Correlation between copy number variation genes (focal events) and molecular subtypes

Colon Adenocarcinoma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1WH2NKJ

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 67 focal events and 12 molecular subtypes across 427 patients, 218 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_2q33.1 cnv correlated to 'CN_CNMF'.
amp_6p21.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'CN_CNMF'.
amp_8p11.21 cnv correlated to 'CN_CNMF'.
amp_8q12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_11p15.5 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q12.13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_13q22.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_16p11.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_16q12.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_17q12 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_17q24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF'.
amp_19q13.11 cnv correlated to 'CN_CNMF'.
amp_20p11.23 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_20q11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_20q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_20q13.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_1p36.11 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_1p33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p13.1 cnv correlated to 'CN_CNMF'.
del_1q43 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_3p26.1 cnv correlated to 'CN_CNMF'.
del_3q26.31 cnv correlated to 'CN_CNMF'.
del_4p16.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_4q22.1 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_4q35.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_5q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_5q21.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_5q23.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_8p23.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_8p22 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_8p11.21 cnv correlated to 'CN_CNMF'.
del_10p15.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_10q21.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
del_10q25.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_12p13.2 cnv correlated to 'CN_CNMF'.
del_14q32.11 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_15q21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_15q22.33 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_17p12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_18p11.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_18q12.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_18q21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_18q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_20p12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_22q13.32 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 67 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 218 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	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	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 20q11 21	306 (72%)	121	7.72e-10 (5.55e-07)	1.47e-11 (1.09e-08)	4.38e-39 (3.49e-36)	2.13e-12 (1.59e-09)	0.000753 (0.426)	0.000114 (0.0709)	2.93e-23 (2.31e-20)	2.01e-21 (1.56e-18)	0.809 (1.00)	0.000105 (0.0661)	2.36e-12 (1.76e-09)	0.146 (1.00)
amp 20q12	307 (72%)	120	8.9e-11 (6.51e-08)	7.64e-12 (5.68e-09)	2.02e-40 (1.61e-37)	1.84e-11 (1.35e-08)	0.000527 (0.303)	2.33e-05 (0.0152)	2.3e-22 (1.81e-19)	6.78e-21 (5.27e-18)	0.764 (1.00)	0.000127 (0.0783)	2.32e-13 (1.75e-10)	0.14 (1.00)
amp 20q13 32	310 (73%)	117	1.49e-09 (1.07e-06)	4.32e-12 (3.22e-09)	6.54e-41 (5.23e-38)	1.84e-11 (1.35e-08)	0.0006 (0.344)	1.41e-05 (0.00928)	4.87e-22 (3.8e-19)	7.33e-21 (5.68e-18)	0.78 (1.00)	0.000275 (0.164)	7.98e-13 (5.98e-10)	0.163 (1.00)
del 14q32 11	140 (33%)	287	1.11e-06 (0.000759)	3.13e-05 (0.0202)	4.19e-25 (3.32e-22)	0.000117 (0.0729)	0.000837 (0.47)	0.0118 (1.00)	4.38e-07 (0.000303)	1.85e-07 (0.000129)	0.197 (1.00)	0.000245 (0.147)	2.17e-05 (0.0142)	0.166 (1.00)
del 17p12	237 (56%)	190	2.85e-08 (2.01e-05)	5.25e-07 (0.000362)	2.19e-34 (1.74e-31)	1.25e-11 (9.25e-09)	0.0125 (1.00)	0.000163 (0.0989)	9.24e-19 (7.11e-16)	1.67e-14 (1.27e-11)	0.659 (1.00)	0.0359 (1.00)	2.38e-11 (1.74e-08)	0.0343 (1.00)
