Correlation between gene mutation status and molecular subtypes

Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

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 (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1CN72XM

Overview

Introduction

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

Summary

Testing the association between mutation status of 73 genes and 10 molecular subtypes across 668 patients, 160 significant findings detected with P value < 0.05 and Q value < 0.25.

TP53 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
PBRM1 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
PTEN mutation correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
BAP1 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
SETD2 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
KDM5C mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
NEFH mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
VHL mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
NF2 mutation correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
HNRNPM mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
MET mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
MUC5B mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
KDM6A mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
TDG mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
NFE2L2 mutation correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
ZNF814 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
DNMT3A mutation correlated to 'MRNASEQ_CNMF'.
CSGALNACT2 mutation correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
MTOR mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
RIMBP3 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.
ZNF598 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
STAG2 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.
SKI mutation correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
ARID1A mutation correlated to 'MIRSEQ_MATURE_CNMF'.
MED16 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.
AHNAK2 mutation correlated to 'MRNA_CHIERARCHICAL', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
STAM mutation correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.
RUFY3 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.
FAM200A mutation correlated to 'MRNASEQ_CHIERARCHICAL'.
NASP mutation correlated to 'MRNASEQ_CNMF'.
PAM mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
CCDC82 mutation correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
OR2L8 mutation correlated to 'MIRSEQ_MATURE_CNMF'.
IDUA mutation correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
GAPDHS mutation correlated to 'MRNASEQ_CHIERARCHICAL'.
GFM1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
FAT1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 73 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 160 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	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
PBRM1	146 (22%)	522	0.015 (0.0925)	0.022 (0.122)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)
BAP1	49 (7%)	619	0.00032 (0.00508)	0.00042 (0.00626)	5e-05 (0.000986)	3e-05 (0.000626)	1e-05 (0.000243)	1e-05 (0.000243)	6e-05 (0.00112)	9e-05 (0.0016)	0.00281 (0.0253)	0.0101 (0.0698)
VHL	174 (26%)	494	0.00031 (0.00503)	0.00073 (0.00969)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)
TP53	38 (6%)	630			2e-05 (0.000442)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)	2e-05 (0.000442)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)
HNRNPM	12 (2%)	656			0.0257 (0.138)	0.00158 (0.017)	0.00079 (0.00985)	0.00173 (0.018)	0.00122 (0.0139)	0.0127 (0.0854)	0.0308 (0.162)	0.0202 (0.116)
MET	19 (3%)	649			0.00923 (0.0668)	3e-05 (0.000626)	1e-05 (0.000243)	1e-05 (0.000243)	2e-05 (0.000442)	1e-05 (0.000243)	0.0008 (0.00985)	0.00015 (0.00255)
MUC5B	30 (4%)	638			0.0061 (0.0489)	0.0001 (0.00174)	8e-05 (0.00146)	1e-05 (0.000243)	1e-05 (0.000243)	1e-05 (0.000243)	0.0231 (0.127)	0.00239 (0.0227)
ZNF814	13 (2%)	655			0.00779 (0.0577)	0.00683 (0.0525)	0.00173 (0.018)	0.0143 (0.09)	0.00977 (0.0686)	0.0159 (0.0959)	0.45 (0.951)	0.304 (0.773)
ZNF598	11 (2%)	657			0.0319 (0.163)	0.00222 (0.0215)	0.00224 (0.0215)	0.00081 (0.00985)	0.00127 (0.0143)	0.197 (0.578)	0.0874 (0.337)	0.00107 (0.0124)
SKI	9 (1%)	659			0.00083 (0.00993)	0.128 (0.434)	0.0003 (0.00498)	0.00217 (0.0214)	0.00073 (0.00969)	0.0408 (0.195)	0.0227 (0.125)	0.0614 (0.27)
AHNAK2	33 (5%)	635	0.278 (0.732)	0.0203 (0.116)	0.544 (1.00)	0.0334 (0.168)	0.00588 (0.0477)	0.00052 (0.0073)	0.017 (0.1)	0.0068 (0.0525)	0.683 (1.00)	0.275 (0.732)
PAM	4 (1%)	664			0.0194 (0.112)	0.00585 (0.0477)	0.0027 (0.0249)	0.0154 (0.0944)	0.0135 (0.0895)	0.00075 (0.00978)
SETD2	58 (9%)	610	0.617 (1.00)	0.662 (1.00)	0.0162 (0.0971)	0.0117 (0.0788)	0.123 (0.424)	6e-05 (0.00112)	0.144 (0.465)	0.00081 (0.00985)	0.0386 (0.187)	0.0636 (0.276)
KDM5C	30 (4%)	638			0.0258 (0.138)	0.018 (0.105)	0.0166 (0.0988)	0.0054 (0.0448)	0.00047 (0.00686)	0.132 (0.441)	0.865 (1.00)	0.74 (1.00)
NEFH	15 (2%)	653			0.0705 (0.294)	0.0136 (0.0895)	0.00211 (0.0211)	0.00433 (0.0368)	0.0234 (0.128)	5e-05 (0.000986)	0.358 (0.844)	0.253 (0.698)
KDM6A	11 (2%)	657			0.154 (0.481)	0.00481 (0.0404)	0.00938 (0.0668)	0.0358 (0.177)	0.026 (0.138)	0.0014 (0.0153)	0.28 (0.732)	0.127 (0.433)
CSGALNACT2	8 (1%)	660			0.0039 (0.0335)	0.248 (0.687)	0.00924 (0.0668)	0.0476 (0.217)	0.0459 (0.211)	0.0429 (0.2)	0.0873 (0.337)	0.235 (0.66)
GFM1	3 (0%)	665			0.277 (0.732)	0.00997 (0.0693)	0.00315 (0.0274)	0.00178 (0.0183)	0.0456 (0.211)	0.00099 (0.0117)
PTEN	28 (4%)	640	0.314 (0.784)	0.787 (1.00)	0.0642 (0.277)	0.425 (0.932)	0.00648 (0.0509)	0.00279 (0.0253)	0.488 (0.999)	0.0311 (0.162)	0.0584 (0.259)	0.00942 (0.0668)
NF2	16 (2%)	652			0.0726 (0.301)	0.109 (0.389)	0.00297 (0.0262)	0.00035 (0.00532)	0.0704 (0.294)	0.173 (0.524)	0.00252 (0.0236)	0.0106 (0.0727)
MTOR	32 (5%)	636			0.00053 (0.0073)	0.00782 (0.0577)	0.146 (0.465)	0.0851 (0.332)	0.00134 (0.0148)	0.00035 (0.00532)	0.445 (0.947)	0.0944 (0.357)
FAT1	22 (3%)	646			0.151 (0.476)	0.0314 (0.162)	0.00049 (0.00701)	0.00184 (0.0187)	0.0254 (0.137)	0.131 (0.441)	0.228 (0.65)	0.068 (0.289)
TDG	5 (1%)	663			0.0327 (0.166)	0.0377 (0.183)	0.0351 (0.174)	0.108 (0.389)	0.121 (0.42)	0.0534 (0.241)	0.101 (0.374)	0.28 (0.732)
IDUA	5 (1%)	663			0.545 (1.00)	0.128 (0.434)	0.00693 (0.0527)	0.0158 (0.0959)	0.0374 (0.183)	0.0531 (0.241)	0.322 (0.795)	0.142 (0.461)
NFE2L2	10 (1%)	658			0.526 (1.00)	0.108 (0.389)	0.0431 (0.2)	0.136 (0.448)	0.5 (1.00)	0.0337 (0.169)	0.294 (0.757)	0.441 (0.946)
STAM	6 (1%)	662			1 (1.00)	0.0141 (0.09)	0.33 (0.807)	0.106 (0.387)	0.32 (0.793)	0.508 (1.00)	0.00298 (0.0262)	0.0575 (0.256)
CCDC82	6 (1%)	662			0.0217 (0.122)	0.303 (0.773)	0.0897 (0.343)	0.0141 (0.09)	0.278 (0.732)	0.509 (1.00)
DNMT3A	10 (1%)	658			1 (1.00)	0.348 (0.832)	0.0313 (0.162)	0.0971 (0.364)	0.762 (1.00)	0.384 (0.88)	0.828 (1.00)	0.438 (0.946)
RIMBP3	5 (1%)	663			0.446 (0.947)	0.173 (0.524)	0.62 (1.00)	0.0143 (0.09)	0.446 (0.947)	0.472 (0.972)
STAG2	14 (2%)	654			1 (1.00)	0.861 (1.00)	0.539 (1.00)	0.00624 (0.0495)	0.197 (0.578)	0.326 (0.802)	0.135 (0.445)	0.191 (0.568)
ARID1A	19 (3%)	649			0.956 (1.00)	0.702 (1.00)	0.0828 (0.328)	0.261 (0.712)	0.793 (1.00)	0.28 (0.732)	0.0139 (0.09)	0.161 (0.495)
MED16	4 (1%)	664			0.461 (0.959)	0.422 (0.932)	0.906 (1.00)	0.0417 (0.198)	0.82 (1.00)	1 (1.00)	0.385 (0.88)	0.207 (0.6)
RUFY3	7 (1%)	661			0.217 (0.622)	0.423 (0.932)	0.245 (0.684)	0.124 (0.426)	0.0766 (0.314)	0.0205 (0.116)
FAM200A	5 (1%)	663			0.452 (0.952)		0.0574 (0.256)	0.00703 (0.0529)	0.199 (0.582)	0.769 (1.00)
NASP	4 (1%)	664			0.32 (0.793)	0.068 (0.289)	0.0407 (0.195)	0.134 (0.445)	0.273 (0.732)	0.103 (0.377)	0.0877 (0.337)	0.145 (0.465)
OR2L8	7 (1%)	661			0.708 (1.00)	0.589 (1.00)	0.602 (1.00)	0.084 (0.332)	0.438 (0.946)	0.677 (1.00)	0.0426 (0.2)	0.144 (0.464)
GAPDHS	5 (1%)	663			0.642 (1.00)	0.26 (0.71)	0.155 (0.482)	0.0144 (0.09)	0.12 (0.42)	0.424 (0.932)
ATM	16 (2%)	652			0.73 (1.00)	0.458 (0.959)	0.383 (0.88)	0.343 (0.827)	0.748 (1.00)	0.354 (0.843)	0.756 (1.00)	0.488 (0.999)
CDK12	9 (1%)	659			1 (1.00)	0.884 (1.00)	0.964 (1.00)	0.993 (1.00)	0.833 (1.00)	0.533 (1.00)	1 (1.00)	0.425 (0.932)
PIK3CA	14 (2%)	654			0.134 (0.445)	0.636 (1.00)	0.12 (0.42)	0.292 (0.754)	0.61 (1.00)	0.0628 (0.274)
KIAA1751	8 (1%)	660			0.903 (1.00)	0.517 (1.00)	0.629 (1.00)	0.652 (1.00)	0.215 (0.618)	0.713 (1.00)
GPR50	5 (1%)	663			1 (1.00)	0.615 (1.00)	0.419 (0.932)	0.555 (1.00)	0.855 (1.00)	0.425 (0.932)
CCDC120	4 (1%)	664			0.461 (0.959)		0.528 (1.00)	0.616 (1.00)	0.355 (0.843)	1 (1.00)
SLC6A14	5 (1%)	663			0.855 (1.00)	0.1 (0.371)	0.757 (1.00)	0.555 (1.00)	0.525 (1.00)	0.423 (0.932)	0.11 (0.391)	0.152 (0.479)
CYP4F11	5 (1%)	663			0.451 (0.951)	0.785 (1.00)	0.371 (0.862)	0.821 (1.00)	0.245 (0.684)	0.77 (1.00)
EGFR	7 (1%)	661			0.306 (0.773)	0.339 (0.82)	0.309 (0.774)	0.528 (1.00)	0.139 (0.456)	0.652 (1.00)
DPCR1	8 (1%)	660			1 (1.00)	0.799 (1.00)	0.829 (1.00)	0.892 (1.00)	1 (1.00)	1 (1.00)
GUSB	4 (1%)	664			0.39 (0.887)		0.637 (1.00)	0.363 (0.85)	0.356 (0.843)	1 (1.00)
PTCH1	8 (1%)	660			0.611 (1.00)	0.718 (1.00)	0.533 (1.00)	0.334 (0.817)	0.305 (0.773)	0.851 (1.00)
RLIM	9 (1%)	659			0.702 (1.00)	0.566 (1.00)	0.584 (1.00)	0.743 (1.00)	0.081 (0.324)	1 (1.00)	0.908 (1.00)	0.887 (1.00)
SLC23A1	7 (1%)	661			0.802 (1.00)	0.516 (1.00)	0.148 (0.469)	0.233 (0.659)	0.894 (1.00)	0.68 (1.00)
RHEB	4 (1%)	664			0.564 (1.00)	1 (1.00)	1 (1.00)	0.178 (0.534)	0.214 (0.618)	1 (1.00)	0.44 (0.946)	1 (1.00)
SLC4A8	6 (1%)	662			0.159 (0.491)	0.363 (0.85)	0.155 (0.482)	0.428 (0.933)	1 (1.00)	0.192 (0.571)
PCK1	6 (1%)	662			0.882 (1.00)	0.427 (0.933)	0.845 (1.00)	0.585 (1.00)	0.584 (1.00)	1 (1.00)
TXNIP	8 (1%)	660			0.181 (0.542)	0.319 (0.793)	0.391 (0.887)	0.61 (1.00)	0.305 (0.773)	0.409 (0.924)	0.583 (1.00)	0.755 (1.00)
RNF128	5 (1%)	663			0.545 (1.00)	0.175 (0.529)	0.705 (1.00)	0.677 (1.00)	0.384 (0.88)	1 (1.00)
ZFYVE26	9 (1%)	659			0.92 (1.00)	0.483 (0.993)	0.781 (1.00)	0.366 (0.854)	0.91 (1.00)	0.639 (1.00)	0.596 (1.00)	0.259 (0.71)
FAM160B2	4 (1%)	664			0.844 (1.00)	1 (1.00)	0.905 (1.00)	0.852 (1.00)	0.445 (0.947)	0.727 (1.00)
FAM47A	6 (1%)	662			0.882 (1.00)	1 (1.00)	0.892 (1.00)	0.683 (1.00)	0.497 (1.00)	0.802 (1.00)
ATP1A1	10 (1%)	658	0.253 (0.698)	0.634 (1.00)	0.14 (0.456)	1 (1.00)	0.124 (0.426)	0.787 (1.00)	0.168 (0.514)	0.503 (1.00)
SH3BP2	4 (1%)	664			0.068 (0.289)	0.275 (0.732)	0.109 (0.389)	0.0922 (0.351)	0.274 (0.732)	0.193 (0.571)
RTL1	7 (1%)	661			0.502 (1.00)	0.885 (1.00)	0.078 (0.317)	0.338 (0.82)	0.493 (0.999)	0.0812 (0.324)	1 (1.00)	0.235 (0.66)
RPL7A	3 (0%)	665			1 (1.00)	0.0987 (0.368)	0.0851 (0.332)	0.0756 (0.312)	0.233 (0.659)	0.107 (0.389)
UIMC1	5 (1%)	663			0.548 (1.00)	0.336 (0.818)	0.931 (1.00)	0.463 (0.959)	0.0956 (0.36)	0.771 (1.00)
TCEB1	3 (0%)	665			0.0686 (0.289)		0.868 (1.00)	0.63 (1.00)	0.164 (0.502)	1 (1.00)
SFMBT1	3 (0%)	665			0.49 (0.999)		0.766 (1.00)	0.745 (1.00)	0.801 (1.00)	0.622 (1.00)
SLC16A1	3 (0%)	665			1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.801 (1.00)	0.626 (1.00)
TMCO3	7 (1%)	661			0.0782 (0.317)	0.273 (0.732)	0.867 (1.00)	0.0806 (0.324)	0.388 (0.885)	1 (1.00)
NFAT5	8 (1%)	660			0.685 (1.00)	0.632 (1.00)	0.548 (1.00)	0.679 (1.00)	0.728 (1.00)	1 (1.00)
HNF1B	3 (0%)	665			0.494 (0.999)	0.786 (1.00)	0.44 (0.946)	0.494 (0.999)	0.802 (1.00)	0.359 (0.844)
ZC3H18	6 (1%)	662			0.882 (1.00)	0.425 (0.932)	0.801 (1.00)	1 (1.00)	0.869 (1.00)	0.377 (0.874)
GPR137	4 (1%)	664			0.204 (0.595)	0.598 (1.00)	0.288 (0.745)	0.346 (0.831)	0.113 (0.397)	0.307 (0.773)
RRP12	9 (1%)	659			0.84 (1.00)	0.419 (0.932)	0.467 (0.967)	0.455 (0.954)	0.287 (0.745)	0.281 (0.732)	0.93 (1.00)	0.56 (1.00)

