TPP2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 0.93

Table S663. Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
TPP2 MUTATED	1	1	0	4	2	0	0
TPP2 WILD-TYPE	232	158	130	201	182	45	18

'TPP2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S664. Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
TPP2 MUTATED	2	2	0	2	2	0
TPP2 WILD-TYPE	261	149	79	259	166	52

'TPP2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.595 (Fisher's exact test), Q value = 0.93

Table S665. Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
TPP2 MUTATED	2	3	2	0	1	0
TPP2 WILD-TYPE	127	240	175	184	183	41

'TPP2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S666. Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
TPP2 MUTATED	0	2	1	2	1	0	2	0	0
TPP2 WILD-TYPE	64	117	155	165	68	111	143	54	73

'TPP2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.487 (Fisher's exact test), Q value = 0.87

Table S667. Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
TPP2 MUTATED	0	0	0	1	3	1
TPP2 WILD-TYPE	114	63	50	119	119	98

'TPP2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S668. Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
TPP2 MUTATED	3	1	1
TPP2 WILD-TYPE	278	170	115

'C17ORF95 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S669. Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
C17ORF95 MUTATED	2	1	1
C17ORF95 WILD-TYPE	225	116	164

'C17ORF95 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S670. Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
C17ORF95 MUTATED	1	2	1
C17ORF95 WILD-TYPE	154	263	88

'C17ORF95 MUTATION STATUS' versus 'CN_CNMF'

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

Table S671. Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
C17ORF95 MUTATED	2	0	2	1	0
C17ORF95 WILD-TYPE	290	118	265	260	25

'C17ORF95 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.953 (Fisher's exact test), Q value = 1

Table S672. Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
C17ORF95 MUTATED	1	1	0	2	1	0	0
C17ORF95 WILD-TYPE	232	158	130	203	183	45	18

'C17ORF95 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.968 (Fisher's exact test), Q value = 1

Table S673. Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
C17ORF95 MUTATED	1	1	0	2	1	0
C17ORF95 WILD-TYPE	262	150	79	259	167	52

'C17ORF95 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 0.88

Table S674. Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
C17ORF95 MUTATED	1	2	2	0	0	0
C17ORF95 WILD-TYPE	128	241	175	184	184	41

'C17ORF95 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.429 (Fisher's exact test), Q value = 0.84

Table S675. Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
C17ORF95 MUTATED	0	2	0	0	0	1	1	0	1
C17ORF95 WILD-TYPE	64	117	156	167	69	110	144	54	72

'RUFY1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S676. Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
RUFY1 MUTATED	1	1	1
RUFY1 WILD-TYPE	226	116	164

'RUFY1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.298 (Fisher's exact test), Q value = 0.77

Table S677. Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
RUFY1 MUTATED	0	3	0
RUFY1 WILD-TYPE	155	262	89

'RUFY1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.83

Table S678. Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
RUFY1 MUTATED	0	1	2	3	0
RUFY1 WILD-TYPE	292	117	265	258	25

'RUFY1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.729 (Fisher's exact test), Q value = 0.99

Table S679. Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
RUFY1 MUTATED	1	2	0	1	0
RUFY1 WILD-TYPE	192	148	122	118	80

'RUFY1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.07 (Fisher's exact test), Q value = 0.42

Table S680. Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
RUFY1 MUTATED	2	0	1	0	1	1	0
RUFY1 WILD-TYPE	150	214	28	199	122	66	10

'RUFY1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.736 (Fisher's exact test), Q value = 0.99

Table S681. Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
RUFY1 MUTATED	2	2	1
RUFY1 WILD-TYPE	213	328	248

'RUFY1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S682. Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
RUFY1 MUTATED	3	1	0	1	1	0	0
RUFY1 WILD-TYPE	230	158	130	204	183	45	18

'RUFY1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.239 (Fisher's exact test), Q value = 0.69

Table S683. Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
RUFY1 MUTATED	0	3	0	2	1	0
RUFY1 WILD-TYPE	263	148	79	259	167	52

'RUFY1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 0.97

Table S684. Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
RUFY1 MUTATED	0	1	1	1	3	0
RUFY1 WILD-TYPE	129	242	176	183	181	41

'RUFY1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.266 (Fisher's exact test), Q value = 0.71

Table S685. Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
RUFY1 MUTATED	1	2	0	0	0	2	1	0	0
RUFY1 WILD-TYPE	63	117	156	167	69	109	144	54	73

'RUFY1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.369 (Fisher's exact test), Q value = 0.83

Table S686. Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
RUFY1 MUTATED	2	0	1	0	1	0
RUFY1 WILD-TYPE	112	63	49	120	121	99

'RUFY1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.431 (Fisher's exact test), Q value = 0.84

Table S687. Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
RUFY1 MUTATED	3	0	1
RUFY1 WILD-TYPE	278	171	115

'MED23 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 0.83

Table S688. Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
MED23 MUTATED	3	3	1
MED23 WILD-TYPE	224	114	164

'MED23 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 0.71

Table S689. Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
MED23 MUTATED	1	6	0
MED23 WILD-TYPE	154	259	89

'MED23 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.73

Table S690. Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
MED23 MUTATED	4	3	6	1	0
MED23 WILD-TYPE	288	115	261	260	25

'MED23 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.64

Table S691. Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
MED23 MUTATED	5	2	1	0	3
MED23 WILD-TYPE	188	148	121	119	77