del 18q21 2	269 (63%)	158	5.08e-11 (3.72e-08)	1.75e-10 (1.27e-07)	2.05e-44 (1.65e-41)	6.96e-14 (5.26e-11)	0.00103 (0.567)	0.000238 (0.143)	3.1e-19 (2.39e-16)	2.42e-19 (1.87e-16)	0.449 (1.00)	0.0692 (1.00)	1.51e-13 (1.14e-10)	0.0668 (1.00)
del 18q22 1	269 (63%)	158	1.3e-10 (9.46e-08)	9.95e-10 (7.14e-07)	1.41e-46 (1.13e-43)	4.09e-14 (3.11e-11)	0.00246 (1.00)	0.000233 (0.14)	4.58e-18 (3.52e-15)	8.21e-19 (6.33e-16)	0.574 (1.00)	0.048 (1.00)	4.21e-14 (3.19e-11)	0.0679 (1.00)
amp 11p15 5	89 (21%)	338	4.77e-05 (0.0304)	0.0015 (0.809)	9.23e-06 (0.00614)	1.74e-05 (0.0114)	0.00106 (0.584)	0.00596 (1.00)	7.55e-05 (0.0478)	1.06e-05 (0.00699)	0.108 (1.00)	6.72e-05 (0.0426)	0.00198 (1.00)	1.09e-05 (0.00721)
amp 13q12 13	261 (61%)	166	1.84e-06 (0.00125)	2.26e-06 (0.00152)	3.88e-38 (3.1e-35)	6.56e-06 (0.00438)	0.00498 (1.00)	0.0126 (1.00)	2.51e-13 (1.89e-10)	9.29e-12 (6.9e-09)	0.563 (1.00)	0.0174 (1.00)	1.23e-07 (8.64e-05)	0.868 (1.00)
amp 16q12 1	105 (25%)	322	4.76e-05 (0.0303)	2.8e-05 (0.0181)	7.95e-21 (6.16e-18)	0.0387 (1.00)	0.11 (1.00)	0.0974 (1.00)	3.72e-05 (0.0238)	1.59e-05 (0.0105)	0.977 (1.00)	0.000121 (0.0752)	0.000106 (0.0665)	0.287 (1.00)
del 8p22	190 (44%)	237	0.0027 (1.00)	0.000179 (0.108)	5.76e-28 (4.57e-25)	3.92e-08 (2.76e-05)	0.00809 (1.00)	0.000135 (0.0832)	2.22e-08 (1.57e-05)	4.66e-09 (3.32e-06)	0.476 (1.00)	0.296 (1.00)	3.42e-07 (0.000237)	0.383 (1.00)
del 15q22 33	153 (36%)	274	0.00016 (0.0973)	0.0005 (0.289)	2.5e-22 (1.96e-19)	2.99e-05 (0.0193)	0.0438 (1.00)	0.0409 (1.00)	4.13e-08 (2.91e-05)	6.26e-10 (4.52e-07)	0.66 (1.00)	0.000102 (0.064)	3.2e-05 (0.0206)	0.29 (1.00)
del 18p11 31	230 (54%)	197	1.04e-11 (7.71e-09)	7.75e-10 (5.57e-07)	2.64e-42 (2.11e-39)	1.19e-15 (9.13e-13)	0.000864 (0.485)	0.00205 (1.00)	4.52e-26 (3.58e-23)	1.67e-24 (1.32e-21)	0.837 (1.00)	0.00498 (1.00)	2.02e-14 (1.53e-11)	0.0195 (1.00)
del 18q12 2	256 (60%)	171	1.76e-11 (1.3e-08)	2.8e-10 (2.03e-07)	1.23e-43 (9.87e-41)	1.39e-17 (1.06e-14)	0.00229 (1.00)	0.000431 (0.253)	1.36e-23 (1.07e-20)	6.27e-24 (4.95e-21)	0.945 (1.00)	0.00271 (1.00)	1.06e-14 (8.08e-12)	0.104 (1.00)
amp 13q22 1	264 (62%)	163	0.000604 (0.345)	4.25e-05 (0.0271)	3.48e-34 (2.77e-31)	8.41e-06 (0.0056)	0.0148 (1.00)	0.0449 (1.00)	1.47e-11 (1.08e-08)	1.33e-10 (9.64e-08)	0.448 (1.00)	0.0328 (1.00)	4.48e-06 (0.003)	0.973 (1.00)
del 1p36 11	159 (37%)	268	8.23e-05 (0.052)	0.00178 (0.956)	3.57e-15 (2.73e-12)	3.19e-06 (0.00215)	0.0227 (1.00)	0.0455 (1.00)	7.21e-08 (5.07e-05)	4.94e-09 (3.51e-06)	0.661 (1.00)	0.0143 (1.00)	1.81e-05 (0.0118)	0.00668 (1.00)
del 8p23 3	176 (41%)	251	0.0119 (1.00)	6.46e-05 (0.041)	2.89e-22 (2.26e-19)	3.4e-07 (0.000236)	0.00457 (1.00)	0.000991 (0.55)	4.67e-07 (0.000323)	3.06e-09 (2.19e-06)	0.219 (1.00)	0.152 (1.00)	2.22e-07 (0.000155)	0.325 (1.00)
amp 16p11 2	119 (28%)	308	0.000469 (0.273)	0.000176 (0.106)	1.56e-21 (1.22e-18)	0.0156 (1.00)	0.0306 (1.00)	0.0388 (1.00)	1.31e-05 (0.00861)	1.05e-05 (0.00693)	0.9 (1.00)	0.00177 (0.951)	0.000399 (0.235)	0.462 (1.00)
del 4q22 1	137 (32%)	290	0.000412 (0.242)	0.00225 (1.00)	2.75e-14 (2.09e-11)	0.000454 (0.266)	0.104 (1.00)	0.145 (1.00)	1.05e-06 (0.000717)	2.3e-07 (0.00016)	0.387 (1.00)	0.0122 (1.00)	0.000181 (0.109)	0.431 (1.00)
del 4q35 1	145 (34%)	282	0.00102 (0.567)	0.00347 (1.00)	3.65e-15 (2.79e-12)	3.67e-06 (0.00247)	0.0137 (1.00)	0.0629 (1.00)	4.39e-05 (0.028)	8.19e-07 (0.000562)	0.357 (1.00)	0.024 (1.00)	1.43e-06 (0.000976)	0.672 (1.00)
del 22q13 32	149 (35%)	278	0.000509 (0.294)	0.000134 (0.0824)	8.41e-18 (6.46e-15)	0.000457 (0.267)	0.117 (1.00)	0.339 (1.00)	7.2e-07 (0.000495)	2.76e-07 (0.000192)	0.358 (1.00)	0.00412 (1.00)	3.42e-06 (0.0023)	0.485 (1.00)
amp 8q12 1	223 (52%)	204	0.482 (1.00)	0.0366 (1.00)	8.52e-22 (6.64e-19)	0.00215 (1.00)	0.0106 (1.00)	0.00158 (0.85)	0.000295 (0.176)	3.76e-05 (0.024)	0.381 (1.00)	0.487 (1.00)	0.000262 (0.157)	0.084 (1.00)
amp 17q24 1	98 (23%)	329	0.0177 (1.00)	0.017 (1.00)	1.18e-10 (8.62e-08)	0.000351 (0.208)	0.0619 (1.00)	0.00786 (1.00)	2.23e-05 (0.0146)	0.00036 (0.213)	0.0118 (1.00)	0.208 (1.00)	0.0563 (1.00)	0.141 (1.00)