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00044

Table S1. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
TP53 MUTATED	22	3	13
TP53 WILD-TYPE	158	239	230

Figure S1. Get High-res Image Gene #1: '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 = 0.00024

Table S2. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
TP53 MUTATED	26	5	3
TP53 WILD-TYPE	77	250	116

Figure S2. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S3. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
TP53 MUTATED	24	8	2	4
TP53 WILD-TYPE	74	166	243	145

Figure S3. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S4. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
TP53 MUTATED	23	6	2	5	1	1
TP53 WILD-TYPE	57	84	175	133	89	90

Figure S4. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00044

Table S5. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
TP53 MUTATED	27	5	6
TP53 WILD-TYPE	187	143	290

Figure S5. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S6. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
TP53 MUTATED	23	12	3
TP53 WILD-TYPE	49	464	107

Figure S6. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S7. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
TP53 MUTATED	2	18	3	3
TP53 WILD-TYPE	74	42	39	96

Figure S7. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S8. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
TP53 MUTATED	0	0	5	3	18
TP53 WILD-TYPE	26	43	57	97	28

Figure S8. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.093

Table S9. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	17	9	14
PBRM1 MUTATED	9	3	1	0
PBRM1 WILD-TYPE	12	14	8	14

Figure S9. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.12

Table S10. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	17	14	10	9
PBRM1 MUTATED	5	3	0	4	1
PBRM1 WILD-TYPE	6	14	14	6	8

Figure S10. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S11. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
PBRM1 MUTATED	5	71	70
PBRM1 WILD-TYPE	175	171	173

Figure S11. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S12. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
PBRM1 MUTATED	1	96	5
PBRM1 WILD-TYPE	102	159	114

Figure S12. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S13. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
PBRM1 MUTATED	2	42	94	7
PBRM1 WILD-TYPE	96	132	151	142

Figure S13. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S14. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
PBRM1 MUTATED	2	6	73	31	32	1
PBRM1 WILD-TYPE	78	84	104	107	58	90

Figure S14. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S15. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
PBRM1 MUTATED	7	24	111
PBRM1 WILD-TYPE	207	124	185

Figure S15. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S16. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
PBRM1 MUTATED	1	139	2
PBRM1 WILD-TYPE	71	337	108

Figure S16. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S17. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
PBRM1 MUTATED	4	1	2	31
PBRM1 WILD-TYPE	72	59	40	68

Figure S17. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S18. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
PBRM1 MUTATED	0	1	5	31	1
PBRM1 WILD-TYPE	26	42	57	69	45

Figure S18. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.314 (Fisher's exact test), Q value = 0.78

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	17	9	14
PTEN MUTATED	0	2	1	1
PTEN WILD-TYPE	21	15	8	13

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	17	14	10	9
PTEN MUTATED	0	2	1	0	1
PTEN WILD-TYPE	11	15	13	10	8

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0642 (Fisher's exact test), Q value = 0.28

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
PTEN MUTATED	12	5	10
PTEN WILD-TYPE	168	237	233

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 0.93

Table S22. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
PTEN MUTATED	6	8	5
PTEN WILD-TYPE	97	247	114

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00648 (Fisher's exact test), Q value = 0.051

Table S23. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
PTEN MUTATED	7	12	3	6
PTEN WILD-TYPE	91	162	242	143

Figure S19. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00279 (Fisher's exact test), Q value = 0.025

Table S24. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
PTEN MUTATED	7	0	4	10	1	6
PTEN WILD-TYPE	73	90	173	128	89	85

Figure S20. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.488 (Fisher's exact test), Q value = 1

Table S25. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
PTEN MUTATED	12	6	10
PTEN WILD-TYPE	202	142	286

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.16

Table S26. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
PTEN MUTATED	7	15	6
PTEN WILD-TYPE	65	461	104

Figure S21. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0584 (Fisher's exact test), Q value = 0.26

Table S27. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
PTEN MUTATED	6	5	0	2
PTEN WILD-TYPE	70	55	42	97

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00942 (Fisher's exact test), Q value = 0.067

Table S28. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
PTEN MUTATED	2	4	0	2	5
PTEN WILD-TYPE	24	39	62	98	41

Figure S22. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0051

Table S29. Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	17	9	14
BAP1 MUTATED	1	8	0	0
BAP1 WILD-TYPE	20	9	9	14

Figure S23. Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0063

Table S30. Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	17	14	10	9
BAP1 MUTATED	0	8	0	1	0
BAP1 WILD-TYPE	11	9	14	9	9

Figure S24. Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00099

Table S31. Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
BAP1 MUTATED	2	20	27
BAP1 WILD-TYPE	178	222	216

Figure S25. Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00063

Table S32. Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
BAP1 MUTATED	0	27	3
BAP1 WILD-TYPE	103	228	116

Figure S26. Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S33. Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
BAP1 MUTATED	0	30	14	5
BAP1 WILD-TYPE	98	144	231	144

Figure S27. Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S34. Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
BAP1 MUTATED	0	4	6	36	3	0
BAP1 WILD-TYPE	80	86	171	102	87	91

Figure S28. Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0011

Table S35. Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
BAP1 MUTATED	5	21	23
BAP1 WILD-TYPE	209	127	273

Figure S29. Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016

Table S36. Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
BAP1 MUTATED	0	47	2
BAP1 WILD-TYPE	72	429	108

Figure S30. Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00281 (Fisher's exact test), Q value = 0.025

Table S37. Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
BAP1 MUTATED	0	0	2	9
BAP1 WILD-TYPE	76	60	40	90

Figure S31. Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.07

Table S38. Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
BAP1 MUTATED	0	0	1	10	0
BAP1 WILD-TYPE	26	43	61	90	46

Figure S32. Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S39. Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	17	9	14
SETD2 MUTATED	2	2	0	0
SETD2 WILD-TYPE	19	15	9	14

'SETD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S40. Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	17	14	10	9
SETD2 MUTATED	1	2	0	1	0
SETD2 WILD-TYPE	10	15	14	9	9

'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.097

Table S41. Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
SETD2 MUTATED	7	24	27
SETD2 WILD-TYPE	173	218	216

Figure S33. Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.079

Table S42. Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
SETD2 MUTATED	3	31	8
SETD2 WILD-TYPE	100	224	111

Figure S34. Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 0.42

Table S43. Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
SETD2 MUTATED	3	18	25	12
SETD2 WILD-TYPE	95	156	220	137

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.0011

Table S44. Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
SETD2 MUTATED	2	13	24	14	5	0
SETD2 WILD-TYPE	78	77	153	124	85	91

Figure S35. Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.46

Table S45. Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
SETD2 MUTATED	12	13	31
SETD2 WILD-TYPE	202	135	265

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0099

Table S46. Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
SETD2 MUTATED	2	52	2
SETD2 WILD-TYPE	70	424	108

Figure S36. Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.19

Table S47. Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
SETD2 MUTATED	5	1	3	14
SETD2 WILD-TYPE	71	59	39	85

Figure S37. Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0636 (Fisher's exact test), Q value = 0.28

Table S48. Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
SETD2 MUTATED	0	2	7	13	1
SETD2 WILD-TYPE	26	41	55	87	45

'KDM5C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.14

Table S49. Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
KDM5C MUTATED	4	8	18
KDM5C WILD-TYPE	176	234	225

Figure S38. Get High-res Image Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KDM5C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.11

Table S50. Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
KDM5C MUTATED	1	17	2
KDM5C WILD-TYPE	102	238	117

Figure S39. Get High-res Image Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.099

Table S51. Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
KDM5C MUTATED	1	12	14	2
KDM5C WILD-TYPE	97	162	231	147

Figure S40. Get High-res Image Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0054 (Fisher's exact test), Q value = 0.045

Table S52. Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
KDM5C MUTATED	1	0	16	7	3	2
KDM5C WILD-TYPE	79	90	161	131	87	89

Figure S41. Get High-res Image Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0069

Table S53. Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
KDM5C MUTATED	3	3	24
KDM5C WILD-TYPE	211	145	272

Figure S42. Get High-res Image Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.44

Table S54. Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
KDM5C MUTATED	1	27	2
KDM5C WILD-TYPE	71	449	108

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S55. Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
KDM5C MUTATED	1	1	0	3
KDM5C WILD-TYPE	75	59	42	96

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S56. Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
KDM5C MUTATED	0	1	0	3	1
KDM5C WILD-TYPE	26	42	62	97	45

'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0705 (Fisher's exact test), Q value = 0.29

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
NEFH MUTATED	8	4	3
NEFH WILD-TYPE	172	238	240

'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.09

Table S58. Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
NEFH MUTATED	1	4	8
NEFH WILD-TYPE	102	251	111