'MED23 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.61

Table S692. Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
MED23 MUTATED	0	1	1	5	2	1	0
MED23 WILD-TYPE	152	213	28	194	121	66	10

'MED23 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0577 (Fisher's exact test), Q value = 0.4

Table S693. Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
MED23 MUTATED	0	4	6
MED23 WILD-TYPE	215	326	243

'MED23 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.63

Table S694. Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
MED23 MUTATED	4	0	3	4	1	2	0
MED23 WILD-TYPE	229	159	127	201	183	43	18

'MED23 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0737 (Fisher's exact test), Q value = 0.42

Table S695. Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
MED23 MUTATED	3	1	1	9	0	0
MED23 WILD-TYPE	260	150	78	252	168	52

'MED23 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.18

Table S696. Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
MED23 MUTATED	2	0	4	5	1	2
MED23 WILD-TYPE	127	243	173	179	183	39

Figure S117. Get High-res Image Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MED23 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 0.56

Table S697. Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
MED23 MUTATED	0	0	3	5	2	1	0	2	1
MED23 WILD-TYPE	64	119	153	162	67	110	145	52	72

'MED23 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 0.71

Table S698. Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
MED23 MUTATED	2	1	2	1	0	1
MED23 WILD-TYPE	112	62	48	119	122	98

'MED23 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.534 (Fisher's exact test), Q value = 0.9

Table S699. Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
MED23 MUTATED	2	3	2
MED23 WILD-TYPE	279	168	114

'PAX2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 0.87

Table S700. Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
PAX2 MUTATED	2	1	0
PAX2 WILD-TYPE	225	116	165

'PAX2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.583 (Fisher's exact test), Q value = 0.93

Table S701. Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
PAX2 MUTATED	2	1	0
PAX2 WILD-TYPE	153	264	89

'PAX2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S702. Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
PAX2 MUTATED	1	0	1	2	0
PAX2 WILD-TYPE	291	118	266	259	25

'PAX2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.805 (Fisher's exact test), Q value = 1

Table S703. Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
PAX2 MUTATED	0	1	0	2	0	0	0
PAX2 WILD-TYPE	152	213	29	197	123	67	10

'PAX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 0.87

Table S704. Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
PAX2 MUTATED	0	1	2
PAX2 WILD-TYPE	215	329	247

'PAX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.83

Table S705. Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
PAX2 MUTATED	3	1	0	0	0	0	0
PAX2 WILD-TYPE	230	158	130	205	184	45	18

'PAX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.75

Table S706. Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
PAX2 MUTATED	2	2	0	0	0	0
PAX2 WILD-TYPE	261	149	79	261	168	52

'PAX2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 0.83

Table S707. Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
PAX2 MUTATED	1	0	1	0	2	0
PAX2 WILD-TYPE	128	243	176	184	182	41

'PAX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.337 (Fisher's exact test), Q value = 0.79

Table S708. Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
PAX2 MUTATED	1	0	0	1	1	1	0	0	0
PAX2 WILD-TYPE	63	119	156	166	68	110	145	54	73

'MED12 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.728 (Fisher's exact test), Q value = 0.99

Table S709. Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
MED12 MUTATED	5	1	2
MED12 WILD-TYPE	222	116	163

'MED12 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.512 (Fisher's exact test), Q value = 0.88

Table S710. Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
MED12 MUTATED	4	3	1
MED12 WILD-TYPE	151	262	88

'MED12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.545 (Fisher's exact test), Q value = 0.91

Table S711. Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
MED12 MUTATED	6	1	9	4	0
MED12 WILD-TYPE	286	117	258	257	25

'MED12 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S712. Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
MED12 MUTATED	4	4	3	2	3
MED12 WILD-TYPE	189	146	119	117	77

'MED12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 0.97

Table S713. Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
MED12 MUTATED	4	5	0	5	2	1	1
MED12 WILD-TYPE	148	209	29	194	121	66	9

'MED12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S714. Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
MED12 MUTATED	4	9	5
MED12 WILD-TYPE	211	321	244

'MED12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.663 (Fisher's exact test), Q value = 0.97

Table S715. Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
MED12 MUTATED	4	5	3	7	2	0	0
MED12 WILD-TYPE	229	154	127	198	182	45	18

'MED12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.41 (Fisher's exact test), Q value = 0.84

Table S716. Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
MED12 MUTATED	8	2	3	4	2	2
MED12 WILD-TYPE	255	149	76	257	166	50

'MED12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.707 (Fisher's exact test), Q value = 0.98

Table S717. Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
MED12 MUTATED	2	3	4	5	6	1
MED12 WILD-TYPE	127	240	173	179	178	40

'MED12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.914 (Fisher's exact test), Q value = 1

Table S718. Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
MED12 MUTATED	2	3	4	5	1	1	2	2	1
MED12 WILD-TYPE	62	116	152	162	68	110	143	52	72

'MED12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.537 (Fisher's exact test), Q value = 0.9

Table S719. Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
MED12 MUTATED	2	1	1	1	1	4
MED12 WILD-TYPE	112	62	49	119	121	95

'MED12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 0.87

Table S720. Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
MED12 MUTATED	4	5	1
MED12 WILD-TYPE	277	166	115