amp 20p11 23	209 (49%)	218	0.0777 (1.00)	0.000396 (0.234)	2.68e-10 (1.94e-07)	0.0746 (1.00)	0.00634 (1.00)	0.182 (1.00)	1.09e-06 (0.000744)	0.000341 (0.202)	0.412 (1.00)	0.0728 (1.00)	0.00207 (1.00)	0.972 (1.00)
del 4p16 2	128 (30%)	299	0.000778 (0.44)	0.00394 (1.00)	6.15e-14 (4.66e-11)	0.00133 (0.724)	0.0264 (1.00)	0.031 (1.00)	5.77e-06 (0.00386)	2.82e-08 (2e-05)	0.357 (1.00)	0.0225 (1.00)	0.000138 (0.0847)	0.465 (1.00)
del 5q11 2	97 (23%)	330	0.00128 (0.699)	0.00131 (0.714)	2.32e-10 (1.68e-07)	0.0104 (1.00)	0.000821 (0.462)	0.00248 (1.00)	0.000151 (0.0918)	1.27e-06 (0.000865)	0.71 (1.00)	0.31 (1.00)	9.16e-05 (0.0577)	0.415 (1.00)
del 15q11 2	166 (39%)	261	0.000483 (0.28)	0.00169 (0.911)	3.99e-22 (3.12e-19)	0.00207 (1.00)	0.0215 (1.00)	0.0443 (1.00)	2.65e-07 (0.000184)	4.27e-09 (3.04e-06)	0.984 (1.00)	0.0019 (1.00)	2.84e-05 (0.0183)	0.747 (1.00)
del 15q21 1	158 (37%)	269	0.0191 (1.00)	0.00823 (1.00)	5.66e-19 (4.37e-16)	0.00124 (0.677)	0.00979 (1.00)	0.0567 (1.00)	7.84e-08 (5.51e-05)	4.02e-09 (2.87e-06)	0.883 (1.00)	0.00272 (1.00)	0.000132 (0.0814)	0.845 (1.00)
del 21q11 2	133 (31%)	294	0.0158 (1.00)	0.0365 (1.00)	2.16e-09 (1.55e-06)	0.036 (1.00)	0.161 (1.00)	0.43 (1.00)	0.000161 (0.098)	7.89e-05 (0.0498)	0.927 (1.00)	0.174 (1.00)	0.000102 (0.0643)	0.181 (1.00)
amp 6p21 1	92 (22%)	335	0.265 (1.00)	0.000142 (0.0868)	5.96e-12 (4.45e-09)	0.0259 (1.00)	0.504 (1.00)	0.18 (1.00)	0.00887 (1.00)	0.000106 (0.0665)	0.705 (1.00)	0.122 (1.00)	0.000811 (0.457)	0.606 (1.00)
amp 8q24 21	247 (58%)	180	0.55 (1.00)	0.068 (1.00)	9.9e-23 (7.78e-20)	0.000189 (0.114)	0.0381 (1.00)	0.0144 (1.00)	0.00104 (0.575)	2.5e-05 (0.0163)	0.702 (1.00)	0.324 (1.00)	0.00065 (0.37)	0.0652 (1.00)
del 1p33	115 (27%)	312	0.0159 (1.00)	0.307 (1.00)	4.34e-13 (3.26e-10)	0.000128 (0.0792)	0.823 (1.00)	0.452 (1.00)	0.00046 (0.268)	3.39e-05 (0.0218)	0.71 (1.00)	0.000943 (0.526)	0.00106 (0.585)	0.00322 (1.00)
del 5q23 1	113 (26%)	314	0.0513 (1.00)	0.0255 (1.00)	1.31e-10 (9.55e-08)	0.00945 (1.00)	0.0251 (1.00)	0.0584 (1.00)	0.000318 (0.189)	3.43e-05 (0.022)	0.855 (1.00)	0.662 (1.00)	0.00238 (1.00)	0.294 (1.00)
del 10q25 2	101 (24%)	326	0.13 (1.00)	0.00215 (1.00)	7.14e-10 (5.14e-07)	0.000473 (0.275)	0.0068 (1.00)	0.14 (1.00)	0.00154 (0.832)	3.15e-06 (0.00213)	0.956 (1.00)	0.0991 (1.00)	1.51e-06 (0.00103)	0.663 (1.00)
del 20p12 1	81 (19%)	346	0.0529 (1.00)	0.194 (1.00)	1.91e-06 (0.00129)	0.000538 (0.309)	0.717 (1.00)	0.292 (1.00)	6.19e-07 (0.000426)	4.71e-06 (0.00316)	0.101 (1.00)	0.0959 (1.00)	0.00446 (1.00)	0.2 (1.00)
amp 17q12	106 (25%)	321	0.0269 (1.00)	0.0512 (1.00)	1.52e-08 (1.08e-05)	0.00051 (0.294)	0.141 (1.00)	0.00476 (1.00)	0.000181 (0.109)	0.00408 (1.00)	0.0365 (1.00)	0.165 (1.00)	0.0425 (1.00)	0.299 (1.00)
del 1q43	51 (12%)	376	0.0616 (1.00)	0.442 (1.00)	2.09e-06 (0.00142)	0.015 (1.00)	0.477 (1.00)	0.517 (1.00)	0.00351 (1.00)	9.6e-06 (0.00637)	0.146 (1.00)	0.00809 (1.00)	0.000953 (0.531)	0.0343 (1.00)
del 5q21 3	122 (29%)	305	0.0663 (1.00)	0.0103 (1.00)	1.22e-11 (9.07e-09)	0.00521 (1.00)	0.0453 (1.00)	0.0567 (1.00)	0.000486 (0.282)	0.000142 (0.0868)	0.961 (1.00)	0.887 (1.00)	0.0187 (1.00)	0.151 (1.00)
del 10p15 3	75 (18%)	352	0.123 (1.00)	0.0986 (1.00)	4.85e-07 (0.000334)	0.00265 (1.00)	0.0225 (1.00)	0.0412 (1.00)	0.0566 (1.00)	0.000108 (0.0675)	0.46 (1.00)	0.000977 (0.543)	0.00119 (0.654)	0.32 (1.00)
del 10q21 1	90 (21%)	337	0.004 (1.00)	0.00919 (1.00)	2.13e-10 (1.55e-07)	0.0155 (1.00)	0.071 (1.00)	0.116 (1.00)	0.00194 (1.00)	0.000404 (0.238)	0.753 (1.00)	0.0986 (1.00)	0.0012 (0.658)	0.79 (1.00)
del 10q23 31	102 (24%)	325	0.104 (1.00)	0.0107 (1.00)	1.72e-07 (0.00012)	0.00724 (1.00)	0.146 (1.00)	0.24 (1.00)	0.00719 (1.00)	0.000938 (0.524)	0.581 (1.00)	0.0136 (1.00)	0.000106 (0.0665)	0.376 (1.00)
amp 2q33 1	84 (20%)	343	0.167 (1.00)	0.0357 (1.00)	0.00015 (0.0914)	0.0381 (1.00)	0.0438 (1.00)	0.0978 (1.00)	0.00128 (0.697)	0.0187 (1.00)	0.289 (1.00)	0.123 (1.00)	0.173 (1.00)	0.141 (1.00)
amp 8p11 23	151 (35%)	276	0.297 (1.00)	0.121 (1.00)	2.63e-13 (1.98e-10)	0.64 (1.00)	0.761 (1.00)	0.799 (1.00)	0.0874 (1.00)	0.0106 (1.00)	0.362 (1.00)	0.365 (1.00)	0.26 (1.00)	1 (1.00)
amp 8p11 21	181 (42%)	246	0.438 (1.00)	0.0714 (1.00)	3.94e-23 (3.1e-20)	0.438 (1.00)	0.176 (1.00)	0.00818 (1.00)	0.172 (1.00)	0.00539 (1.00)	0.668 (1.00)	0.498 (1.00)	0.221 (1.00)	0.587 (1.00)