Figure S43. Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.021

Table S59. Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
NEFH MUTATED	1	1	3	10
NEFH WILD-TYPE	97	173	242	139

Figure S44. Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00433 (Fisher's exact test), Q value = 0.037

Table S60. Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
NEFH MUTATED	0	6	2	2	0	5
NEFH WILD-TYPE	80	84	175	136	90	86

Figure S45. Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.13

Table S61. Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
NEFH MUTATED	10	2	3
NEFH WILD-TYPE	204	146	293

Figure S46. Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00099

Table S62. Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
NEFH MUTATED	0	5	10
NEFH WILD-TYPE	72	471	100

Figure S47. Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.358 (Fisher's exact test), Q value = 0.84

Table S63. Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
NEFH MUTATED	3	0	0	3
NEFH WILD-TYPE	73	60	42	96

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.7

Table S64. Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
NEFH MUTATED	0	3	1	2	0
NEFH WILD-TYPE	26	40	61	98	46

'VHL MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.005

Table S65. Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	17	9	14
VHL MUTATED	13	5	1	0
VHL WILD-TYPE	8	12	8	14

Figure S48. Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'VHL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0097

Table S66. Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	17	14	10	9
VHL MUTATED	7	5	0	6	1
VHL WILD-TYPE	4	12	14	4	8

Figure S49. Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S67. Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
VHL MUTATED	4	93	77
VHL WILD-TYPE	176	149	166

Figure S50. Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'VHL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S68. Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
VHL MUTATED	1	114	1
VHL WILD-TYPE	102	141	118

Figure S51. Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'VHL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S69. Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
VHL MUTATED	4	58	110	2
VHL WILD-TYPE	94	116	135	147

Figure S52. Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'VHL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S70. Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
VHL MUTATED	2	2	78	52	40	0
VHL WILD-TYPE	78	88	99	86	50	91

Figure S53. Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S71. Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
VHL MUTATED	4	46	120
VHL WILD-TYPE	210	102	176

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

'VHL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
VHL MUTATED	1	169	0
VHL WILD-TYPE	71	307	110

Figure S55. Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S73. Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
VHL MUTATED	0	1	0	47
VHL WILD-TYPE	76	59	42	52

Figure S56. Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S74. Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
VHL MUTATED	0	0	0	47	1
VHL WILD-TYPE	26	43	62	53	45

Figure S57. Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0726 (Fisher's exact test), Q value = 0.3

Table S75. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
NF2 MUTATED	7	2	7
NF2 WILD-TYPE	173	240	236

'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.39

Table S76. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
NF2 MUTATED	4	3	5
NF2 WILD-TYPE	99	252	114

'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00297 (Fisher's exact test), Q value = 0.026

Table S77. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
NF2 MUTATED	1	5	1	9
NF2 WILD-TYPE	97	169	244	140

Figure S58. Get High-res Image Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0053

Table S78. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
NF2 MUTATED	0	8	1	3	0	4
NF2 WILD-TYPE	80	82	176	135	90	87

Figure S59. Get High-res Image Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0704 (Fisher's exact test), Q value = 0.29

Table S79. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
NF2 MUTATED	9	4	3
NF2 WILD-TYPE	205	144	293

'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.52

Table S80. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
NF2 MUTATED	0	11	5
NF2 WILD-TYPE	72	465	105

'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00252 (Fisher's exact test), Q value = 0.024

Table S81. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
NF2 MUTATED	3	0	4	0
NF2 WILD-TYPE	73	60	38	99

Figure S60. Get High-res Image Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.073

Table S82. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
NF2 MUTATED	0	3	4	0	0
NF2 WILD-TYPE	26	40	58	100	46

Figure S61. Get High-res Image Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HNRNPM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.14

Table S83. Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
HNRNPM MUTATED	7	4	1
HNRNPM WILD-TYPE	173	238	242

Figure S62. Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'HNRNPM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.017

Table S84. Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
HNRNPM MUTATED	4	1	7
HNRNPM WILD-TYPE	99	254	112

Figure S63. Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0099

Table S85. Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
HNRNPM MUTATED	2	2	0	8
HNRNPM WILD-TYPE	96	172	245	141

Figure S64. Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00173 (Fisher's exact test), Q value = 0.018

Table S86. Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
HNRNPM MUTATED	2	5	0	1	0	4
HNRNPM WILD-TYPE	78	85	177	137	90	87

Figure S65. Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.014

Table S87. Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
HNRNPM MUTATED	8	4	0
HNRNPM WILD-TYPE	206	144	296

Figure S66. Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.085

Table S88. Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
HNRNPM MUTATED	1	5	6
HNRNPM WILD-TYPE	71	471	104

Figure S67. Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.16

Table S89. Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
HNRNPM MUTATED	5	3	2	0
HNRNPM WILD-TYPE	71	57	40	99

Figure S68. Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0202 (Fisher's exact test), Q value = 0.12

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
HNRNPM MUTATED	2	3	4	0	1
HNRNPM WILD-TYPE	24	40	58	100	45

Figure S69. Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.067

Table S91. Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
MET MUTATED	11	4	3
MET WILD-TYPE	169	238	240

Figure S70. Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00063

Table S92. Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
MET MUTATED	1	3	13
MET WILD-TYPE	102	252	106

Figure S71. Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S93. Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
MET MUTATED	0	1	1	17
MET WILD-TYPE	98	173	244	132

Figure S72. Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'MET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S94. Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
MET MUTATED	0	4	1	0	0	14
MET WILD-TYPE	80	86	176	138	90	77

Figure S73. Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00044

Table S95. Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
MET MUTATED	15	3	1
MET WILD-TYPE	199	145	295

Figure S74. Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S96. Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
MET MUTATED	0	5	14
MET WILD-TYPE	72	471	96

Figure S75. Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0099

Table S97. Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
MET MUTATED	9	0	3	1
MET WILD-TYPE	67	60	39	98

Figure S76. Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0025

Table S98. Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
MET MUTATED	4	5	4	0	0
MET WILD-TYPE	22	38	58	100	46

Figure S77. Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MUC5B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0061 (Fisher's exact test), Q value = 0.049

Table S99. Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
MUC5B MUTATED	16	6	8
MUC5B WILD-TYPE	164	236	235

Figure S78. Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MUC5B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0017

Table S100. Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
MUC5B MUTATED	13	5	11
MUC5B WILD-TYPE	90	250	108

Figure S79. Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MUC5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S101. Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
MUC5B MUTATED	10	3	4	13
MUC5B WILD-TYPE	88	171	241	136

Figure S80. Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'MUC5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S102. Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
MUC5B MUTATED	10	10	4	1	0	5
MUC5B WILD-TYPE	70	80	173	137	90	86

Figure S81. Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MUC5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S103. Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
MUC5B MUTATED	23	2	5
MUC5B WILD-TYPE	191	146	291

Figure S82. Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MUC5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S104. Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
MUC5B MUTATED	10	10	10
MUC5B WILD-TYPE	62	466	100

Figure S83. Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.13

Table S105. Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
MUC5B MUTATED	8	8	4	2
MUC5B WILD-TYPE	68	52	38	97

Figure S84. Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00239 (Fisher's exact test), Q value = 0.023

Table S106. Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
MUC5B MUTATED	3	4	6	1	8
MUC5B WILD-TYPE	23	39	56	99	38

Figure S85. Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.48

Table S107. Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
KDM6A MUTATED	6	3	2
KDM6A WILD-TYPE	174	239	241

'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00481 (Fisher's exact test), Q value = 0.04

Table S108. Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
KDM6A MUTATED	1	1	6
KDM6A WILD-TYPE	102	254	113

Figure S86. Get High-res Image Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00938 (Fisher's exact test), Q value = 0.067

Table S109. Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
KDM6A MUTATED	1	0	3	7
KDM6A WILD-TYPE	97	174	242	142

Figure S87. Get High-res Image Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0358 (Fisher's exact test), Q value = 0.18

Table S110. Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
KDM6A MUTATED	0	4	1	1	1	4
KDM6A WILD-TYPE	80	86	176	137	89	87

Figure S88. Get High-res Image Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.14

Table S111. Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
KDM6A MUTATED	8	1	2
KDM6A WILD-TYPE	206	147	294

Figure S89. Get High-res Image Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.015

Table S112. Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
KDM6A MUTATED	0	4	7
KDM6A WILD-TYPE	72	472	103

Figure S90. Get High-res Image Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.73

Table S113. Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
KDM6A MUTATED	2	1	0	0
KDM6A WILD-TYPE	74	59	42	99

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.43

Table S114. Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
KDM6A MUTATED	0	2	1	0	0
KDM6A WILD-TYPE	26	41	61	100	46

'TDG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.17

Table S115. Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
TDG MUTATED	4	0	1
TDG WILD-TYPE	176	242	242

Figure S91. Get High-res Image Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TDG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.18

Table S116. Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
TDG MUTATED	0	1	4
TDG WILD-TYPE	103	254	115

Figure S92. Get High-res Image Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TDG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.17

Table S117. Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
TDG MUTATED	0	0	1	4
TDG WILD-TYPE	98	174	244	145

Figure S93. Get High-res Image Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TDG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 0.39

Table S118. Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
TDG MUTATED	0	2	0	1	0	2
TDG WILD-TYPE	80	88	177	137	90	89

'TDG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.42

Table S119. Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
TDG MUTATED	4	0	1
TDG WILD-TYPE	210	148	295

'TDG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0534 (Fisher's exact test), Q value = 0.24

Table S120. Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
TDG MUTATED	0	2	3
TDG WILD-TYPE	72	474	107

'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.37

Table S121. Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
TDG MUTATED	4	0	0	1
TDG WILD-TYPE	72	60	42	98

'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 0.73

Table S122. Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
TDG MUTATED	1	2	1	1	0
TDG WILD-TYPE	25	41	61	99	46

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 1

Table S123. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
NFE2L2 MUTATED	4	2	4
NFE2L2 WILD-TYPE	176	240	239

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 0.39

Table S124. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
NFE2L2 MUTATED	0	3	4
NFE2L2 WILD-TYPE	103	252	115

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 0.2

Table S125. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
NFE2L2 MUTATED	0	4	1	5
NFE2L2 WILD-TYPE	98	170	244	144

Figure S94. Get High-res Image Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test), Q value = 0.45

Table S126. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
NFE2L2 MUTATED	0	2	1	4	0	3
NFE2L2 WILD-TYPE	80	88	176	134	90	88

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.5 (Fisher's exact test), Q value = 1

Table S127. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
NFE2L2 MUTATED	5	2	3
NFE2L2 WILD-TYPE	209	146	293

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.17

Table S128. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
NFE2L2 MUTATED	0	5	5
NFE2L2 WILD-TYPE	72	471	105

Figure S95. Get High-res Image Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.294 (Fisher's exact test), Q value = 0.76

Table S129. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
NFE2L2 MUTATED	3	0	0	1
NFE2L2 WILD-TYPE	73	60	42	98

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.441 (Fisher's exact test), Q value = 0.95

Table S130. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
NFE2L2 MUTATED	0	2	1	1	0
NFE2L2 WILD-TYPE	26	41	61	99	46

'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S131. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
ATM MUTATED	3	7	6
ATM WILD-TYPE	177	235	237

'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 0.96

Table S132. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
ATM MUTATED	3	8	1
ATM WILD-TYPE	100	247	118

'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.383 (Fisher's exact test), Q value = 0.88

Table S133. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
ATM MUTATED	3	4	8	1
ATM WILD-TYPE	95	170	237	148

'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.343 (Fisher's exact test), Q value = 0.83

Table S134. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
ATM MUTATED	3	0	5	3	4	1
ATM WILD-TYPE	77	90	172	135	86	90

'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.748 (Fisher's exact test), Q value = 1

Table S135. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
ATM MUTATED	5	2	8
ATM WILD-TYPE	209	146	288

'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.84

Table S136. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
ATM MUTATED	3	11	1
ATM WILD-TYPE	69	465	109

'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.756 (Fisher's exact test), Q value = 1

Table S137. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
ATM MUTATED	1	2	0	2
ATM WILD-TYPE	75	58	42	97

'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.488 (Fisher's exact test), Q value = 1

Table S138. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
ATM MUTATED	0	1	0	2	2
ATM WILD-TYPE	26	42	62	98	44

'ZNF814 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00779 (Fisher's exact test), Q value = 0.058

Table S139. Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
ZNF814 MUTATED	6	0	7
ZNF814 WILD-TYPE	174	242	236

Figure S96. Get High-res Image Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZNF814 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00683 (Fisher's exact test), Q value = 0.052

Table S140. Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
ZNF814 MUTATED	4	2	7
ZNF814 WILD-TYPE	99	253	112

Figure S97. Get High-res Image Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.018

Table S141. Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
ZNF814 MUTATED	3	1	1	8
ZNF814 WILD-TYPE	95	173	244	141

Figure S98. Get High-res Image Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.09