'CHD4 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S721. Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
CHD4 MUTATED	3	2	4
CHD4 WILD-TYPE	224	115	161

'CHD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.87

Table S722. Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
CHD4 MUTATED	1	6	2
CHD4 WILD-TYPE	154	259	87

'CHD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.68

Table S723. Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
CHD4 MUTATED	3	2	9	4	1
CHD4 WILD-TYPE	289	116	258	257	24

'CHD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0616 (Fisher's exact test), Q value = 0.4

Table S724. Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
CHD4 MUTATED	1	5	4	1	4
CHD4 WILD-TYPE	192	145	118	118	76

'CHD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.715 (Fisher's exact test), Q value = 0.98

Table S725. Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
CHD4 MUTATED	4	2	0	4	4	1	0
CHD4 WILD-TYPE	148	212	29	195	119	66	10

'CHD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S726. Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
CHD4 MUTATED	4	6	5
CHD4 WILD-TYPE	211	324	244

'CHD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.27

Table S727. Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
CHD4 MUTATED	0	4	5	6	3	0	1
CHD4 WILD-TYPE	233	155	125	199	181	45	17

Figure S118. Get High-res Image Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CHD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.269 (Fisher's exact test), Q value = 0.72

Table S728. Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
CHD4 MUTATED	2	5	3	6	3	0
CHD4 WILD-TYPE	261	146	76	255	165	52

'CHD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.873 (Fisher's exact test), Q value = 1

Table S729. Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
CHD4 MUTATED	3	3	4	5	4	0
CHD4 WILD-TYPE	126	240	173	179	180	41

'CHD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0669 (Fisher's exact test), Q value = 0.41

Table S730. Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
CHD4 MUTATED	0	5	8	2	0	1	3	0	0
CHD4 WILD-TYPE	64	114	148	165	69	110	142	54	73

'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S731. Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
CHD4 MUTATED	1	2	1	2	2	3
CHD4 WILD-TYPE	113	61	49	118	120	96

'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 0.77

Table S732. Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
CHD4 MUTATED	3	5	3
CHD4 WILD-TYPE	278	166	113

'PFKP MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 0.56

Table S733. Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
PFKP MUTATED	1	0	4
PFKP WILD-TYPE	226	117	161

'PFKP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0587 (Fisher's exact test), Q value = 0.4

Table S734. Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
PFKP MUTATED	1	1	3
PFKP WILD-TYPE	154	264	86

'PFKP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 0.97

Table S735. Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
PFKP MUTATED	2	0	1	3	0
PFKP WILD-TYPE	290	118	266	258	25

'PFKP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 0.77

Table S736. Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
PFKP MUTATED	2	0	0	1	0	1	0
PFKP WILD-TYPE	150	214	29	198	123	66	10

'PFKP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.687 (Fisher's exact test), Q value = 0.97

Table S737. Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
PFKP MUTATED	2	1	1
PFKP WILD-TYPE	213	329	248

'PFKP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.587 (Fisher's exact test), Q value = 0.93

Table S738. Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
PFKP MUTATED	2	0	0	1	3	0	0
PFKP WILD-TYPE	231	159	130	204	181	45	18

'PFKP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.302 (Fisher's exact test), Q value = 0.77

Table S739. Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
PFKP MUTATED	2	1	0	0	3	0
PFKP WILD-TYPE	261	150	79	261	165	52

'PFKP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 0.84

Table S740. Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
PFKP MUTATED	0	4	1	0	1	0
PFKP WILD-TYPE	129	239	176	184	183	41

'PFKP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 0.57

Table S741. Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
PFKP MUTATED	1	2	0	0	0	0	3	0	0
PFKP WILD-TYPE	63	117	156	167	69	111	142	54	73

'RHBG MUTATION STATUS' versus 'CN_CNMF'

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

Table S742. Gene #66: 'RHBG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
RHBG MUTATED	2	0	1	1	0
RHBG WILD-TYPE	290	118	266	260	25

'RHBG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.66

Table S743. Gene #66: 'RHBG MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
RHBG MUTATED	0	2	0	0	2	0	0
RHBG WILD-TYPE	233	157	130	205	182	45	18

'RHBG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 0.53

Table S744. Gene #66: 'RHBG MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
RHBG MUTATED	0	2	0	0	2	0
RHBG WILD-TYPE	263	149	79	261	166	52

'RHBG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.679 (Fisher's exact test), Q value = 0.97

Table S745. Gene #66: 'RHBG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
RHBG MUTATED	1	2	0	0	1	0
RHBG WILD-TYPE	128	241	177	184	183	41

'RHBG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 0.75

Table S746. Gene #66: 'RHBG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
RHBG MUTATED	0	2	0	0	0	0	2	0	0
RHBG WILD-TYPE	64	117	156	167	69	111	143	54	73

'PSIP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 0.97

Table S747. Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
PSIP1 MUTATED	2	0	2
PSIP1 WILD-TYPE	225	117	163

'PSIP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S748. Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
PSIP1 MUTATED	1	2	1
PSIP1 WILD-TYPE	154	263	88

'PSIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 0.96

Table S749. Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
PSIP1 MUTATED	3	2	2	1	0
PSIP1 WILD-TYPE	289	116	265	260	25

'PSIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S750. Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
PSIP1 MUTATED	2	1	1	0	1
PSIP1 WILD-TYPE	191	149	121	119	79