amp 19p13 2	70 (16%)	357	0.0669 (1.00)	0.0249 (1.00)	6.89e-06 (0.00459)	0.0213 (1.00)	0.67 (1.00)	0.284 (1.00)	0.72 (1.00)	0.0396 (1.00)	0.335 (1.00)	0.0146 (1.00)	0.0108 (1.00)	0.274 (1.00)
amp 19q13 11	88 (21%)	339	0.187 (1.00)	0.0238 (1.00)	2.77e-05 (0.018)	0.104 (1.00)	0.0341 (1.00)	0.564 (1.00)	0.0721 (1.00)	0.0283 (1.00)	0.45 (1.00)	0.0833 (1.00)	0.0302 (1.00)	0.221 (1.00)
del 1p13 1	110 (26%)	317	0.0886 (1.00)	0.256 (1.00)	5.97e-12 (4.45e-09)	0.012 (1.00)	0.678 (1.00)	0.649 (1.00)	0.0019 (1.00)	0.000614 (0.35)	0.786 (1.00)	0.0147 (1.00)	0.0435 (1.00)	0.0165 (1.00)
del 3p26 1	65 (15%)	362	0.122 (1.00)	0.277 (1.00)	2.58e-05 (0.0168)	0.109 (1.00)	0.744 (1.00)	0.856 (1.00)	0.032 (1.00)	0.0276 (1.00)	0.826 (1.00)	0.0883 (1.00)	0.0014 (0.759)	0.558 (1.00)
del 3q26 31	44 (10%)	383	0.708 (1.00)	0.934 (1.00)	0.000144 (0.0881)	0.125 (1.00)	0.507 (1.00)	0.383 (1.00)	0.0769 (1.00)	0.154 (1.00)	0.43 (1.00)	0.696 (1.00)	0.00721 (1.00)	0.0333 (1.00)
del 8p11 21	44 (10%)	383	0.0261 (1.00)	0.377 (1.00)	1.3e-05 (0.00859)	0.282 (1.00)	0.0434 (1.00)	0.0216 (1.00)	0.105 (1.00)	0.0142 (1.00)	0.349 (1.00)	0.345 (1.00)	0.0569 (1.00)	0.335 (1.00)
del 12p13 2	54 (13%)	373	0.0101 (1.00)	0.00427 (1.00)	6.93e-11 (5.08e-08)	0.0215 (1.00)	0.311 (1.00)	0.907 (1.00)	0.00272 (1.00)	0.00294 (1.00)	0.779 (1.00)	0.267 (1.00)	0.00496 (1.00)	0.29 (1.00)
amp 5p13 2	82 (19%)	345	0.374 (1.00)	0.273 (1.00)	0.000666 (0.378)	0.493 (1.00)	0.00475 (1.00)	0.686 (1.00)	0.0323 (1.00)	0.000914 (0.512)	0.723 (1.00)	0.107 (1.00)	0.0657 (1.00)	0.398 (1.00)
amp 5q22 3	41 (10%)	386	0.924 (1.00)	0.804 (1.00)	0.00735 (1.00)	0.861 (1.00)	0.333 (1.00)	0.466 (1.00)	0.324 (1.00)	0.00367 (1.00)	0.962 (1.00)	0.852 (1.00)	0.218 (1.00)	0.446 (1.00)
amp 12p13 33	105 (25%)	322	0.659 (1.00)	0.605 (1.00)	0.104 (1.00)	0.234 (1.00)	0.425 (1.00)	0.951 (1.00)	0.954 (1.00)	0.981 (1.00)	0.509 (1.00)	0.696 (1.00)	0.678 (1.00)	0.563 (1.00)
del 2p21	16 (4%)	411	0.594 (1.00)	0.876 (1.00)	0.656 (1.00)	0.837 (1.00)	0.807 (1.00)	0.833 (1.00)	0.609 (1.00)	0.368 (1.00)	0.0902 (1.00)	0.524 (1.00)	0.269 (1.00)	0.791 (1.00)
del 2q22 1	20 (5%)	407	0.81 (1.00)	0.388 (1.00)	0.494 (1.00)	0.93 (1.00)	0.0287 (1.00)	0.0686 (1.00)	0.907 (1.00)	0.844 (1.00)	0.684 (1.00)	0.935 (1.00)	0.305 (1.00)	0.803 (1.00)
del 2q37 2	21 (5%)	406	0.805 (1.00)	0.0652 (1.00)	0.449 (1.00)	0.288 (1.00)	0.36 (1.00)	0.208 (1.00)	0.991 (1.00)	0.93 (1.00)	0.24 (1.00)	0.366 (1.00)	1 (1.00)	0.787 (1.00)
del 3p14 2	80 (19%)	347	0.561 (1.00)	0.557 (1.00)	0.0243 (1.00)	0.389 (1.00)	0.52 (1.00)	0.215 (1.00)	0.142 (1.00)	0.00446 (1.00)	0.647 (1.00)	0.804 (1.00)	0.00404 (1.00)	0.775 (1.00)
del 6p25 3	54 (13%)	373	0.873 (1.00)	0.714 (1.00)	0.315 (1.00)	0.0776 (1.00)	0.0432 (1.00)	0.86 (1.00)	0.922 (1.00)	0.902 (1.00)	0.652 (1.00)	0.512 (1.00)	0.177 (1.00)	0.53 (1.00)
del 6q26	59 (14%)	368	0.581 (1.00)	0.359 (1.00)	0.803 (1.00)	0.391 (1.00)	0.0848 (1.00)	0.24 (1.00)	0.0839 (1.00)	0.47 (1.00)	0.664 (1.00)	0.137 (1.00)	0.448 (1.00)	0.354 (1.00)
del 7q31 1	12 (3%)	415	1 (1.00)	0.504 (1.00)	0.12 (1.00)	0.66 (1.00)	0.165 (1.00)	0.0916 (1.00)	0.222 (1.00)	0.445 (1.00)	0.759 (1.00)	0.931 (1.00)	0.629 (1.00)	0.853 (1.00)
del 9p21 3	57 (13%)	370	0.447 (1.00)	0.0262 (1.00)	0.0006 (0.344)	0.141 (1.00)	0.814 (1.00)	0.141 (1.00)	0.0437 (1.00)	0.0142 (1.00)	0.607 (1.00)	0.552 (1.00)	0.0465 (1.00)	0.666 (1.00)
del 13q14 13	18 (4%)	409	0.275 (1.00)	0.876 (1.00)	0.228 (1.00)	0.18 (1.00)	0.24 (1.00)	0.34 (1.00)	0.495 (1.00)	1 (1.00)	0.655 (1.00)	0.86 (1.00)	0.632 (1.00)	0.787 (1.00)
del 16p13 3	51 (12%)	376	0.23 (1.00)	0.364 (1.00)	0.0771 (1.00)	0.102 (1.00)	0.392 (1.00)	0.867 (1.00)	0.236 (1.00)	0.0309 (1.00)	0.836 (1.00)	0.486 (1.00)	0.134 (1.00)	0.422 (1.00)
del 16q23 1	55 (13%)	372	0.279 (1.00)	0.00599 (1.00)	0.0788 (1.00)	0.583 (1.00)	0.144 (1.00)	0.862 (1.00)	0.177 (1.00)	0.178 (1.00)	0.528 (1.00)	0.858 (1.00)	0.808 (1.00)	0.773 (1.00)
del 17q24 3	62 (15%)	365	0.0957 (1.00)	0.686 (1.00)	0.00354 (1.00)	0.0024 (1.00)	0.831 (1.00)	0.479 (1.00)	0.00578 (1.00)	0.00185 (0.989)	0.698 (1.00)	0.807 (1.00)	0.0117 (1.00)	0.201 (1.00)
del 19p13 3	59 (14%)	368	0.13 (1.00)	0.0411 (1.00)	0.000684 (0.388)	0.287 (1.00)	0.967 (1.00)	0.0695 (1.00)	0.0112 (1.00)	0.00238 (1.00)	0.635 (1.00)	0.631 (1.00)	0.0289 (1.00)	0.272 (1.00)