Table S142. Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
ZNF814 MUTATED	3	5	1	1	0	3
ZNF814 WILD-TYPE	77	85	176	137	90	88

Figure S99. Get High-res Image Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00977 (Fisher's exact test), Q value = 0.069

Table S143. Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
ZNF814 MUTATED	7	5	1
ZNF814 WILD-TYPE	207	143	295

Figure S100. Get High-res Image Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.096

Table S144. Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
ZNF814 MUTATED	3	5	5
ZNF814 WILD-TYPE	69	471	105

Figure S101. Get High-res Image Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 0.95

Table S145. Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
ZNF814 MUTATED	5	2	1	2
ZNF814 WILD-TYPE	71	58	41	97

'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 0.77

Table S146. Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
ZNF814 MUTATED	1	2	4	1	2
ZNF814 WILD-TYPE	25	41	58	99	44

'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

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

Table S147. Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
DNMT3A MUTATED	2	4	4
DNMT3A WILD-TYPE	178	238	239

'DNMT3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.83

Table S148. Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
DNMT3A MUTATED	0	5	3
DNMT3A WILD-TYPE	103	250	116

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.16

Table S149. Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
DNMT3A MUTATED	0	0	5	5
DNMT3A WILD-TYPE	98	174	240	144

Figure S102. Get High-res Image Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0971 (Fisher's exact test), Q value = 0.36

Table S150. Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
DNMT3A MUTATED	0	2	2	0	3	3
DNMT3A WILD-TYPE	80	88	175	138	87	88

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S151. Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
DNMT3A MUTATED	4	2	3
DNMT3A WILD-TYPE	210	146	293

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.384 (Fisher's exact test), Q value = 0.88

Table S152. Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
DNMT3A MUTATED	0	6	3
DNMT3A WILD-TYPE	72	470	107

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S153. Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
DNMT3A MUTATED	2	1	0	1
DNMT3A WILD-TYPE	74	59	42	98

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.438 (Fisher's exact test), Q value = 0.95

Table S154. Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
DNMT3A MUTATED	0	2	1	1	0
DNMT3A WILD-TYPE	26	41	61	99	46

'CDK12 MUTATION STATUS' versus 'CN_CNMF'

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

Table S155. Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
CDK12 MUTATED	2	3	4
CDK12 WILD-TYPE	178	239	239

'CDK12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.884 (Fisher's exact test), Q value = 1

Table S156. Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
CDK12 MUTATED	2	4	1
CDK12 WILD-TYPE	101	251	118

'CDK12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.964 (Fisher's exact test), Q value = 1

Table S157. Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
CDK12 MUTATED	1	3	3	2
CDK12 WILD-TYPE	97	171	242	147

'CDK12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.993 (Fisher's exact test), Q value = 1

Table S158. Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
CDK12 MUTATED	1	1	2	3	1	1
CDK12 WILD-TYPE	79	89	175	135	89	90

'CDK12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S159. Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
CDK12 MUTATED	3	1	5
CDK12 WILD-TYPE	211	147	291

'CDK12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S160. Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
CDK12 MUTATED	1	8	0
CDK12 WILD-TYPE	71	468	110

'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S161. Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
CDK12 MUTATED	1	1	1	2
CDK12 WILD-TYPE	75	59	41	97

'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 0.93

Table S162. Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
CDK12 MUTATED	1	0	0	3	1
CDK12 WILD-TYPE	25	43	62	97	45

'CSGALNACT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0039 (Fisher's exact test), Q value = 0.033

Table S163. Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
CSGALNACT2 MUTATED	6	0	2
CSGALNACT2 WILD-TYPE	174	242	241

Figure S103. Get High-res Image Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 0.69

Table S164. Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
CSGALNACT2 MUTATED	3	2	3
CSGALNACT2 WILD-TYPE	100	253	116

'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00924 (Fisher's exact test), Q value = 0.067

Table S165. Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
CSGALNACT2 MUTATED	3	1	0	4
CSGALNACT2 WILD-TYPE	95	173	245	145

Figure S104. Get High-res Image Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0476 (Fisher's exact test), Q value = 0.22

Table S166. Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
CSGALNACT2 MUTATED	2	3	0	1	0	2
CSGALNACT2 WILD-TYPE	78	87	177	137	90	89

Figure S105. Get High-res Image Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.21

Table S167. Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
CSGALNACT2 MUTATED	6	1	1
CSGALNACT2 WILD-TYPE	208	147	295

Figure S106. Get High-res Image Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0429 (Fisher's exact test), Q value = 0.2

Table S168. Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
CSGALNACT2 MUTATED	2	3	3
CSGALNACT2 WILD-TYPE	70	473	107

Figure S107. Get High-res Image Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0873 (Fisher's exact test), Q value = 0.34

Table S169. Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
CSGALNACT2 MUTATED	0	2	1	0
CSGALNACT2 WILD-TYPE	76	58	41	99

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 0.66

Table S170. Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
CSGALNACT2 MUTATED	0	0	2	0	1
CSGALNACT2 WILD-TYPE	26	43	60	100	45

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.44

Table S171. Gene #21: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
PIK3CA MUTATED	1	5	8
PIK3CA WILD-TYPE	179	237	235

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.636 (Fisher's exact test), Q value = 1

Table S172. Gene #21: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
PIK3CA MUTATED	1	6	1
PIK3CA WILD-TYPE	102	249	118

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.42

Table S173. Gene #21: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
PIK3CA MUTATED	0	6	7	1
PIK3CA WILD-TYPE	98	168	238	148

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 0.75

Table S174. Gene #21: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
PIK3CA MUTATED	0	1	3	5	4	1
PIK3CA WILD-TYPE	80	89	174	133	86	90

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S175. Gene #21: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
PIK3CA MUTATED	3	4	7
PIK3CA WILD-TYPE	211	144	289

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0628 (Fisher's exact test), Q value = 0.27

Table S176. Gene #21: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
PIK3CA MUTATED	0	14	0
PIK3CA WILD-TYPE	72	462	110

'KIAA1751 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S177. Gene #22: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
KIAA1751 MUTATED	2	2	4
KIAA1751 WILD-TYPE	178	240	239

'KIAA1751 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S178. Gene #22: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
KIAA1751 MUTATED	0	5	2
KIAA1751 WILD-TYPE	103	250	117

'KIAA1751 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 1

Table S179. Gene #22: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
KIAA1751 MUTATED	0	1	4	2
KIAA1751 WILD-TYPE	98	173	241	147

'KIAA1751 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S180. Gene #22: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
KIAA1751 MUTATED	0	0	3	1	1	2
KIAA1751 WILD-TYPE	80	90	174	137	89	89

'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.62

Table S181. Gene #22: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
KIAA1751 MUTATED	2	0	6
KIAA1751 WILD-TYPE	212	148	290

'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.713 (Fisher's exact test), Q value = 1

Table S182. Gene #22: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
KIAA1751 MUTATED	0	6	2
KIAA1751 WILD-TYPE	72	470	108

'MTOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0073

Table S183. Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
MTOR MUTATED	1	11	20
MTOR WILD-TYPE	179	231	223

Figure S108. Get High-res Image Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MTOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00782 (Fisher's exact test), Q value = 0.058

Table S184. Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
MTOR MUTATED	5	21	1
MTOR WILD-TYPE	98	234	118

Figure S109. Get High-res Image Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MTOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.46

Table S185. Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
MTOR MUTATED	3	12	14	3
MTOR WILD-TYPE	95	162	231	146

'MTOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0851 (Fisher's exact test), Q value = 0.33

Table S186. Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
MTOR MUTATED	2	4	7	9	9	1
MTOR WILD-TYPE	78	86	170	129	81	90

'MTOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.015

Table S187. Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
MTOR MUTATED	2	9	21
MTOR WILD-TYPE	212	139	275

Figure S110. Get High-res Image Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MTOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0053

Table S188. Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
MTOR MUTATED	0	32	0
MTOR WILD-TYPE	72	444	110

Figure S111. Get High-res Image Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.445 (Fisher's exact test), Q value = 0.95

Table S189. Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
MTOR MUTATED	1	2	2	6
MTOR WILD-TYPE	75	58	40	93

'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0944 (Fisher's exact test), Q value = 0.36

Table S190. Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
MTOR MUTATED	0	0	4	7	0
MTOR WILD-TYPE	26	43	58	93	46

'RIMBP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 0.95

Table S191. Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
RIMBP3 MUTATED	0	2	3
RIMBP3 WILD-TYPE	180	240	240

'RIMBP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 0.52

Table S192. Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
RIMBP3 MUTATED	2	1	0
RIMBP3 WILD-TYPE	101	254	119

'RIMBP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.62 (Fisher's exact test), Q value = 1

Table S193. Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
RIMBP3 MUTATED	1	1	3	0
RIMBP3 WILD-TYPE	97	173	242	149

'RIMBP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.09

Table S194. Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
RIMBP3 MUTATED	1	1	0	0	3	0
RIMBP3 WILD-TYPE	79	89	177	138	87	91

Figure S112. Get High-res Image Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RIMBP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 0.95

Table S195. Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
RIMBP3 MUTATED	1	2	1
RIMBP3 WILD-TYPE	213	146	295

'RIMBP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.472 (Fisher's exact test), Q value = 0.97

Table S196. Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
RIMBP3 MUTATED	1	3	0
RIMBP3 WILD-TYPE	71	473	110

'ZNF598 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.16

Table S197. Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
ZNF598 MUTATED	7	2	2
ZNF598 WILD-TYPE	173	240	241

Figure S113. Get High-res Image Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZNF598 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.022

Table S198. Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
ZNF598 MUTATED	2	1	7
ZNF598 WILD-TYPE	101	254	112

Figure S114. Get High-res Image Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.022

Table S199. Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
ZNF598 MUTATED	1	1	1	8
ZNF598 WILD-TYPE	97	173	244	141

Figure S115. Get High-res Image Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0099

Table S200. Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
ZNF598 MUTATED	1	3	0	1	0	6
ZNF598 WILD-TYPE	79	87	177	137	90	85

Figure S116. Get High-res Image Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.014

Table S201. Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
ZNF598 MUTATED	8	3	0
ZNF598 WILD-TYPE	206	145	296

Figure S117. Get High-res Image Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.58

Table S202. Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
ZNF598 MUTATED	1	6	4
ZNF598 WILD-TYPE	71	470	106

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0874 (Fisher's exact test), Q value = 0.34

Table S203. Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
ZNF598 MUTATED	3	3	4	1
ZNF598 WILD-TYPE	73	57	38	98

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.012

Table S204. Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
ZNF598 MUTATED	5	0	4	1	1
ZNF598 WILD-TYPE	21	43	58	99	45

Figure S118. Get High-res Image Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GPR50 MUTATION STATUS' versus 'CN_CNMF'

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

Table S205. Gene #26: 'GPR50 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
GPR50 MUTATED	1	2	2
GPR50 WILD-TYPE	179	240	241

'GPR50 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.615 (Fisher's exact test), Q value = 1

Table S206. Gene #26: 'GPR50 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
GPR50 MUTATED	2	2	1
GPR50 WILD-TYPE	101	253	118

'GPR50 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.419 (Fisher's exact test), Q value = 0.93

Table S207. Gene #26: 'GPR50 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
GPR50 MUTATED	2	1	1	1
GPR50 WILD-TYPE	96	173	244	148

'GPR50 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S208. Gene #26: 'GPR50 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
GPR50 MUTATED	1	1	0	1	1	1
GPR50 WILD-TYPE	79	89	177	137	89	90

'GPR50 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S209. Gene #26: 'GPR50 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
GPR50 MUTATED	1	1	3
GPR50 WILD-TYPE	213	147	293

'GPR50 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 0.93

Table S210. Gene #26: 'GPR50 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
GPR50 MUTATED	1	3	1
GPR50 WILD-TYPE	71	473	109

'CCDC120 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.461 (Fisher's exact test), Q value = 0.96

Table S211. Gene #27: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
CCDC120 MUTATED	0	1	3
CCDC120 WILD-TYPE	180	241	240

'CCDC120 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.528 (Fisher's exact test), Q value = 1

Table S212. Gene #27: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
CCDC120 MUTATED	0	1	3	0
CCDC120 WILD-TYPE	98	173	242	149

'CCDC120 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S213. Gene #27: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
CCDC120 MUTATED	0	0	3	1	0	0
CCDC120 WILD-TYPE	80	90	174	137	90	91

'CCDC120 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 0.84

Table S214. Gene #27: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
CCDC120 MUTATED	0	1	3
CCDC120 WILD-TYPE	214	147	293

'CCDC120 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S215. Gene #27: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
CCDC120 MUTATED	0	4	0
CCDC120 WILD-TYPE	72	472	110

'SLC6A14 MUTATION STATUS' versus 'CN_CNMF'

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

Table S216. Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
SLC6A14 MUTATED	2	1	2
SLC6A14 WILD-TYPE	178	241	241