'PSIP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.592 (Fisher's exact test), Q value = 0.93

Table S751. Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
PSIP1 MUTATED	0	2	0	1	2	1	0
PSIP1 WILD-TYPE	152	212	29	198	121	66	10

'PSIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 0.93

Table S752. Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
PSIP1 MUTATED	1	4	1
PSIP1 WILD-TYPE	214	326	248

'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 0.92

Table S753. Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
PSIP1 MUTATED	1	1	0	3	2	1	0
PSIP1 WILD-TYPE	232	158	130	202	182	44	18

'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.935 (Fisher's exact test), Q value = 1

Table S754. Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
PSIP1 MUTATED	3	2	0	2	1	0
PSIP1 WILD-TYPE	260	149	79	259	167	52

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.411 (Fisher's exact test), Q value = 0.84

Table S755. Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
PSIP1 MUTATED	2	0	2	1	2	0
PSIP1 WILD-TYPE	127	243	175	183	182	41

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.909 (Fisher's exact test), Q value = 1

Table S756. Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
PSIP1 MUTATED	0	1	2	2	0	1	0	0	1
PSIP1 WILD-TYPE	64	118	154	165	69	110	145	54	72

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S757. Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
PSIP1 MUTATED	1	0	0	2	1	0
PSIP1 WILD-TYPE	113	63	50	118	121	99

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.429 (Fisher's exact test), Q value = 0.84

Table S758. Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
PSIP1 MUTATED	3	0	1
PSIP1 WILD-TYPE	278	171	115

'LRIG2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 0.92

Table S759. Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
LRIG2 MUTATED	3	0	1
LRIG2 WILD-TYPE	224	117	164

'LRIG2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0643 (Fisher's exact test), Q value = 0.41

Table S760. Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
LRIG2 MUTATED	3	0	1
LRIG2 WILD-TYPE	152	265	88

'LRIG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 0.95

Table S761. Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
LRIG2 MUTATED	4	0	1	2	0
LRIG2 WILD-TYPE	288	118	266	259	25

'LRIG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 0.93

Table S762. Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
LRIG2 MUTATED	1	1	0	2	0
LRIG2 WILD-TYPE	192	149	122	117	80

'LRIG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.84

Table S763. Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
LRIG2 MUTATED	1	3	1	1	0	0	0
LRIG2 WILD-TYPE	151	211	28	198	123	67	10

'LRIG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.584 (Fisher's exact test), Q value = 0.93

Table S764. Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
LRIG2 MUTATED	1	4	1
LRIG2 WILD-TYPE	214	326	248

'LRIG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 0.83

Table S765. Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
LRIG2 MUTATED	4	2	0	0	1	0	0
LRIG2 WILD-TYPE	229	157	130	205	183	45	18

'LRIG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S766. Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
LRIG2 MUTATED	2	1	0	2	1	1
LRIG2 WILD-TYPE	261	150	79	259	167	51

'LRIG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.79

Table S767. Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
LRIG2 MUTATED	2	2	1	0	1	1
LRIG2 WILD-TYPE	127	241	176	184	183	40

'LRIG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S768. Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
LRIG2 MUTATED	1	1	1	1	0	2	1	0	0
LRIG2 WILD-TYPE	63	118	155	166	69	109	144	54	73

'LRIG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S769. Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
LRIG2 MUTATED	1	0	0	1	1	0
LRIG2 WILD-TYPE	113	63	50	119	121	99

'LRIG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S770. Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
LRIG2 MUTATED	2	1	0
LRIG2 WILD-TYPE	279	170	116

'RIBC1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 0.81

Table S771. Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
RIBC1 MUTATED	3	1	0
RIBC1 WILD-TYPE	224	116	165

'RIBC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.653 (Fisher's exact test), Q value = 0.96

Table S772. Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
RIBC1 MUTATED	2	2	0
RIBC1 WILD-TYPE	153	263	89

'RIBC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 0.97

Table S773. Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
RIBC1 MUTATED	2	0	2	0	0
RIBC1 WILD-TYPE	290	118	265	261	25

'RIBC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.32

Table S774. Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
RIBC1 MUTATED	0	1	0	0	2
RIBC1 WILD-TYPE	193	149	122	119	78

Figure S119. Get High-res Image Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'RIBC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.685 (Fisher's exact test), Q value = 0.97

Table S775. Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
RIBC1 MUTATED	1	0	1	2	0	0	0
RIBC1 WILD-TYPE	232	159	129	203	184	45	18

'RIBC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.608 (Fisher's exact test), Q value = 0.94

Table S776. Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
RIBC1 MUTATED	1	0	0	3	0	0
RIBC1 WILD-TYPE	262	151	79	258	168	52

'RIBC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 0.83

Table S777. Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
RIBC1 MUTATED	1	0	1	0	2	0
RIBC1 WILD-TYPE	128	243	176	184	182	41

'RIBC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 0.84

Table S778. Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
RIBC1 MUTATED	0	1	1	0	1	0	0	0	1
RIBC1 WILD-TYPE	64	118	155	167	68	111	145	54	72

'PLK2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 0.94

Table S779. Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
PLK2 MUTATED	1	0	2
PLK2 WILD-TYPE	226	117	163

'PLK2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.84

Table S780. Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
PLK2 MUTATED	0	2	1
PLK2 WILD-TYPE	155	263	88