'amp_2q33.1' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.091

Table S1. Gene #1: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 1(2Q33.1) MUTATED	50	23	11
AMP PEAK 1(2Q33.1) WILD-TYPE	121	172	50

Figure S1. Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.000142 (Fisher's exact test), Q value = 0.087

Table S2. Gene #4: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 4(6P21.1) MUTATED	7	3	19
AMP PEAK 4(6P21.1) WILD-TYPE	49	40	28

Figure S2. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 5.96e-12 (Fisher's exact test), Q value = 4.4e-09

Table S3. Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 4(6P21.1) MUTATED	65	15	12
AMP PEAK 4(6P21.1) WILD-TYPE	106	180	49

Figure S3. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000106 (Fisher's exact test), Q value = 0.066

Table S4. Gene #4: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
AMP PEAK 4(6P21.1) MUTATED	36	8	48
AMP PEAK 4(6P21.1) WILD-TYPE	128	90	113

Figure S4. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 2.63e-13 (Fisher's exact test), Q value = 2e-10

Table S5. Gene #5: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 5(8P11.23) MUTATED	59	45	47
AMP PEAK 5(8P11.23) WILD-TYPE	112	150	14

Figure S5. Get High-res Image Gene #5: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 3.94e-23 (Fisher's exact test), Q value = 3.1e-20

Table S6. Gene #6: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 6(8P11.21) MUTATED	74	49	58
AMP PEAK 6(8P11.21) WILD-TYPE	97	146	3

Figure S6. Get High-res Image Gene #6: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q12.1' versus 'CN_CNMF'

P value = 8.52e-22 (Fisher's exact test), Q value = 6.6e-19

Table S7. Gene #7: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 7(8Q12.1) MUTATED	105	60	58
AMP PEAK 7(8Q12.1) WILD-TYPE	66	135	3

Figure S7. Get High-res Image Gene #7: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q12.1' versus 'MRNASEQ_CNMF'

P value = 0.000295 (Chi-square test), Q value = 0.18

Table S8. Gene #7: 'amp_8q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 7(8Q12.1) MUTATED	16	74	42	31	58
AMP PEAK 7(8Q12.1) WILD-TYPE	17	39	29	59	58

Figure S8. Get High-res Image Gene #7: 'amp_8q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.76e-05 (Fisher's exact test), Q value = 0.024

Table S9. Gene #7: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
AMP PEAK 7(8Q12.1) MUTATED	79	37	105
AMP PEAK 7(8Q12.1) WILD-TYPE	85	61	56

Figure S9. Get High-res Image Gene #7: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000262 (Fisher's exact test), Q value = 0.16

Table S10. Gene #7: 'amp_8q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 7(8Q12.1) MUTATED	53	29	40
AMP PEAK 7(8Q12.1) WILD-TYPE	26	49	23

Figure S10. Get High-res Image Gene #7: 'amp_8q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 9.9e-23 (Fisher's exact test), Q value = 7.8e-20

Table S11. Gene #8: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 8(8Q24.21) MUTATED	117	70	60
AMP PEAK 8(8Q24.21) WILD-TYPE	54	125	1

Figure S11. Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.000189 (Fisher's exact test), Q value = 0.11

Table S12. Gene #8: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 8(8Q24.21) MUTATED	86	42	39
AMP PEAK 8(8Q24.21) WILD-TYPE	28	46	29

Figure S12. Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.5e-05 (Fisher's exact test), Q value = 0.016

Table S13. Gene #8: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
AMP PEAK 8(8Q24.21) MUTATED	89	42	114
AMP PEAK 8(8Q24.21) WILD-TYPE	75	56	47

Figure S13. Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'MRNA_CNMF'

P value = 4.77e-05 (Fisher's exact test), Q value = 0.03

Table S14. Gene #9: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 9(11P15.5) MUTATED	2	18	3	12
AMP PEAK 9(11P15.5) WILD-TYPE	33	43	26	9

Figure S14. Get High-res Image Gene #9: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11p15.5' versus 'CN_CNMF'

P value = 9.23e-06 (Fisher's exact test), Q value = 0.0061

Table S15. Gene #9: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 9(11P15.5) MUTATED	54	22	13
AMP PEAK 9(11P15.5) WILD-TYPE	117	173	48

Figure S15. Get High-res Image Gene #9: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p15.5' versus 'METHLYATION_CNMF'

P value = 1.74e-05 (Fisher's exact test), Q value = 0.011

Table S16. Gene #9: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 9(11P15.5) MUTATED	35	5	11
AMP PEAK 9(11P15.5) WILD-TYPE	79	83	57

Figure S16. Get High-res Image Gene #9: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CNMF'

P value = 7.55e-05 (Chi-square test), Q value = 0.048

Table S17. Gene #9: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 9(11P15.5) MUTATED	6	33	15	3	31
AMP PEAK 9(11P15.5) WILD-TYPE	27	80	56	87	85

Figure S17. Get High-res Image Gene #9: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.007

Table S18. Gene #9: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
AMP PEAK 9(11P15.5) MUTATED	42	5	41
AMP PEAK 9(11P15.5) WILD-TYPE	122	93	120

Figure S18. Get High-res Image Gene #9: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.72e-05 (Fisher's exact test), Q value = 0.043

Table S19. Gene #9: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
AMP PEAK 9(11P15.5) MUTATED	4	46	34
AMP PEAK 9(11P15.5) WILD-TYPE	76	128	109

Figure S19. Get High-res Image Gene #9: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0072

Table S20. Gene #9: 'amp_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	21	86	113
AMP PEAK 9(11P15.5) MUTATED	12	16	11
AMP PEAK 9(11P15.5) WILD-TYPE	9	70	102

Figure S20. Get High-res Image Gene #9: 'amp_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q12.13' versus 'MRNA_CNMF'

P value = 1.84e-06 (Fisher's exact test), Q value = 0.0012

Table S21. Gene #11: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 11(13Q12.13) MUTATED	15	51	10	16
AMP PEAK 11(13Q12.13) WILD-TYPE	20	10	19	5

Figure S21. Get High-res Image Gene #11: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q12.13' versus 'MRNA_CHIERARCHICAL'

P value = 2.26e-06 (Fisher's exact test), Q value = 0.0015

Table S22. Gene #11: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 11(13Q12.13) MUTATED	39	14	39
AMP PEAK 11(13Q12.13) WILD-TYPE	17	29	8