'SLC6A14 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.1 (Fisher's exact test), Q value = 0.37

Table S217. Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
SLC6A14 MUTATED	1	0	2
SLC6A14 WILD-TYPE	102	255	117

'SLC6A14 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.757 (Fisher's exact test), Q value = 1

Table S218. Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
SLC6A14 MUTATED	1	2	1	1
SLC6A14 WILD-TYPE	97	172	244	148

'SLC6A14 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S219. Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
SLC6A14 MUTATED	1	1	0	1	1	1
SLC6A14 WILD-TYPE	79	89	177	137	89	90

'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.525 (Fisher's exact test), Q value = 1

Table S220. Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
SLC6A14 MUTATED	2	2	1
SLC6A14 WILD-TYPE	212	146	295

'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.423 (Fisher's exact test), Q value = 0.93

Table S221. Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
SLC6A14 MUTATED	1	3	1
SLC6A14 WILD-TYPE	71	473	109

'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.39

Table S222. Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
SLC6A14 MUTATED	1	1	2	0
SLC6A14 WILD-TYPE	75	59	40	99

'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.152 (Fisher's exact test), Q value = 0.48

Table S223. Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
SLC6A14 MUTATED	1	0	2	0	1
SLC6A14 WILD-TYPE	25	43	60	100	45

'CYP4F11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.451 (Fisher's exact test), Q value = 0.95

Table S224. Gene #29: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
CYP4F11 MUTATED	0	2	3
CYP4F11 WILD-TYPE	180	240	240

'CYP4F11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.785 (Fisher's exact test), Q value = 1

Table S225. Gene #29: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
CYP4F11 MUTATED	1	2	0
CYP4F11 WILD-TYPE	102	253	119

'CYP4F11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.86

Table S226. Gene #29: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
CYP4F11 MUTATED	0	3	2	0
CYP4F11 WILD-TYPE	98	171	243	149

'CYP4F11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S227. Gene #29: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
CYP4F11 MUTATED	0	1	1	2	1	0
CYP4F11 WILD-TYPE	80	89	176	136	89	91

'CYP4F11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 0.68

Table S228. Gene #29: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
CYP4F11 MUTATED	0	2	3
CYP4F11 WILD-TYPE	214	146	293

'CYP4F11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S229. Gene #29: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
CYP4F11 MUTATED	0	5	0
CYP4F11 WILD-TYPE	72	471	110

'STAG2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S230. Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
STAG2 MUTATED	4	5	5
STAG2 WILD-TYPE	176	237	238

'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.861 (Fisher's exact test), Q value = 1

Table S231. Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
STAG2 MUTATED	3	7	2
STAG2 WILD-TYPE	100	248	117

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 1

Table S232. Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
STAG2 MUTATED	3	5	3	3
STAG2 WILD-TYPE	95	169	242	146

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00624 (Fisher's exact test), Q value = 0.05

Table S233. Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
STAG2 MUTATED	0	6	1	4	3	0
STAG2 WILD-TYPE	80	84	176	134	87	91

Figure S119. Get High-res Image Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.58

Table S234. Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
STAG2 MUTATED	4	6	4
STAG2 WILD-TYPE	210	142	292

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 0.8

Table S235. Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
STAG2 MUTATED	0	13	1
STAG2 WILD-TYPE	72	463	109

'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.44

Table S236. Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
STAG2 MUTATED	1	1	4	3
STAG2 WILD-TYPE	75	59	38	96

'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.57

Table S237. Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
STAG2 MUTATED	0	1	5	3	0
STAG2 WILD-TYPE	26	42	57	97	46

'SKI MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0099

Table S238. Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
SKI MUTATED	7	2	0
SKI WILD-TYPE	173	240	243

Figure S120. Get High-res Image Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SKI MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.43

Table S239. Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
SKI MUTATED	2	2	4
SKI WILD-TYPE	101	253	115

'SKI MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.005

Table S240. Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
SKI MUTATED	3	0	0	6
SKI WILD-TYPE	95	174	245	143

Figure S121. Get High-res Image Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SKI MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00217 (Fisher's exact test), Q value = 0.021

Table S241. Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
SKI MUTATED	3	3	0	0	0	3
SKI WILD-TYPE	77	87	177	138	90	88

Figure S122. Get High-res Image Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SKI MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0097

Table S242. Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
SKI MUTATED	8	1	0
SKI WILD-TYPE	206	147	296

Figure S123. Get High-res Image Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SKI MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.19

Table S243. Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
SKI MUTATED	3	4	2
SKI WILD-TYPE	69	472	108

Figure S124. Get High-res Image Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.13

Table S244. Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
SKI MUTATED	1	2	3	0
SKI WILD-TYPE	75	58	39	99

Figure S125. Get High-res Image Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0614 (Fisher's exact test), Q value = 0.27

Table S245. Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
SKI MUTATED	0	1	4	0	1
SKI WILD-TYPE	26	42	58	100	45

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.956 (Fisher's exact test), Q value = 1

Table S246. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
ARID1A MUTATED	5	6	8
ARID1A WILD-TYPE	175	236	235

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S247. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
ARID1A MUTATED	2	9	5
ARID1A WILD-TYPE	101	246	114

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0828 (Fisher's exact test), Q value = 0.33

Table S248. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
ARID1A MUTATED	0	5	6	8
ARID1A WILD-TYPE	98	169	239	141

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S249. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
ARID1A MUTATED	0	4	3	4	4	4
ARID1A WILD-TYPE	80	86	174	134	86	87

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S250. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
ARID1A MUTATED	7	3	9
ARID1A WILD-TYPE	207	145	287

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 0.73

Table S251. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
ARID1A MUTATED	0	15	4
ARID1A WILD-TYPE	72	461	106

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.09

Table S252. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
ARID1A MUTATED	4	0	5	2
ARID1A WILD-TYPE	72	60	37	97

Figure S126. Get High-res Image Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.49

Table S253. Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
ARID1A MUTATED	3	2	3	3	0
ARID1A WILD-TYPE	23	41	59	97	46

'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 0.77

Table S254. Gene #33: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
EGFR MUTATED	0	3	4
EGFR WILD-TYPE	180	239	239

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.82

Table S255. Gene #33: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
EGFR MUTATED	0	4	0
EGFR WILD-TYPE	103	251	119

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 0.77

Table S256. Gene #33: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
EGFR MUTATED	0	3	4	0
EGFR WILD-TYPE	98	171	241	149

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.528 (Fisher's exact test), Q value = 1

Table S257. Gene #33: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
EGFR MUTATED	0	0	3	3	1	0
EGFR WILD-TYPE	80	90	174	135	89	91

'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.46

Table S258. Gene #33: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
EGFR MUTATED	0	2	4
EGFR WILD-TYPE	214	146	292

'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S259. Gene #33: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
EGFR MUTATED	0	6	0
EGFR WILD-TYPE	72	470	110

'DPCR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S260. Gene #34: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
DPCR1 MUTATED	2	3	3
DPCR1 WILD-TYPE	178	239	240

'DPCR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.799 (Fisher's exact test), Q value = 1

Table S261. Gene #34: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
DPCR1 MUTATED	2	5	1
DPCR1 WILD-TYPE	101	250	118

'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.829 (Fisher's exact test), Q value = 1

Table S262. Gene #34: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
DPCR1 MUTATED	2	2	3	1
DPCR1 WILD-TYPE	96	172	242	148

'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S263. Gene #34: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
DPCR1 MUTATED	1	1	2	3	0	1
DPCR1 WILD-TYPE	79	89	175	135	90	90

'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S264. Gene #34: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
DPCR1 MUTATED	2	2	4
DPCR1 WILD-TYPE	212	146	292

'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S265. Gene #34: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
DPCR1 MUTATED	1	6	1
DPCR1 WILD-TYPE	71	470	109

'GUSB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 0.89

Table S266. Gene #35: 'GUSB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
GUSB MUTATED	0	3	1
GUSB WILD-TYPE	180	239	242

'GUSB MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S267. Gene #35: 'GUSB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
GUSB MUTATED	0	2	2	0
GUSB WILD-TYPE	98	172	243	149

'GUSB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 0.85

Table S268. Gene #35: 'GUSB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
GUSB MUTATED	0	0	1	3	0	0
GUSB WILD-TYPE	80	90	176	135	90	91

'GUSB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.356 (Fisher's exact test), Q value = 0.84

Table S269. Gene #35: 'GUSB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
GUSB MUTATED	0	1	3
GUSB WILD-TYPE	214	147	293

'GUSB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S270. Gene #35: 'GUSB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
GUSB MUTATED	0	4	0
GUSB WILD-TYPE	72	472	110

'MED16 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.461 (Fisher's exact test), Q value = 0.96

Table S271. Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
MED16 MUTATED	0	1	3
MED16 WILD-TYPE	180	241	240

'MED16 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.422 (Fisher's exact test), Q value = 0.93

Table S272. Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
MED16 MUTATED	1	1	2
MED16 WILD-TYPE	102	254	117

'MED16 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S273. Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
MED16 MUTATED	1	1	1	1
MED16 WILD-TYPE	97	173	244	148

'MED16 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0417 (Fisher's exact test), Q value = 0.2

Table S274. Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
MED16 MUTATED	0	3	1	0	0	0
MED16 WILD-TYPE	80	87	176	138	90	91

Figure S127. Get High-res Image Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MED16 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S275. Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
MED16 MUTATED	2	1	1
MED16 WILD-TYPE	212	147	295

'MED16 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S276. Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
MED16 MUTATED	0	4	0
MED16 WILD-TYPE	72	472	110

'MED16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 0.88

Table S277. Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
MED16 MUTATED	1	1	1	0
MED16 WILD-TYPE	75	59	41	99

'MED16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 0.6

Table S278. Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
MED16 MUTATED	0	1	2	0	0
MED16 WILD-TYPE	26	42	60	100	46

'PTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 1

Table S279. Gene #37: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
PTCH1 MUTATED	1	3	4
PTCH1 WILD-TYPE	179	239	239

'PTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S280. Gene #37: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
PTCH1 MUTATED	0	4	1
PTCH1 WILD-TYPE	103	251	118

'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S281. Gene #37: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
PTCH1 MUTATED	0	2	5	1
PTCH1 WILD-TYPE	98	172	240	148

'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 0.82

Table S282. Gene #37: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
PTCH1 MUTATED	0	0	5	2	0	1
PTCH1 WILD-TYPE	80	90	172	136	90	90

'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 0.77

Table S283. Gene #37: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
PTCH1 MUTATED	1	1	6
PTCH1 WILD-TYPE	213	147	290

'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S284. Gene #37: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
PTCH1 MUTATED	0	7	1
PTCH1 WILD-TYPE	72	469	109

'AHNAK2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.73

Table S285. Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	17	9	14
AHNAK2 MUTATED	3	0	0	2
AHNAK2 WILD-TYPE	18	17	9	12

'AHNAK2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.12

Table S286. Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	17	14	10	9
AHNAK2 MUTATED	0	0	2	3	0
AHNAK2 WILD-TYPE	11	17	12	7	9

Figure S128. Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'AHNAK2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S287. Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
AHNAK2 MUTATED	10	9	14
AHNAK2 WILD-TYPE	170	233	229

'AHNAK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.17

Table S288. Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
AHNAK2 MUTATED	11	10	4
AHNAK2 WILD-TYPE	92	245	115

Figure S129. Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'AHNAK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00588 (Fisher's exact test), Q value = 0.048

Table S289. Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
AHNAK2 MUTATED	10	2	12	9
AHNAK2 WILD-TYPE	88	172	233	140

Figure S130. Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'AHNAK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0073

Table S290. Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
AHNAK2 MUTATED	10	6	4	1	8	4
AHNAK2 WILD-TYPE	70	84	173	137	82	87

Figure S131. Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.1

Table S291. Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
AHNAK2 MUTATED	18	3	12
AHNAK2 WILD-TYPE	196	145	284

Figure S132. Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0068 (Fisher's exact test), Q value = 0.052

Table S292. Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
AHNAK2 MUTATED	9	17	7
AHNAK2 WILD-TYPE	63	459	103

Figure S133. Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S293. Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
AHNAK2 MUTATED	5	5	2	4
AHNAK2 WILD-TYPE	71	55	40	95

'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.73

Table S294. Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
AHNAK2 MUTATED	1	4	3	3	5
AHNAK2 WILD-TYPE	25	39	59	97	41

'RLIM MUTATION STATUS' versus 'CN_CNMF'

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

Table S295. Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
RLIM MUTATED	3	4	2
RLIM WILD-TYPE	177	238	241

'RLIM MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S296. Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
RLIM MUTATED	2	3	3
RLIM WILD-TYPE	101	252	116

'RLIM MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S297. Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
RLIM MUTATED	2	2	2	3
RLIM WILD-TYPE	96	172	243	146