'PLK2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S781. Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
PLK2 MUTATED	3	1	3	2	0
PLK2 WILD-TYPE	289	117	264	259	25

'PLK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S782. Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
PLK2 MUTATED	2	1	1	2	1
PLK2 WILD-TYPE	191	149	121	117	79

'PLK2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.8

Table S783. Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
PLK2 MUTATED	0	2	1	1	1	1	0
PLK2 WILD-TYPE	152	212	28	198	122	66	10

'PLK2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S784. Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
PLK2 MUTATED	1	3	2
PLK2 WILD-TYPE	214	327	247

'PLK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S785. Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
PLK2 MUTATED	1	2	1	3	2	0	0
PLK2 WILD-TYPE	232	157	129	202	182	45	18

'PLK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S786. Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
PLK2 MUTATED	1	2	1	3	2	0
PLK2 WILD-TYPE	262	149	78	258	166	52

'PLK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.982 (Fisher's exact test), Q value = 1

Table S787. Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
PLK2 MUTATED	1	3	2	2	1	0
PLK2 WILD-TYPE	128	240	175	182	183	41

'PLK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 0.93

Table S788. Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
PLK2 MUTATED	0	3	2	1	0	0	2	1	0
PLK2 WILD-TYPE	64	116	154	166	69	111	143	53	73

'PLK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.829 (Fisher's exact test), Q value = 1

Table S789. Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
PLK2 MUTATED	1	1	0	0	1	1
PLK2 WILD-TYPE	113	62	50	120	121	98

'PLK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.671 (Fisher's exact test), Q value = 0.97

Table S790. Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
PLK2 MUTATED	2	2	0
PLK2 WILD-TYPE	279	169	116

'ANKRD20A4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.607 (Fisher's exact test), Q value = 0.94

Table S791. Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
ANKRD20A4 MUTATED	1	0	2
ANKRD20A4 WILD-TYPE	226	117	163

'ANKRD20A4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S792. Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
ANKRD20A4 MUTATED	1	2	0
ANKRD20A4 WILD-TYPE	154	263	89

'ANKRD20A4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 0.94

Table S793. Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
ANKRD20A4 MUTATED	1	0	3	3	0
ANKRD20A4 WILD-TYPE	291	118	264	258	25

'ANKRD20A4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 0.84

Table S794. Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
ANKRD20A4 MUTATED	3	0	1	0	1
ANKRD20A4 WILD-TYPE	190	150	121	119	79

'ANKRD20A4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S795. Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
ANKRD20A4 MUTATED	1	2	0	1	1	1	0
ANKRD20A4 WILD-TYPE	151	212	29	198	122	66	10

'ANKRD20A4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S796. Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
ANKRD20A4 MUTATED	2	2	2
ANKRD20A4 WILD-TYPE	213	328	247

'ANKRD20A4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0725 (Fisher's exact test), Q value = 0.42

Table S797. Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
ANKRD20A4 MUTATED	0	3	2	1	0	1	0
ANKRD20A4 WILD-TYPE	233	156	128	204	184	44	18

'ANKRD20A4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.332 (Fisher's exact test), Q value = 0.79

Table S798. Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
ANKRD20A4 MUTATED	2	0	1	3	0	1
ANKRD20A4 WILD-TYPE	261	151	78	258	168	51

'ANKRD20A4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S799. Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
ANKRD20A4 MUTATED	2	1	1	2	1	0
ANKRD20A4 WILD-TYPE	127	242	176	182	183	41

'ANKRD20A4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.813 (Fisher's exact test), Q value = 1

Table S800. Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
ANKRD20A4 MUTATED	0	1	2	2	0	1	0	1	0
ANKRD20A4 WILD-TYPE	64	118	154	165	69	110	145	53	73

'ANKRD20A4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.97

Table S801. Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
ANKRD20A4 MUTATED	0	1	1	1	1	1
ANKRD20A4 WILD-TYPE	114	62	49	119	121	98

'ANKRD20A4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.23

Table S802. Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
ANKRD20A4 MUTATED	0	4	1
ANKRD20A4 WILD-TYPE	281	167	115

Figure S120. Get High-res Image Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PHACTR1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.56

Table S803. Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
PHACTR1 MUTATED	1	0	4
PHACTR1 WILD-TYPE	226	117	161

'PHACTR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S804. Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
PHACTR1 MUTATED	1	3	1
PHACTR1 WILD-TYPE	154	262	88

'PHACTR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S805. Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
PHACTR1 MUTATED	1	1	2	2	0
PHACTR1 WILD-TYPE	291	117	265	259	25

'PHACTR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 0.69

Table S806. Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
PHACTR1 MUTATED	0	2	0	1	1
PHACTR1 WILD-TYPE	193	148	122	118	79

'PHACTR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 0.63

Table S807. Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
PHACTR1 MUTATED	4	1	0	0	1	1	0
PHACTR1 WILD-TYPE	148	213	29	199	122	66	10

'PHACTR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0851 (Fisher's exact test), Q value = 0.45

Table S808. Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
PHACTR1 MUTATED	4	3	0
PHACTR1 WILD-TYPE	211	327	249

'PHACTR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.57

Table S809. Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
PHACTR1 MUTATED	0	4	0	1	2	0	0
PHACTR1 WILD-TYPE	233	155	130	204	182	45	18

'PHACTR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0784 (Fisher's exact test), Q value = 0.44