Figure S22. Get High-res Image Gene #11: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q12.13' versus 'CN_CNMF'

P value = 3.88e-38 (Fisher's exact test), Q value = 3.1e-35

Table S23. Gene #11: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 11(13Q12.13) MUTATED	161	61	39
AMP PEAK 11(13Q12.13) WILD-TYPE	10	134	22

Figure S23. Get High-res Image Gene #11: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'METHLYATION_CNMF'

P value = 6.56e-06 (Fisher's exact test), Q value = 0.0044

Table S24. Gene #11: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 11(13Q12.13) MUTATED	89	42	35
AMP PEAK 11(13Q12.13) WILD-TYPE	25	46	33

Figure S24. Get High-res Image Gene #11: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CNMF'

P value = 2.51e-13 (Chi-square test), Q value = 1.9e-10

Table S25. Gene #11: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 11(13Q12.13) MUTATED	24	88	41	24	82
AMP PEAK 11(13Q12.13) WILD-TYPE	9	25	30	66	34

Figure S25. Get High-res Image Gene #11: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.29e-12 (Fisher's exact test), Q value = 6.9e-09

Table S26. Gene #11: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
AMP PEAK 11(13Q12.13) MUTATED	103	32	124
AMP PEAK 11(13Q12.13) WILD-TYPE	61	66	37

Figure S26. Get High-res Image Gene #11: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.23e-07 (Fisher's exact test), Q value = 8.6e-05

Table S27. Gene #11: 'amp_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 11(13Q12.13) MUTATED	63	29	43
AMP PEAK 11(13Q12.13) WILD-TYPE	16	49	20

Figure S27. Get High-res Image Gene #11: 'amp_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 4.25e-05 (Fisher's exact test), Q value = 0.027

Table S28. Gene #12: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 12(13Q22.1) MUTATED	39	15	37
AMP PEAK 12(13Q22.1) WILD-TYPE	17	28	10

Figure S28. Get High-res Image Gene #12: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 3.48e-34 (Fisher's exact test), Q value = 2.8e-31

Table S29. Gene #12: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 12(13Q22.1) MUTATED	159	65	40
AMP PEAK 12(13Q22.1) WILD-TYPE	12	130	21

Figure S29. Get High-res Image Gene #12: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 8.41e-06 (Fisher's exact test), Q value = 0.0056

Table S30. Gene #12: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 12(13Q22.1) MUTATED	90	44	35
AMP PEAK 12(13Q22.1) WILD-TYPE	24	44	33

Figure S30. Get High-res Image Gene #12: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 1.47e-11 (Chi-square test), Q value = 1.1e-08

Table S31. Gene #12: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 12(13Q22.1) MUTATED	23	89	42	27	81
AMP PEAK 12(13Q22.1) WILD-TYPE	10	24	29	63	35

Figure S31. Get High-res Image Gene #12: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.33e-10 (Fisher's exact test), Q value = 9.6e-08

Table S32. Gene #12: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
AMP PEAK 12(13Q22.1) MUTATED	102	35	125
AMP PEAK 12(13Q22.1) WILD-TYPE	62	63	36

Figure S32. Get High-res Image Gene #12: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.48e-06 (Fisher's exact test), Q value = 0.003

Table S33. Gene #12: 'amp_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 12(13Q22.1) MUTATED	63	33	43
AMP PEAK 12(13Q22.1) WILD-TYPE	16	45	20

Figure S33. Get High-res Image Gene #12: 'amp_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_16p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.000176 (Fisher's exact test), Q value = 0.11

Table S34. Gene #13: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 13(16P11.2) MUTATED	14	6	25
AMP PEAK 13(16P11.2) WILD-TYPE	42	37	22

Figure S34. Get High-res Image Gene #13: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1.56e-21 (Fisher's exact test), Q value = 1.2e-18

Table S35. Gene #13: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 13(16P11.2) MUTATED	91	17	11
AMP PEAK 13(16P11.2) WILD-TYPE	80	178	50

Figure S35. Get High-res Image Gene #13: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 1.31e-05 (Chi-square test), Q value = 0.0086

Table S36. Gene #13: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 13(16P11.2) MUTATED	8	42	19	7	43
AMP PEAK 13(16P11.2) WILD-TYPE	25	71	52	83	73

Figure S36. Get High-res Image Gene #13: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0069

Table S37. Gene #13: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
AMP PEAK 13(16P11.2) MUTATED	54	10	55
AMP PEAK 13(16P11.2) WILD-TYPE	110	88	106

Figure S37. Get High-res Image Gene #13: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000399 (Fisher's exact test), Q value = 0.24

Table S38. Gene #13: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 13(16P11.2) MUTATED	31	10	21
AMP PEAK 13(16P11.2) WILD-TYPE	48	68	42

Figure S38. Get High-res Image Gene #13: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_16q12.1' versus 'MRNA_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.03

Table S39. Gene #14: 'amp_16q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 14(16Q12.1) MUTATED	4	22	2	12
AMP PEAK 14(16Q12.1) WILD-TYPE	31	39	27	9

Figure S39. Get High-res Image Gene #14: 'amp_16q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 2.8e-05 (Fisher's exact test), Q value = 0.018

Table S40. Gene #14: 'amp_16q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 14(16Q12.1) MUTATED	14	3	23
AMP PEAK 14(16Q12.1) WILD-TYPE	42	40	24

Figure S40. Get High-res Image Gene #14: 'amp_16q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_16q12.1' versus 'CN_CNMF'

P value = 7.95e-21 (Fisher's exact test), Q value = 6.2e-18

Table S41. Gene #14: 'amp_16q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 14(16Q12.1) MUTATED	83	13	9
AMP PEAK 14(16Q12.1) WILD-TYPE	88	182	52

Figure S41. Get High-res Image Gene #14: 'amp_16q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16q12.1' versus 'MRNASEQ_CNMF'

P value = 3.72e-05 (Chi-square test), Q value = 0.024

Table S42. Gene #14: 'amp_16q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 14(16Q12.1) MUTATED	8	37	17	5	38
AMP PEAK 14(16Q12.1) WILD-TYPE	25	76	54	85	78

Figure S42. Get High-res Image Gene #14: 'amp_16q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.01

Table S43. Gene #14: 'amp_16q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
AMP PEAK 14(16Q12.1) MUTATED	47	8	50
AMP PEAK 14(16Q12.1) WILD-TYPE	117	90	111

Figure S43. Get High-res Image Gene #14: 'amp_16q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000121 (Fisher's exact test), Q value = 0.075

Table S44. Gene #14: 'amp_16q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
AMP PEAK 14(16Q12.1) MUTATED	7	46	47
AMP PEAK 14(16Q12.1) WILD-TYPE	73	128	96