'RLIM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S298. Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
RLIM MUTATED	2	2	2	2	0	1
RLIM WILD-TYPE	78	88	175	136	90	90

'RLIM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.081 (Fisher's exact test), Q value = 0.32

Table S299. Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
RLIM MUTATED	6	0	3
RLIM WILD-TYPE	208	148	293

'RLIM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S300. Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
RLIM MUTATED	1	7	1
RLIM WILD-TYPE	71	469	109

'RLIM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S301. Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
RLIM MUTATED	1	1	1	1
RLIM WILD-TYPE	75	59	41	98

'RLIM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S302. Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
RLIM MUTATED	0	1	1	1	1
RLIM WILD-TYPE	26	42	61	99	45

'SLC23A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S303. Gene #40: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
SLC23A1 MUTATED	1	3	3
SLC23A1 WILD-TYPE	179	239	240

'SLC23A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S304. Gene #40: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
SLC23A1 MUTATED	0	3	2
SLC23A1 WILD-TYPE	103	252	117

'SLC23A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 0.47

Table S305. Gene #40: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
SLC23A1 MUTATED	0	0	5	2
SLC23A1 WILD-TYPE	98	174	240	147

'SLC23A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 0.66

Table S306. Gene #40: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
SLC23A1 MUTATED	0	1	2	0	3	1
SLC23A1 WILD-TYPE	80	89	175	138	87	90

'SLC23A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S307. Gene #40: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
SLC23A1 MUTATED	2	1	4
SLC23A1 WILD-TYPE	212	147	292

'SLC23A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S308. Gene #40: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
SLC23A1 MUTATED	0	5	2
SLC23A1 WILD-TYPE	72	471	108

'STAM MUTATION STATUS' versus 'CN_CNMF'

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

Table S309. Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
STAM MUTATED	2	2	2
STAM WILD-TYPE	178	240	241

'STAM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.09

Table S310. Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
STAM MUTATED	4	1	0
STAM WILD-TYPE	99	254	119

Figure S134. Get High-res Image Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'STAM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 0.81

Table S311. Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
STAM MUTATED	2	2	2	0
STAM WILD-TYPE	96	172	243	149

'STAM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.106 (Fisher's exact test), Q value = 0.39

Table S312. Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
STAM MUTATED	1	3	1	0	1	0
STAM WILD-TYPE	79	87	176	138	89	91

'STAM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 0.79

Table S313. Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
STAM MUTATED	1	3	2
STAM WILD-TYPE	213	145	294

'STAM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.508 (Fisher's exact test), Q value = 1

Table S314. Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
STAM MUTATED	1	5	0
STAM WILD-TYPE	71	471	110

'STAM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00298 (Fisher's exact test), Q value = 0.026

Table S315. Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
STAM MUTATED	0	0	3	0
STAM WILD-TYPE	76	60	39	99

Figure S135. Get High-res Image Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'STAM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0575 (Fisher's exact test), Q value = 0.26

Table S316. Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
STAM MUTATED	0	0	3	0	0
STAM WILD-TYPE	26	43	59	100	46

'RHEB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 1

Table S317. Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
RHEB MUTATED	0	2	2
RHEB WILD-TYPE	180	240	241

'RHEB MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S318. Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
RHEB MUTATED	0	2	1
RHEB WILD-TYPE	103	253	118

'RHEB MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S319. Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
RHEB MUTATED	0	1	2	1
RHEB WILD-TYPE	98	173	243	148

'RHEB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.178 (Fisher's exact test), Q value = 0.53

Table S320. Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
RHEB MUTATED	0	1	0	1	2	0
RHEB WILD-TYPE	80	89	177	137	88	91

'RHEB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.62

Table S321. Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
RHEB MUTATED	0	2	2
RHEB WILD-TYPE	214	146	294

'RHEB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S322. Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
RHEB MUTATED	0	4	0
RHEB WILD-TYPE	72	472	110

'RHEB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.95

Table S323. Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
RHEB MUTATED	0	0	1	2
RHEB WILD-TYPE	76	60	41	97

'RHEB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S324. Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
RHEB MUTATED	0	0	1	2	0
RHEB WILD-TYPE	26	43	61	98	46

'SLC4A8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 0.49

Table S325. Gene #43: 'SLC4A8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
SLC4A8 MUTATED	2	0	4
SLC4A8 WILD-TYPE	178	242	239

'SLC4A8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 0.85

Table S326. Gene #43: 'SLC4A8 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
SLC4A8 MUTATED	2	4	0
SLC4A8 WILD-TYPE	101	251	119

'SLC4A8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.48

Table S327. Gene #43: 'SLC4A8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
SLC4A8 MUTATED	2	3	1	0
SLC4A8 WILD-TYPE	96	171	244	149

'SLC4A8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.428 (Fisher's exact test), Q value = 0.93

Table S328. Gene #43: 'SLC4A8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
SLC4A8 MUTATED	2	0	2	2	0	0
SLC4A8 WILD-TYPE	78	90	175	136	90	91

'SLC4A8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S329. Gene #43: 'SLC4A8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
SLC4A8 MUTATED	2	1	3
SLC4A8 WILD-TYPE	212	147	293

'SLC4A8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 0.57

Table S330. Gene #43: 'SLC4A8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
SLC4A8 MUTATED	2	4	0
SLC4A8 WILD-TYPE	70	472	110

'RUFY3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 0.62

Table S331. Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
RUFY3 MUTATED	4	2	1
RUFY3 WILD-TYPE	176	240	242

'RUFY3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.93

Table S332. Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
RUFY3 MUTATED	1	1	2
RUFY3 WILD-TYPE	102	254	117

'RUFY3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 0.68

Table S333. Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
RUFY3 MUTATED	2	1	1	3
RUFY3 WILD-TYPE	96	173	244	146

'RUFY3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 0.43

Table S334. Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
RUFY3 MUTATED	2	0	1	1	0	3
RUFY3 WILD-TYPE	78	90	176	137	90	88

'RUFY3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0766 (Fisher's exact test), Q value = 0.31

Table S335. Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
RUFY3 MUTATED	5	0	2
RUFY3 WILD-TYPE	209	148	294

'RUFY3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.12

Table S336. Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
RUFY3 MUTATED	2	2	3
RUFY3 WILD-TYPE	70	474	107

Figure S136. Get High-res Image Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PCK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S337. Gene #45: 'PCK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
PCK1 MUTATED	1	2	3
PCK1 WILD-TYPE	179	240	240

'PCK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 0.93

Table S338. Gene #45: 'PCK1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
PCK1 MUTATED	0	3	0
PCK1 WILD-TYPE	103	252	119

'PCK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.845 (Fisher's exact test), Q value = 1

Table S339. Gene #45: 'PCK1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
PCK1 MUTATED	0	2	3	1
PCK1 WILD-TYPE	98	172	242	148

'PCK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S340. Gene #45: 'PCK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
PCK1 MUTATED	0	0	1	2	2	1
PCK1 WILD-TYPE	80	90	176	136	88	90

'PCK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S341. Gene #45: 'PCK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
PCK1 MUTATED	1	1	4
PCK1 WILD-TYPE	213	147	292

'PCK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S342. Gene #45: 'PCK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
PCK1 MUTATED	0	5	1
PCK1 WILD-TYPE	72	471	109

'TXNIP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 0.54

Table S343. Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
TXNIP MUTATED	0	4	4
TXNIP WILD-TYPE	180	238	239

'TXNIP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.79

Table S344. Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
TXNIP MUTATED	2	5	0
TXNIP WILD-TYPE	101	250	119

'TXNIP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 0.89

Table S345. Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
TXNIP MUTATED	2	2	4	0
TXNIP WILD-TYPE	96	172	241	149

'TXNIP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S346. Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
TXNIP MUTATED	0	2	2	3	1	0
TXNIP WILD-TYPE	80	88	175	135	89	91

'TXNIP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 0.77

Table S347. Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
TXNIP MUTATED	1	1	6
TXNIP WILD-TYPE	213	147	290

'TXNIP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 0.92

Table S348. Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
TXNIP MUTATED	0	8	0
TXNIP WILD-TYPE	72	468	110

'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 1

Table S349. Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
TXNIP MUTATED	0	1	1	2
TXNIP WILD-TYPE	76	59	41	97

'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S350. Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
TXNIP MUTATED	0	0	2	2	0
TXNIP WILD-TYPE	26	43	60	98	46

'RNF128 MUTATION STATUS' versus 'CN_CNMF'

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

Table S351. Gene #47: 'RNF128 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
RNF128 MUTATED	1	3	1
RNF128 WILD-TYPE	179	239	242

'RNF128 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 0.53

Table S352. Gene #47: 'RNF128 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
RNF128 MUTATED	2	1	0
RNF128 WILD-TYPE	101	254	119

'RNF128 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S353. Gene #47: 'RNF128 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
RNF128 MUTATED	1	1	1	2
RNF128 WILD-TYPE	97	173	244	147

'RNF128 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S354. Gene #47: 'RNF128 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
RNF128 MUTATED	1	1	2	0	0	1
RNF128 WILD-TYPE	79	89	175	138	90	90

'RNF128 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.88

Table S355. Gene #47: 'RNF128 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
RNF128 MUTATED	3	0	2
RNF128 WILD-TYPE	211	148	294

'RNF128 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S356. Gene #47: 'RNF128 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
RNF128 MUTATED	0	4	1
RNF128 WILD-TYPE	72	472	109

'ZFYVE26 MUTATION STATUS' versus 'CN_CNMF'

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

Table S357. Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
ZFYVE26 MUTATED	2	4	3
ZFYVE26 WILD-TYPE	178	238	240

'ZFYVE26 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 0.99

Table S358. Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
ZFYVE26 MUTATED	0	5	1
ZFYVE26 WILD-TYPE	103	250	118

'ZFYVE26 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S359. Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
ZFYVE26 MUTATED	0	3	4	2
ZFYVE26 WILD-TYPE	98	171	241	147

'ZFYVE26 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.366 (Fisher's exact test), Q value = 0.85

Table S360. Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
ZFYVE26 MUTATED	0	0	4	3	0	2
ZFYVE26 WILD-TYPE	80	90	173	135	90	89

'ZFYVE26 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S361. Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
ZFYVE26 MUTATED	2	2	5
ZFYVE26 WILD-TYPE	212	146	291

'ZFYVE26 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S362. Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
ZFYVE26 MUTATED	0	7	2
ZFYVE26 WILD-TYPE	72	469	108

'ZFYVE26 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S363. Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
ZFYVE26 MUTATED	2	0	0	1
ZFYVE26 WILD-TYPE	74	60	42	98

'ZFYVE26 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.259 (Fisher's exact test), Q value = 0.71

Table S364. Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
ZFYVE26 MUTATED	0	2	0	1	0
ZFYVE26 WILD-TYPE	26	41	62	99	46

'FAM160B2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.844 (Fisher's exact test), Q value = 1

Table S365. Gene #49: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
FAM160B2 MUTATED	1	2	1
FAM160B2 WILD-TYPE	179	240	242

'FAM160B2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S366. Gene #49: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
FAM160B2 MUTATED	1	2	1
FAM160B2 WILD-TYPE	102	253	118

'FAM160B2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S367. Gene #49: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
FAM160B2 MUTATED	1	1	1	1
FAM160B2 WILD-TYPE	97	173	244	148

'FAM160B2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S368. Gene #49: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
FAM160B2 MUTATED	1	0	1	1	0	1
FAM160B2 WILD-TYPE	79	90	176	137	90	90

'FAM160B2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.445 (Fisher's exact test), Q value = 0.95

Table S369. Gene #49: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
FAM160B2 MUTATED	1	2	1
FAM160B2 WILD-TYPE	213	146	295

'FAM160B2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.727 (Fisher's exact test), Q value = 1

Table S370. Gene #49: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
FAM160B2 MUTATED	0	3	1
FAM160B2 WILD-TYPE	72	473	109

'FAM47A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S371. Gene #50: 'FAM47A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
FAM47A MUTATED	1	2	3
FAM47A WILD-TYPE	179	240	240

'FAM47A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S372. Gene #50: 'FAM47A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
FAM47A MUTATED	1	2	1
FAM47A WILD-TYPE	102	253	118

'FAM47A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S373. Gene #50: 'FAM47A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
FAM47A MUTATED	1	1	2	2
FAM47A WILD-TYPE	97	173	243	147

'FAM47A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S374. Gene #50: 'FAM47A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
FAM47A MUTATED	1	1	1	1	2	0
FAM47A WILD-TYPE	79	89	176	137	88	91

'FAM47A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 1

Table S375. Gene #50: 'FAM47A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
FAM47A MUTATED	2	0	4
FAM47A WILD-TYPE	212	148	292

'FAM47A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S376. Gene #50: 'FAM47A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
FAM47A MUTATED	1	4	1
FAM47A WILD-TYPE	71	472	109