Table S810. Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
PHACTR1 MUTATED	0	3	0	1	2	1
PHACTR1 WILD-TYPE	263	148	79	260	166	51

'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.757 (Fisher's exact test), Q value = 1

Table S811. Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
PHACTR1 MUTATED	1	3	0	1	2	0
PHACTR1 WILD-TYPE	128	240	177	183	182	41

'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0417 (Fisher's exact test), Q value = 0.32

Table S812. Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
PHACTR1 MUTATED	0	2	0	0	2	0	1	0	2
PHACTR1 WILD-TYPE	64	117	156	167	67	111	144	54	71

Figure S121. Get High-res Image Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S813. Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
PHACTR1 MUTATED	1	0	0	0	1	1
PHACTR1 WILD-TYPE	113	63	50	120	121	98

'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S814. Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
PHACTR1 MUTATED	2	1	0
PHACTR1 WILD-TYPE	279	170	116

'DLG1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S815. Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
DLG1 MUTATED	3	1	3
DLG1 WILD-TYPE	224	116	162

'DLG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 0.7

Table S816. Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
DLG1 MUTATED	1	6	0
DLG1 WILD-TYPE	154	259	89

'DLG1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S817. Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
DLG1 MUTATED	3	1	4	5	0
DLG1 WILD-TYPE	289	117	263	256	25

'DLG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.57

Table S818. Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
DLG1 MUTATED	1	1	4	3	0
DLG1 WILD-TYPE	192	149	118	116	80

'DLG1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.634 (Fisher's exact test), Q value = 0.95

Table S819. Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
DLG1 MUTATED	2	3	0	2	4	2	0
DLG1 WILD-TYPE	150	211	29	197	119	65	10

'DLG1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.827 (Fisher's exact test), Q value = 1

Table S820. Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
DLG1 MUTATED	4	6	3
DLG1 WILD-TYPE	211	324	246

'DLG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.71

Table S821. Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
DLG1 MUTATED	2	4	2	1	2	1	1
DLG1 WILD-TYPE	231	155	128	204	182	44	17

'DLG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 0.63

Table S822. Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
DLG1 MUTATED	1	3	1	5	1	2
DLG1 WILD-TYPE	262	148	78	256	167	50

'DLG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S823. Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
DLG1 MUTATED	2	4	2	3	1	0
DLG1 WILD-TYPE	127	239	175	181	183	41

'DLG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.13

Table S824. Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
DLG1 MUTATED	0	4	0	3	0	0	1	0	4
DLG1 WILD-TYPE	64	115	156	164	69	111	144	54	69

Figure S122. Get High-res Image Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'DLG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 0.84

Table S825. Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
DLG1 MUTATED	0	2	1	1	2	2
DLG1 WILD-TYPE	114	61	49	119	120	97

'DLG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S826. Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
DLG1 MUTATED	4	2	2
DLG1 WILD-TYPE	277	169	114

'GPRASP2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 0.84

Table S827. Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
GPRASP2 MUTATED	3	0	3
GPRASP2 WILD-TYPE	224	117	162

'GPRASP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 0.79

Table S828. Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
GPRASP2 MUTATED	1	5	0
GPRASP2 WILD-TYPE	154	260	89

'GPRASP2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.66 (Fisher's exact test), Q value = 0.97

Table S829. Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
GPRASP2 MUTATED	4	1	1	4	0
GPRASP2 WILD-TYPE	288	117	266	257	25

'GPRASP2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 0.96

Table S830. Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
GPRASP2 MUTATED	2	1	2	0	0
GPRASP2 WILD-TYPE	191	149	120	119	80

'GPRASP2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.84

Table S831. Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
GPRASP2 MUTATED	3	5	0	1	0	0	0
GPRASP2 WILD-TYPE	149	209	29	198	123	67	10

'GPRASP2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.44 (Fisher's exact test), Q value = 0.84

Table S832. Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
GPRASP2 MUTATED	3	5	1
GPRASP2 WILD-TYPE	212	325	248

'GPRASP2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.59

Table S833. Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
GPRASP2 MUTATED	1	3	0	4	1	0	1
GPRASP2 WILD-TYPE	232	156	130	201	183	45	17

'GPRASP2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.71

Table S834. Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
GPRASP2 MUTATED	1	4	0	3	1	1
GPRASP2 WILD-TYPE	262	147	79	258	167	51

'GPRASP2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00291 (Fisher's exact test), Q value = 0.042

Table S835. Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
GPRASP2 MUTATED	2	4	0	1	0	3
GPRASP2 WILD-TYPE	127	239	177	183	184	38

Figure S123. Get High-res Image Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'GPRASP2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.231 (Fisher's exact test), Q value = 0.68

Table S836. Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
GPRASP2 MUTATED	0	1	3	0	2	3	1	0	0
GPRASP2 WILD-TYPE	64	118	153	167	67	108	144	54	73

'GPRASP2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 0.83

Table S837. Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
GPRASP2 MUTATED	2	1	0	0	0	1
GPRASP2 WILD-TYPE	112	62	50	120	122	98

'GPRASP2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.672 (Fisher's exact test), Q value = 0.97

Table S838. Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
GPRASP2 MUTATED	2	2	0
GPRASP2 WILD-TYPE	279	169	116