Figure S44. Get High-res Image Gene #14: 'amp_16q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000106 (Fisher's exact test), Q value = 0.066

Table S45. Gene #14: 'amp_16q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 14(16Q12.1) MUTATED	27	7	21
AMP PEAK 14(16Q12.1) WILD-TYPE	52	71	42

Figure S45. Get High-res Image Gene #14: 'amp_16q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 1.52e-08 (Fisher's exact test), Q value = 1.1e-05

Table S46. Gene #15: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 15(17Q12) MUTATED	65	23	18
AMP PEAK 15(17Q12) WILD-TYPE	106	172	43

Figure S46. Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.000181 (Chi-square test), Q value = 0.11

Table S47. Gene #15: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 15(17Q12) MUTATED	9	44	12	11	29
AMP PEAK 15(17Q12) WILD-TYPE	24	69	59	79	87

Figure S47. Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q24.1' versus 'CN_CNMF'

P value = 1.18e-10 (Fisher's exact test), Q value = 8.6e-08

Table S48. Gene #16: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 16(17Q24.1) MUTATED	63	17	18
AMP PEAK 16(17Q24.1) WILD-TYPE	108	178	43

Figure S48. Get High-res Image Gene #16: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.1' versus 'METHLYATION_CNMF'

P value = 0.000351 (Fisher's exact test), Q value = 0.21

Table S49. Gene #16: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 16(17Q24.1) MUTATED	41	16	8
AMP PEAK 16(17Q24.1) WILD-TYPE	73	72	60

Figure S49. Get High-res Image Gene #16: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CNMF'

P value = 2.23e-05 (Chi-square test), Q value = 0.015

Table S50. Gene #16: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 16(17Q24.1) MUTATED	10	43	8	11	26
AMP PEAK 16(17Q24.1) WILD-TYPE	23	70	63	79	90

Figure S50. Get High-res Image Gene #16: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.21

Table S51. Gene #16: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
AMP PEAK 16(17Q24.1) MUTATED	38	10	50
AMP PEAK 16(17Q24.1) WILD-TYPE	126	88	111

Figure S51. Get High-res Image Gene #16: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 6.89e-06 (Fisher's exact test), Q value = 0.0046

Table S52. Gene #17: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 17(19P13.2) MUTATED	46	16	8
AMP PEAK 17(19P13.2) WILD-TYPE	125	179	53

Figure S52. Get High-res Image Gene #17: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.11' versus 'CN_CNMF'

P value = 2.77e-05 (Fisher's exact test), Q value = 0.018

Table S53. Gene #18: 'amp_19q13.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 18(19Q13.11) MUTATED	54	24	10
AMP PEAK 18(19Q13.11) WILD-TYPE	117	171	51

Figure S53. Get High-res Image Gene #18: 'amp_19q13.11' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.23' versus 'MRNA_CHIERARCHICAL'

P value = 0.000396 (Fisher's exact test), Q value = 0.23

Table S54. Gene #19: 'amp_20p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 19(20P11.23) MUTATED	36	11	26
AMP PEAK 19(20P11.23) WILD-TYPE	20	32	21

Figure S54. Get High-res Image Gene #19: 'amp_20p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p11.23' versus 'CN_CNMF'

P value = 2.68e-10 (Fisher's exact test), Q value = 1.9e-07

Table S55. Gene #19: 'amp_20p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 19(20P11.23) MUTATED	114	63	32
AMP PEAK 19(20P11.23) WILD-TYPE	57	132	29

Figure S55. Get High-res Image Gene #19: 'amp_20p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.23' versus 'MRNASEQ_CNMF'

P value = 1.09e-06 (Chi-square test), Q value = 0.00074

Table S56. Gene #19: 'amp_20p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 19(20P11.23) MUTATED	22	67	31	22	64
AMP PEAK 19(20P11.23) WILD-TYPE	11	46	40	68	52

Figure S56. Get High-res Image Gene #19: 'amp_20p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000341 (Fisher's exact test), Q value = 0.2

Table S57. Gene #19: 'amp_20p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
AMP PEAK 19(20P11.23) MUTATED	84	31	91
AMP PEAK 19(20P11.23) WILD-TYPE	80	67	70

Figure S57. Get High-res Image Gene #19: 'amp_20p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 7.72e-10 (Fisher's exact test), Q value = 5.6e-07

Table S58. Gene #20: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 20(20Q11.21) MUTATED	13	58	16	18
AMP PEAK 20(20Q11.21) WILD-TYPE	22	3	13	3

Figure S58. Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 1.47e-11 (Fisher's exact test), Q value = 1.1e-08

Table S59. Gene #20: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 20(20Q11.21) MUTATED	50	13	42
AMP PEAK 20(20Q11.21) WILD-TYPE	6	30	5

Figure S59. Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 4.38e-39 (Fisher's exact test), Q value = 3.5e-36

Table S60. Gene #20: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 20(20Q11.21) MUTATED	170	84	52
AMP PEAK 20(20Q11.21) WILD-TYPE	1	111	9

Figure S60. Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 2.13e-12 (Fisher's exact test), Q value = 1.6e-09

Table S61. Gene #20: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 20(20Q11.21) MUTATED	107	46	42
AMP PEAK 20(20Q11.21) WILD-TYPE	7	42	26

Figure S61. Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.000114 (Fisher's exact test), Q value = 0.071

Table S62. Gene #20: 'amp_20q11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
AMP PEAK 20(20Q11.21) MUTATED	13	29	53	133
AMP PEAK 20(20Q11.21) WILD-TYPE	13	27	10	47

Figure S62. Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 2.93e-23 (Chi-square test), Q value = 2.3e-20

Table S63. Gene #20: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 20(20Q11.21) MUTATED	26	110	50	28	89
AMP PEAK 20(20Q11.21) WILD-TYPE	7	3	21	62	27

Figure S63. Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.01e-21 (Fisher's exact test), Q value = 1.6e-18

Table S64. Gene #20: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
AMP PEAK 20(20Q11.21) MUTATED	118	36	149
AMP PEAK 20(20Q11.21) WILD-TYPE	46	62	12

Figure S64. Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000105 (Fisher's exact test), Q value = 0.066

Table S65. Gene #20: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
AMP PEAK 20(20Q11.21) MUTATED	43	125	116
AMP PEAK 20(20Q11.21) WILD-TYPE	37	49	27

Figure S65. Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.36e-12 (Fisher's exact test), Q value = 1.8e-09

Table S66. Gene #20: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 20(20Q11.21) MUTATED	74	34	51
AMP PEAK 20(20Q11.21) WILD-TYPE	5	44	12

Figure S66. Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q12' versus 'MRNA_CNMF'