'ATP1A1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.253 (Fisher's exact test), Q value = 0.7

Table S377. Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	17	9	14
ATP1A1 MUTATED	0	1	1	2
ATP1A1 WILD-TYPE	21	16	8	12

'ATP1A1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S378. Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	17	14	10	9
ATP1A1 MUTATED	0	1	2	0	1
ATP1A1 WILD-TYPE	11	16	12	10	8

'ATP1A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.46

Table S379. Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
ATP1A1 MUTATED	5	4	1
ATP1A1 WILD-TYPE	175	238	242

'ATP1A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S380. Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
ATP1A1 MUTATED	0	2	1
ATP1A1 WILD-TYPE	103	253	118

'ATP1A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.43

Table S381. Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
ATP1A1 MUTATED	2	0	4	4
ATP1A1 WILD-TYPE	96	174	241	145

'ATP1A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S382. Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
ATP1A1 MUTATED	1	1	3	1	1	3
ATP1A1 WILD-TYPE	79	89	174	137	89	88

'ATP1A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.51

Table S383. Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
ATP1A1 MUTATED	5	0	5
ATP1A1 WILD-TYPE	209	148	291

'ATP1A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S384. Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
ATP1A1 MUTATED	1	6	3
ATP1A1 WILD-TYPE	71	470	107

'SH3BP2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.068 (Fisher's exact test), Q value = 0.29

Table S385. Gene #52: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
SH3BP2 MUTATED	3	1	0
SH3BP2 WILD-TYPE	177	241	243

'SH3BP2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.73

Table S386. Gene #52: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
SH3BP2 MUTATED	0	1	2
SH3BP2 WILD-TYPE	103	254	117

'SH3BP2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.39

Table S387. Gene #52: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
SH3BP2 MUTATED	0	0	1	3
SH3BP2 WILD-TYPE	98	174	244	146

'SH3BP2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0922 (Fisher's exact test), Q value = 0.35

Table S388. Gene #52: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
SH3BP2 MUTATED	0	1	0	0	1	2
SH3BP2 WILD-TYPE	80	89	177	138	89	89

'SH3BP2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.73

Table S389. Gene #52: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
SH3BP2 MUTATED	3	0	1
SH3BP2 WILD-TYPE	211	148	295

'SH3BP2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.57

Table S390. Gene #52: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
SH3BP2 MUTATED	0	2	2
SH3BP2 WILD-TYPE	72	474	108

'FAM200A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 0.95

Table S391. Gene #53: 'FAM200A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
FAM200A MUTATED	0	2	3
FAM200A WILD-TYPE	180	240	240

'FAM200A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0574 (Fisher's exact test), Q value = 0.26

Table S392. Gene #53: 'FAM200A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
FAM200A MUTATED	0	0	5	0
FAM200A WILD-TYPE	98	174	240	149

'FAM200A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00703 (Fisher's exact test), Q value = 0.053

Table S393. Gene #53: 'FAM200A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
FAM200A MUTATED	0	0	1	0	4	0
FAM200A WILD-TYPE	80	90	176	138	86	91

Figure S137. Get High-res Image Gene #53: 'FAM200A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FAM200A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.58

Table S394. Gene #53: 'FAM200A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
FAM200A MUTATED	0	1	4
FAM200A WILD-TYPE	214	147	292

'FAM200A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.769 (Fisher's exact test), Q value = 1

Table S395. Gene #53: 'FAM200A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
FAM200A MUTATED	0	5	0
FAM200A WILD-TYPE	72	471	110

'RTL1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S396. Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
RTL1 MUTATED	2	1	4
RTL1 WILD-TYPE	178	241	239

'RTL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S397. Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
RTL1 MUTATED	2	4	1
RTL1 WILD-TYPE	101	251	118

'RTL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.078 (Fisher's exact test), Q value = 0.32

Table S398. Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
RTL1 MUTATED	2	3	0	2
RTL1 WILD-TYPE	96	171	245	147

'RTL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.338 (Fisher's exact test), Q value = 0.82

Table S399. Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
RTL1 MUTATED	2	2	1	2	0	0
RTL1 WILD-TYPE	78	88	176	136	90	91

'RTL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S400. Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
RTL1 MUTATED	4	1	2
RTL1 WILD-TYPE	210	147	294

'RTL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0812 (Fisher's exact test), Q value = 0.32

Table S401. Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
RTL1 MUTATED	2	3	2
RTL1 WILD-TYPE	70	473	108

'RTL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S402. Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
RTL1 MUTATED	1	1	0	1
RTL1 WILD-TYPE	75	59	42	98

'RTL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 0.66

Table S403. Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
RTL1 MUTATED	0	0	2	0	1
RTL1 WILD-TYPE	26	43	60	100	45

'NASP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 0.79

Table S404. Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
NASP MUTATED	2	0	2
NASP WILD-TYPE	178	242	241

'NASP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.068 (Fisher's exact test), Q value = 0.29

Table S405. Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
NASP MUTATED	3	1	0
NASP WILD-TYPE	100	254	119

'NASP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.19

Table S406. Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
NASP MUTATED	2	2	0	0
NASP WILD-TYPE	96	172	245	149

Figure S138. Get High-res Image Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NASP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.44

Table S407. Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
NASP MUTATED	2	1	0	1	0	0
NASP WILD-TYPE	78	89	177	137	90	91

'NASP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.73

Table S408. Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
NASP MUTATED	3	0	1
NASP WILD-TYPE	211	148	295

'NASP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.38

Table S409. Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
NASP MUTATED	2	2	0
NASP WILD-TYPE	70	474	110

'NASP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0877 (Fisher's exact test), Q value = 0.34

Table S410. Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
NASP MUTATED	0	2	1	0
NASP WILD-TYPE	76	58	41	99

'NASP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.46

Table S411. Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
NASP MUTATED	0	0	1	0	2
NASP WILD-TYPE	26	43	61	100	44

'RPL7A MUTATION STATUS' versus 'CN_CNMF'

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

Table S412. Gene #56: 'RPL7A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
RPL7A MUTATED	1	1	1
RPL7A WILD-TYPE	179	241	242

'RPL7A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0987 (Fisher's exact test), Q value = 0.37

Table S413. Gene #56: 'RPL7A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
RPL7A MUTATED	1	0	2
RPL7A WILD-TYPE	102	255	117

'RPL7A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0851 (Fisher's exact test), Q value = 0.33

Table S414. Gene #56: 'RPL7A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
RPL7A MUTATED	1	0	0	2
RPL7A WILD-TYPE	97	174	245	147

'RPL7A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0756 (Fisher's exact test), Q value = 0.31

Table S415. Gene #56: 'RPL7A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
RPL7A MUTATED	0	2	0	0	0	1
RPL7A WILD-TYPE	80	88	177	138	90	90

'RPL7A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 0.66

Table S416. Gene #56: 'RPL7A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
RPL7A MUTATED	2	1	0
RPL7A WILD-TYPE	212	147	296

'RPL7A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 0.39

Table S417. Gene #56: 'RPL7A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
RPL7A MUTATED	0	1	2
RPL7A WILD-TYPE	72	475	108

'UIMC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 1

Table S418. Gene #57: 'UIMC1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
UIMC1 MUTATED	1	3	1
UIMC1 WILD-TYPE	179	239	242

'UIMC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.82

Table S419. Gene #57: 'UIMC1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
UIMC1 MUTATED	0	4	0
UIMC1 WILD-TYPE	103	251	119

'UIMC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S420. Gene #57: 'UIMC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
UIMC1 MUTATED	0	2	2	1
UIMC1 WILD-TYPE	98	172	243	148

'UIMC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.463 (Fisher's exact test), Q value = 0.96

Table S421. Gene #57: 'UIMC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
UIMC1 MUTATED	0	1	1	3	0	0
UIMC1 WILD-TYPE	80	89	176	135	90	91

'UIMC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0956 (Fisher's exact test), Q value = 0.36

Table S422. Gene #57: 'UIMC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
UIMC1 MUTATED	0	3	2
UIMC1 WILD-TYPE	214	145	294

'UIMC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S423. Gene #57: 'UIMC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
UIMC1 MUTATED	0	5	0
UIMC1 WILD-TYPE	72	471	110

'TCEB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0686 (Fisher's exact test), Q value = 0.29

Table S424. Gene #58: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
TCEB1 MUTATED	0	3	0
TCEB1 WILD-TYPE	180	239	243

'TCEB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S425. Gene #58: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
TCEB1 MUTATED	0	1	2	0
TCEB1 WILD-TYPE	98	173	243	149

'TCEB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S426. Gene #58: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
TCEB1 MUTATED	0	0	2	0	1	0
TCEB1 WILD-TYPE	80	90	175	138	89	91

'TCEB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.5

Table S427. Gene #58: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
TCEB1 MUTATED	0	2	1
TCEB1 WILD-TYPE	214	146	295

'TCEB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S428. Gene #58: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
TCEB1 MUTATED	0	3	0
TCEB1 WILD-TYPE	72	473	110

'SFMBT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S429. Gene #59: 'SFMBT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
SFMBT1 MUTATED	1	0	2
SFMBT1 WILD-TYPE	179	242	241

'SFMBT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 1

Table S430. Gene #59: 'SFMBT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
SFMBT1 MUTATED	0	0	2	1
SFMBT1 WILD-TYPE	98	174	243	148

'SFMBT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S431. Gene #59: 'SFMBT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
SFMBT1 MUTATED	0	0	1	0	1	1
SFMBT1 WILD-TYPE	80	90	176	138	89	90

'SFMBT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S432. Gene #59: 'SFMBT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
SFMBT1 MUTATED	1	0	2
SFMBT1 WILD-TYPE	213	148	294

'SFMBT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S433. Gene #59: 'SFMBT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
SFMBT1 MUTATED	0	2	1
SFMBT1 WILD-TYPE	72	474	109

'SLC16A1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S434. Gene #60: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
SLC16A1 MUTATED	1	1	1
SLC16A1 WILD-TYPE	179	241	242

'SLC16A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S435. Gene #60: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
SLC16A1 MUTATED	0	2	1
SLC16A1 WILD-TYPE	103	253	118

'SLC16A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S436. Gene #60: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
SLC16A1 MUTATED	0	1	1	1
SLC16A1 WILD-TYPE	98	173	244	148

'SLC16A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S437. Gene #60: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
SLC16A1 MUTATED	0	0	1	1	0	1
SLC16A1 WILD-TYPE	80	90	176	137	90	90

'SLC16A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S438. Gene #60: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
SLC16A1 MUTATED	1	0	2
SLC16A1 WILD-TYPE	213	148	294

'SLC16A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S439. Gene #60: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
SLC16A1 MUTATED	0	2	1
SLC16A1 WILD-TYPE	72	474	109

'PAM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.11

Table S440. Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
PAM MUTATED	3	0	0
PAM WILD-TYPE	177	242	243

Figure S139. Get High-res Image Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PAM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00585 (Fisher's exact test), Q value = 0.048

Table S441. Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
PAM MUTATED	0	0	4
PAM WILD-TYPE	103	255	115

Figure S140. Get High-res Image Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PAM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0027 (Fisher's exact test), Q value = 0.025

Table S442. Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
PAM MUTATED	0	0	0	4
PAM WILD-TYPE	98	174	245	145

Figure S141. Get High-res Image Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PAM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.094

Table S443. Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
PAM MUTATED	0	1	0	0	0	3
PAM WILD-TYPE	80	89	177	138	90	88

Figure S142. Get High-res Image Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PAM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.09

Table S444. Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
PAM MUTATED	4	0	0
PAM WILD-TYPE	210	148	296

Figure S143. Get High-res Image Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PAM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0098

Table S445. Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
PAM MUTATED	0	0	4
PAM WILD-TYPE	72	476	106

Figure S144. Get High-res Image Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TMCO3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0782 (Fisher's exact test), Q value = 0.32

Table S446. Gene #62: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
TMCO3 MUTATED	2	0	5
TMCO3 WILD-TYPE	178	242	238

'TMCO3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.73

Table S447. Gene #62: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
TMCO3 MUTATED	0	1	2
TMCO3 WILD-TYPE	103	254	117

'TMCO3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S448. Gene #62: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
TMCO3 MUTATED	0	2	3	2
TMCO3 WILD-TYPE	98	172	242	147

'TMCO3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0806 (Fisher's exact test), Q value = 0.32

Table S449. Gene #62: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
TMCO3 MUTATED	0	1	0	1	3	2
TMCO3 WILD-TYPE	80	89	177	137	87	89

'TMCO3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 0.88

Table S450. Gene #62: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
TMCO3 MUTATED	3	0	4
TMCO3 WILD-TYPE	211	148	292

'TMCO3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S451. Gene #62: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
TMCO3 MUTATED	0	6	1
TMCO3 WILD-TYPE	72	470	109