'CCDC82 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 0.65

Table S839. Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
CCDC82 MUTATED	1	0	3
CCDC82 WILD-TYPE	226	117	162

'CCDC82 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.302 (Fisher's exact test), Q value = 0.77

Table S840. Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
CCDC82 MUTATED	0	4	0
CCDC82 WILD-TYPE	155	261	89

'CCDC82 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S841. Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
CCDC82 MUTATED	2	1	1	2	0
CCDC82 WILD-TYPE	290	117	266	259	25

'CCDC82 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.14

Table S842. Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
CCDC82 MUTATED	4	0	0	0	0	2	0
CCDC82 WILD-TYPE	148	214	29	199	123	65	10

Figure S124. Get High-res Image Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CCDC82 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.586 (Fisher's exact test), Q value = 0.93

Table S843. Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
CCDC82 MUTATED	1	4	1
CCDC82 WILD-TYPE	214	326	248

'CCDC82 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.412 (Fisher's exact test), Q value = 0.84

Table S844. Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
CCDC82 MUTATED	4	1	0	0	1	0	0
CCDC82 WILD-TYPE	229	158	130	205	183	45	18

'CCDC82 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00255 (Fisher's exact test), Q value = 0.038

Table S845. Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
CCDC82 MUTATED	0	5	0	0	1	0
CCDC82 WILD-TYPE	263	146	79	261	167	52

Figure S125. Get High-res Image Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CCDC82 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 0.83

Table S846. Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
CCDC82 MUTATED	2	2	0	0	2	0
CCDC82 WILD-TYPE	127	241	177	184	182	41

'CCDC82 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0592 (Fisher's exact test), Q value = 0.4

Table S847. Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
CCDC82 MUTATED	2	1	0	0	1	0	1	1	0
CCDC82 WILD-TYPE	62	118	156	167	68	111	144	53	73

'CCDC82 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.896 (Fisher's exact test), Q value = 1

Table S848. Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
CCDC82 MUTATED	1	0	0	0	1	1
CCDC82 WILD-TYPE	113	63	50	120	121	98

'CCDC82 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S849. Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
CCDC82 MUTATED	2	1	0
CCDC82 WILD-TYPE	279	170	116

'CCDC27 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.65

Table S850. Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
CCDC27 MUTATED	1	0	3
CCDC27 WILD-TYPE	226	117	162

'CCDC27 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.402 (Fisher's exact test), Q value = 0.84

Table S851. Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
CCDC27 MUTATED	0	3	1
CCDC27 WILD-TYPE	155	262	88

'CCDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.57

Table S852. Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
CCDC27 MUTATED	2	0	0	5	0
CCDC27 WILD-TYPE	290	118	267	256	25

'CCDC27 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.26

Table S853. Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
CCDC27 MUTATED	0	0	2	3	0
CCDC27 WILD-TYPE	193	150	120	116	80

Figure S126. Get High-res Image Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CCDC27 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0813 (Fisher's exact test), Q value = 0.44

Table S854. Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
CCDC27 MUTATED	2	0	0	0	1	2	0
CCDC27 WILD-TYPE	150	214	29	199	122	65	10

'CCDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 0.58

Table S855. Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
CCDC27 MUTATED	3	2	0
CCDC27 WILD-TYPE	212	328	249

'CCDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.32

Table S856. Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
CCDC27 MUTATED	0	3	0	0	4	0	0
CCDC27 WILD-TYPE	233	156	130	205	180	45	18

Figure S127. Get High-res Image Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CCDC27 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.71

Table S857. Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
CCDC27 MUTATED	1	1	0	1	4	0
CCDC27 WILD-TYPE	262	150	79	260	164	52

'CCDC27 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.65

Table S858. Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
CCDC27 MUTATED	2	4	0	1	0	0
CCDC27 WILD-TYPE	127	239	177	183	184	41

'CCDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0553 (Fisher's exact test), Q value = 0.39

Table S859. Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
CCDC27 MUTATED	0	0	0	1	0	0	4	0	2
CCDC27 WILD-TYPE	64	119	156	166	69	111	141	54	71

'CCDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 0.68

Table S860. Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
CCDC27 MUTATED	0	1	0	0	2	0
CCDC27 WILD-TYPE	114	62	50	120	120	99

'CCDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.312 (Fisher's exact test), Q value = 0.77

Table S861. Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
CCDC27 MUTATED	3	0	0
CCDC27 WILD-TYPE	278	171	116

'RHOA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.35

Table S862. Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
RHOA MUTATED	0	0	3
RHOA WILD-TYPE	227	117	162

Figure S128. Get High-res Image Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'RHOA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.439 (Fisher's exact test), Q value = 0.84

Table S863. Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
RHOA MUTATED	0	2	1
RHOA WILD-TYPE	155	263	88

'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 0.89

Table S864. Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
RHOA MUTATED	1	2	2	1	0
RHOA WILD-TYPE	291	116	265	260	25

'RHOA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.69

Table S865. Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
RHOA MUTATED	0	2	0	1	1
RHOA WILD-TYPE	193	148	122	118	79

'RHOA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 0.87

Table S866. Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
RHOA MUTATED	2	1	1	1	1	0	0
RHOA WILD-TYPE	150	213	28	198	122	67	10

'RHOA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.508 (Fisher's exact test), Q value = 0.88

Table S867. Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
RHOA MUTATED	3	2	1
RHOA WILD-TYPE	212	328	248