'CCDC82 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.12

Table S452. Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
CCDC82 MUTATED	1	5	0
CCDC82 WILD-TYPE	179	237	243

Figure S145. Get High-res Image Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CCDC82 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 0.77

Table S453. Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
CCDC82 MUTATED	1	5	0
CCDC82 WILD-TYPE	102	250	119

'CCDC82 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0897 (Fisher's exact test), Q value = 0.34

Table S454. Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
CCDC82 MUTATED	1	0	5	0
CCDC82 WILD-TYPE	97	174	240	149

'CCDC82 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.09

Table S455. Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
CCDC82 MUTATED	1	0	1	0	4	0
CCDC82 WILD-TYPE	79	90	176	138	86	91

Figure S146. Get High-res Image Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CCDC82 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.73

Table S456. Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
CCDC82 MUTATED	1	0	5
CCDC82 WILD-TYPE	213	148	291

'CCDC82 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.509 (Fisher's exact test), Q value = 1

Table S457. Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
CCDC82 MUTATED	1	5	0
CCDC82 WILD-TYPE	71	471	110

'NFAT5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S458. Gene #64: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
NFAT5 MUTATED	3	3	2
NFAT5 WILD-TYPE	177	239	241

'NFAT5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 1

Table S459. Gene #64: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
NFAT5 MUTATED	1	6	1
NFAT5 WILD-TYPE	102	249	118

'NFAT5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 1

Table S460. Gene #64: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
NFAT5 MUTATED	1	4	2	1
NFAT5 WILD-TYPE	97	170	243	148

'NFAT5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 1

Table S461. Gene #64: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
NFAT5 MUTATED	1	1	4	2	0	0
NFAT5 WILD-TYPE	79	89	173	136	90	91

'NFAT5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.728 (Fisher's exact test), Q value = 1

Table S462. Gene #64: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
NFAT5 MUTATED	2	1	5
NFAT5 WILD-TYPE	212	147	291

'NFAT5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S463. Gene #64: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
NFAT5 MUTATED	1	6	1
NFAT5 WILD-TYPE	71	470	109

'HNF1B MUTATION STATUS' versus 'CN_CNMF'

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

Table S464. Gene #65: 'HNF1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
HNF1B MUTATED	1	0	2
HNF1B WILD-TYPE	179	242	241

'HNF1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.786 (Fisher's exact test), Q value = 1

Table S465. Gene #65: 'HNF1B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
HNF1B MUTATED	1	2	0
HNF1B WILD-TYPE	102	253	119

'HNF1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.95

Table S466. Gene #65: 'HNF1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
HNF1B MUTATED	1	0	2	0
HNF1B WILD-TYPE	97	174	243	149

'HNF1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S467. Gene #65: 'HNF1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
HNF1B MUTATED	1	0	2	0	0	0
HNF1B WILD-TYPE	79	90	175	138	90	91

'HNF1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S468. Gene #65: 'HNF1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
HNF1B MUTATED	1	0	2
HNF1B WILD-TYPE	213	148	294

'HNF1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.359 (Fisher's exact test), Q value = 0.84

Table S469. Gene #65: 'HNF1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
HNF1B MUTATED	1	2	0
HNF1B WILD-TYPE	71	474	110

'OR2L8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.708 (Fisher's exact test), Q value = 1

Table S470. Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
OR2L8 MUTATED	3	2	2
OR2L8 WILD-TYPE	177	240	241

'OR2L8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S471. Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
OR2L8 MUTATED	1	3	3
OR2L8 WILD-TYPE	102	252	116

'OR2L8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S472. Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
OR2L8 MUTATED	1	1	2	3
OR2L8 WILD-TYPE	97	173	243	146

'OR2L8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.084 (Fisher's exact test), Q value = 0.33

Table S473. Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
OR2L8 MUTATED	0	1	0	1	2	3
OR2L8 WILD-TYPE	80	89	177	137	88	88

'OR2L8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 0.95

Table S474. Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
OR2L8 MUTATED	2	3	2
OR2L8 WILD-TYPE	212	145	294

'OR2L8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S475. Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
OR2L8 MUTATED	0	5	2
OR2L8 WILD-TYPE	72	471	108

'OR2L8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.2

Table S476. Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
OR2L8 MUTATED	2	0	2	0
OR2L8 WILD-TYPE	74	60	40	99

Figure S147. Get High-res Image Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'OR2L8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.46

Table S477. Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
OR2L8 MUTATED	1	1	2	0	0
OR2L8 WILD-TYPE	25	42	60	100	46

'IDUA MUTATION STATUS' versus 'CN_CNMF'

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

Table S478. Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
IDUA MUTATED	1	3	1
IDUA WILD-TYPE	179	239	242

'IDUA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.43

Table S479. Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
IDUA MUTATED	1	1	3
IDUA WILD-TYPE	102	254	116

'IDUA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00693 (Fisher's exact test), Q value = 0.053

Table S480. Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
IDUA MUTATED	1	0	0	4
IDUA WILD-TYPE	97	174	245	145

Figure S148. Get High-res Image Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'IDUA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.096

Table S481. Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
IDUA MUTATED	1	3	0	0	0	1
IDUA WILD-TYPE	79	87	177	138	90	90

Figure S149. Get High-res Image Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'IDUA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.18

Table S482. Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
IDUA MUTATED	4	1	0
IDUA WILD-TYPE	210	147	296

Figure S150. Get High-res Image Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'IDUA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0531 (Fisher's exact test), Q value = 0.24

Table S483. Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
IDUA MUTATED	0	2	3
IDUA WILD-TYPE	72	474	107

'IDUA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 0.79

Table S484. Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
IDUA MUTATED	2	1	1	0
IDUA WILD-TYPE	74	59	41	99

'IDUA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.142 (Fisher's exact test), Q value = 0.46

Table S485. Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
IDUA MUTATED	1	1	2	0	0
IDUA WILD-TYPE	25	42	60	100	46

'ZC3H18 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S486. Gene #68: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
ZC3H18 MUTATED	1	2	3
ZC3H18 WILD-TYPE	179	240	240

'ZC3H18 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 0.93

Table S487. Gene #68: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
ZC3H18 MUTATED	0	3	0
ZC3H18 WILD-TYPE	103	252	119

'ZC3H18 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S488. Gene #68: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
ZC3H18 MUTATED	0	2	2	2
ZC3H18 WILD-TYPE	98	172	243	147

'ZC3H18 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S489. Gene #68: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
ZC3H18 MUTATED	0	1	2	1	1	1
ZC3H18 WILD-TYPE	80	89	175	137	89	90

'ZC3H18 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S490. Gene #68: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
ZC3H18 MUTATED	2	2	2
ZC3H18 WILD-TYPE	212	146	294

'ZC3H18 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 0.87

Table S491. Gene #68: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
ZC3H18 MUTATED	0	4	2
ZC3H18 WILD-TYPE	72	472	108

'GAPDHS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S492. Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
GAPDHS MUTATED	1	1	3
GAPDHS WILD-TYPE	179	241	240

'GAPDHS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 0.71

Table S493. Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
GAPDHS MUTATED	2	1	2
GAPDHS WILD-TYPE	101	254	117

'GAPDHS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.48

Table S494. Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
GAPDHS MUTATED	1	0	1	3
GAPDHS WILD-TYPE	97	174	244	146

'GAPDHS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.09

Table S495. Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
GAPDHS MUTATED	1	3	0	0	1	0
GAPDHS WILD-TYPE	79	87	177	138	89	91

Figure S151. Get High-res Image Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'GAPDHS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.42

Table S496. Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
GAPDHS MUTATED	4	0	1
GAPDHS WILD-TYPE	210	148	295

'GAPDHS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.424 (Fisher's exact test), Q value = 0.93

Table S497. Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
GAPDHS MUTATED	1	3	1
GAPDHS WILD-TYPE	71	473	109

'GPR137 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 0.59

Table S498. Gene #70: 'GPR137 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
GPR137 MUTATED	1	0	3
GPR137 WILD-TYPE	179	242	240

'GPR137 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S499. Gene #70: 'GPR137 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
GPR137 MUTATED	1	1	1
GPR137 WILD-TYPE	102	254	118

'GPR137 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.75

Table S500. Gene #70: 'GPR137 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
GPR137 MUTATED	1	2	0	1
GPR137 WILD-TYPE	97	172	245	148

'GPR137 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.346 (Fisher's exact test), Q value = 0.83

Table S501. Gene #70: 'GPR137 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
GPR137 MUTATED	1	0	0	2	0	1
GPR137 WILD-TYPE	79	90	177	136	90	90

'GPR137 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 0.4

Table S502. Gene #70: 'GPR137 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
GPR137 MUTATED	2	2	0
GPR137 WILD-TYPE	212	146	296

'GPR137 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 0.77

Table S503. Gene #70: 'GPR137 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
GPR137 MUTATED	1	2	1
GPR137 WILD-TYPE	71	474	109

'GFM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 0.73

Table S504. Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
GFM1 MUTATED	2	0	1
GFM1 WILD-TYPE	178	242	242

'GFM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00997 (Fisher's exact test), Q value = 0.069

Table S505. Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
GFM1 MUTATED	3	0	0
GFM1 WILD-TYPE	100	255	119

Figure S152. Get High-res Image Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'GFM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.027

Table S506. Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
GFM1 MUTATED	3	0	0	0
GFM1 WILD-TYPE	95	174	245	149

Figure S153. Get High-res Image Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'GFM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00178 (Fisher's exact test), Q value = 0.018

Table S507. Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
GFM1 MUTATED	3	0	0	0	0	0
GFM1 WILD-TYPE	77	90	177	138	90	91

Figure S154. Get High-res Image Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'GFM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.21

Table S508. Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
GFM1 MUTATED	3	0	0
GFM1 WILD-TYPE	211	148	296

Figure S155. Get High-res Image Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'GFM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.012

Table S509. Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
GFM1 MUTATED	3	0	0
GFM1 WILD-TYPE	69	476	110

Figure S156. Get High-res Image Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.48

Table S510. Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
FAT1 MUTATED	10	5	7
FAT1 WILD-TYPE	170	237	236

'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.16

Table S511. Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
FAT1 MUTATED	4	5	9
FAT1 WILD-TYPE	99	250	110

Figure S157. Get High-res Image Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FAT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.007

Table S512. Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
FAT1 MUTATED	2	5	2	13
FAT1 WILD-TYPE	96	169	243	136

Figure S158. Get High-res Image Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.019

Table S513. Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
FAT1 MUTATED	1	9	2	3	1	6
FAT1 WILD-TYPE	79	81	175	135	89	85

Figure S159. Get High-res Image Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.14

Table S514. Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
FAT1 MUTATED	13	4	5
FAT1 WILD-TYPE	201	144	291

Figure S160. Get High-res Image Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 0.44

Table S515. Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
FAT1 MUTATED	1	14	7
FAT1 WILD-TYPE	71	462	103

'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.228 (Fisher's exact test), Q value = 0.65

Table S516. Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
FAT1 MUTATED	5	1	3	2
FAT1 WILD-TYPE	71	59	39	97

'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.068 (Fisher's exact test), Q value = 0.29

Table S517. Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
FAT1 MUTATED	1	2	6	1	1
FAT1 WILD-TYPE	25	41	56	99	45

'RRP12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 1

Table S518. Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	180	242	243
RRP12 MUTATED	3	3	3
RRP12 WILD-TYPE	177	239	240

'RRP12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.419 (Fisher's exact test), Q value = 0.93

Table S519. Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	103	255	119
RRP12 MUTATED	1	2	3
RRP12 WILD-TYPE	102	253	116

'RRP12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.97

Table S520. Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	174	245	149
RRP12 MUTATED	1	1	3	4
RRP12 WILD-TYPE	97	173	242	145

'RRP12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 0.95

Table S521. Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	80	90	177	138	90	91
RRP12 MUTATED	1	1	1	1	2	3
RRP12 WILD-TYPE	79	89	176	137	88	88

'RRP12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.287 (Fisher's exact test), Q value = 0.75

Table S522. Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	214	148	296
RRP12 MUTATED	5	2	2
RRP12 WILD-TYPE	209	146	294

'RRP12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.281 (Fisher's exact test), Q value = 0.73

Table S523. Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	476	110
RRP12 MUTATED	1	5	3
RRP12 WILD-TYPE	71	471	107

'RRP12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S524. Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	60	42	99
RRP12 MUTATED	2	1	0	2
RRP12 WILD-TYPE	74	59	42	97

'RRP12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S525. Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	43	62	100	46
RRP12 MUTATED	1	1	0	2	1
RRP12 WILD-TYPE	25	42	62	98	45

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/KIPAN-TP/15639742/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIPAN-TP/15165233/KIPAN-TP.transferedmergedcluster.txt
Number of patients = 668
Number of significantly mutated genes = 73
Number of Molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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