'RHOA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S868. Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
RHOA MUTATED	2	2	0	1	1	0	0
RHOA WILD-TYPE	231	157	130	204	183	45	18

'RHOA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.71

Table S869. Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
RHOA MUTATED	0	2	0	2	1	1
RHOA WILD-TYPE	263	149	79	259	167	51

'RHOA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 0.99

Table S870. Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
RHOA MUTATED	0	2	0	2	2	0
RHOA WILD-TYPE	129	241	177	182	182	41

'RHOA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 0.83

Table S871. Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
RHOA MUTATED	1	2	1	0	0	0	1	1	0
RHOA WILD-TYPE	63	117	155	167	69	111	144	53	73

'MAMLD1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.83

Table S872. Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
MAMLD1 MUTATED	1	2	3
MAMLD1 WILD-TYPE	226	115	162

'MAMLD1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 0.63

Table S873. Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
MAMLD1 MUTATED	0	4	2
MAMLD1 WILD-TYPE	155	261	87

'MAMLD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.601 (Fisher's exact test), Q value = 0.93

Table S874. Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
MAMLD1 MUTATED	1	1	3	4	0
MAMLD1 WILD-TYPE	291	117	264	257	25

'MAMLD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.87

Table S875. Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
MAMLD1 MUTATED	1	0	1	2	1
MAMLD1 WILD-TYPE	192	150	121	117	79

'MAMLD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 0.59

Table S876. Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
MAMLD1 MUTATED	3	3	0	0	0	2	0
MAMLD1 WILD-TYPE	149	211	29	199	123	65	10

'MAMLD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.5 (Fisher's exact test), Q value = 0.87

Table S877. Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
MAMLD1 MUTATED	3	4	1
MAMLD1 WILD-TYPE	212	326	248

'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 0.95

Table S878. Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
MAMLD1 MUTATED	3	0	1	2	4	0	0
MAMLD1 WILD-TYPE	230	159	129	203	180	45	18

'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.653 (Fisher's exact test), Q value = 0.96

Table S879. Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
MAMLD1 MUTATED	2	1	0	3	4	0
MAMLD1 WILD-TYPE	261	150	79	258	164	52

'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.757 (Fisher's exact test), Q value = 1

Table S880. Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
MAMLD1 MUTATED	1	5	1	2	1	0
MAMLD1 WILD-TYPE	128	238	176	182	183	41

'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.727 (Fisher's exact test), Q value = 0.99

Table S881. Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
MAMLD1 MUTATED	0	1	1	3	0	1	4	0	0
MAMLD1 WILD-TYPE	64	118	155	164	69	110	141	54	73

'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.671 (Fisher's exact test), Q value = 0.97

Table S882. Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	114	63	50	120	122	99
MAMLD1 MUTATED	0	0	1	1	1	1
MAMLD1 WILD-TYPE	114	63	49	119	121	98

'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S883. Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	281	171	116
MAMLD1 MUTATED	2	1	1
MAMLD1 WILD-TYPE	279	170	115

'OR8D1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 0.97

Table S884. Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	117	165
OR8D1 MUTATED	2	0	2
OR8D1 WILD-TYPE	225	117	163

'OR8D1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.34

Table S885. Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	265	89
OR8D1 MUTATED	2	0	2
OR8D1 WILD-TYPE	153	265	87

Figure S129. Get High-res Image Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'OR8D1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 1

Table S886. Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	292	118	267	261	25
OR8D1 MUTATED	1	1	1	1	0
OR8D1 WILD-TYPE	291	117	266	260	25

'OR8D1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 0.89

Table S887. Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	193	150	122	119	80
OR8D1 MUTATED	2	0	1	2	0
OR8D1 WILD-TYPE	191	150	121	117	80

'OR8D1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.188 (Fisher's exact test), Q value = 0.63

Table S888. Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	152	214	29	199	123	67	10
OR8D1 MUTATED	1	2	0	0	0	2	0
OR8D1 WILD-TYPE	151	212	29	199	123	65	10

'OR8D1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.59

Table S889. Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	330	249
OR8D1 MUTATED	3	2	0
OR8D1 WILD-TYPE	212	328	249

'OR8D1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.243 (Fisher's exact test), Q value = 0.69

Table S890. Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	233	159	130	205	184	45	18
OR8D1 MUTATED	0	0	0	2	3	0	0
OR8D1 WILD-TYPE	233	159	130	203	181	45	18

'OR8D1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 0.63

Table S891. Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	263	151	79	261	168	52
OR8D1 MUTATED	2	0	0	0	3	0
OR8D1 WILD-TYPE	261	151	79	261	165	52

'OR8D1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.475 (Fisher's exact test), Q value = 0.87

Table S892. Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	129	243	177	184	184	41
OR8D1 MUTATED	1	1	2	0	0	0
OR8D1 WILD-TYPE	128	242	175	184	184	41

'OR8D1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S893. Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	64	119	156	167	69	111	145	54	73
OR8D1 MUTATED	0	1	1	1	0	0	1	0	0
OR8D1 WILD-TYPE	64	118	155	166	69	111	144	54	73

Methods & Data

Input

Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BRCA-TP/22824019/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/22595637/BRCA-TP.transferedmergedcluster.txt
Number of patients = 977
Number of significantly mutated genes = 79
Number of Molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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