P value = 8.9e-11 (Fisher's exact test), Q value = 6.5e-08

Table S67. Gene #21: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 21(20Q12) MUTATED	12	58	15	18
AMP PEAK 21(20Q12) WILD-TYPE	23	3	14	3

Figure S67. Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q12' versus 'MRNA_CHIERARCHICAL'

P value = 7.64e-12 (Fisher's exact test), Q value = 5.7e-09

Table S68. Gene #21: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 21(20Q12) MUTATED	49	12	42
AMP PEAK 21(20Q12) WILD-TYPE	7	31	5

Figure S68. Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q12' versus 'CN_CNMF'

P value = 2.02e-40 (Fisher's exact test), Q value = 1.6e-37

Table S69. Gene #21: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 21(20Q12) MUTATED	170	83	54
AMP PEAK 21(20Q12) WILD-TYPE	1	112	7

Figure S69. Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q12' versus 'METHLYATION_CNMF'

P value = 1.84e-11 (Fisher's exact test), Q value = 1.4e-08

Table S70. Gene #21: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 21(20Q12) MUTATED	107	48	43
AMP PEAK 21(20Q12) WILD-TYPE	7	40	25

Figure S70. Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q12' versus 'RPPA_CHIERARCHICAL'

P value = 2.33e-05 (Fisher's exact test), Q value = 0.015

Table S71. Gene #21: 'amp_20q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
AMP PEAK 21(20Q12) MUTATED	13	29	55	132
AMP PEAK 21(20Q12) WILD-TYPE	13	27	8	48

Figure S71. Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q12' versus 'MRNASEQ_CNMF'

P value = 2.3e-22 (Chi-square test), Q value = 1.8e-19

Table S72. Gene #21: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 21(20Q12) MUTATED	26	110	52	29	87
AMP PEAK 21(20Q12) WILD-TYPE	7	3	19	61	29

Figure S72. Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.78e-21 (Fisher's exact test), Q value = 5.3e-18

Table S73. Gene #21: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
AMP PEAK 21(20Q12) MUTATED	116	38	150
AMP PEAK 21(20Q12) WILD-TYPE	48	60	11

Figure S73. Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000127 (Fisher's exact test), Q value = 0.078

Table S74. Gene #21: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
AMP PEAK 21(20Q12) MUTATED	44	124	117
AMP PEAK 21(20Q12) WILD-TYPE	36	50	26

Figure S74. Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.32e-13 (Fisher's exact test), Q value = 1.8e-10

Table S75. Gene #21: 'amp_20q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 21(20Q12) MUTATED	75	34	52
AMP PEAK 21(20Q12) WILD-TYPE	4	44	11

Figure S75. Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.32' versus 'MRNA_CNMF'

P value = 1.49e-09 (Fisher's exact test), Q value = 1.1e-06

Table S76. Gene #22: 'amp_20q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 22(20Q13.32) MUTATED	13	58	17	18
AMP PEAK 22(20Q13.32) WILD-TYPE	22	3	12	3

Figure S76. Get High-res Image Gene #22: 'amp_20q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 4.32e-12 (Fisher's exact test), Q value = 3.2e-09

Table S77. Gene #22: 'amp_20q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 22(20Q13.32) MUTATED	51	13	42
AMP PEAK 22(20Q13.32) WILD-TYPE	5	30	5

Figure S77. Get High-res Image Gene #22: 'amp_20q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.32' versus 'CN_CNMF'

P value = 6.54e-41 (Fisher's exact test), Q value = 5.2e-38

Table S78. Gene #22: 'amp_20q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
AMP PEAK 22(20Q13.32) MUTATED	170	84	56
AMP PEAK 22(20Q13.32) WILD-TYPE	1	111	5

Figure S78. Get High-res Image Gene #22: 'amp_20q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.32' versus 'METHLYATION_CNMF'

P value = 1.84e-11 (Fisher's exact test), Q value = 1.4e-08

Table S79. Gene #22: 'amp_20q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 22(20Q13.32) MUTATED	107	48	43
AMP PEAK 22(20Q13.32) WILD-TYPE	7	40	25

Figure S79. Get High-res Image Gene #22: 'amp_20q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.0093

Table S80. Gene #22: 'amp_20q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
AMP PEAK 22(20Q13.32) MUTATED	13	29	55	135
AMP PEAK 22(20Q13.32) WILD-TYPE	13	27	8	45

Figure S80. Get High-res Image Gene #22: 'amp_20q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.32' versus 'MRNASEQ_CNMF'

P value = 4.87e-22 (Chi-square test), Q value = 3.8e-19

Table S81. Gene #22: 'amp_20q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 22(20Q13.32) MUTATED	26	110	52	30	89
AMP PEAK 22(20Q13.32) WILD-TYPE	7	3	19	60	27

Figure S81. Get High-res Image Gene #22: 'amp_20q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.33e-21 (Fisher's exact test), Q value = 5.7e-18

Table S82. Gene #22: 'amp_20q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
AMP PEAK 22(20Q13.32) MUTATED	119	38	150
AMP PEAK 22(20Q13.32) WILD-TYPE	45	60	11

Figure S82. Get High-res Image Gene #22: 'amp_20q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000275 (Fisher's exact test), Q value = 0.16

Table S83. Gene #22: 'amp_20q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
AMP PEAK 22(20Q13.32) MUTATED	45	126	117
AMP PEAK 22(20Q13.32) WILD-TYPE	35	48	26

Figure S83. Get High-res Image Gene #22: 'amp_20q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.98e-13 (Fisher's exact test), Q value = 6e-10

Table S84. Gene #22: 'amp_20q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 22(20Q13.32) MUTATED	75	35	52
AMP PEAK 22(20Q13.32) WILD-TYPE	4	43	11

Figure S84. Get High-res Image Gene #22: 'amp_20q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 8.23e-05 (Fisher's exact test), Q value = 0.052

Table S85. Gene #23: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 1(1P36.11) MUTATED	9	36	4	10
DEL PEAK 1(1P36.11) WILD-TYPE	26	25	25	11

Figure S85. Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 3.57e-15 (Fisher's exact test), Q value = 2.7e-12

Table S86. Gene #23: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 1(1P36.11) MUTATED	102	37	20
DEL PEAK 1(1P36.11) WILD-TYPE	69	158	41

Figure S86. Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 3.19e-06 (Fisher's exact test), Q value = 0.0022

Table S87. Gene #23: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 1(1P36.11) MUTATED	60	17	21
DEL PEAK 1(1P36.11) WILD-TYPE	54	71	47

Figure S87. Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 7.21e-08 (Chi-square test), Q value = 5.1e-05

Table S88. Gene #23: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 1(1P36.11) MUTATED	11	58	27	10	52
DEL PEAK 1(1P36.11) WILD-TYPE	22	55	44	80	64

Figure S88. Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.94e-09 (Fisher's exact test), Q value = 3.5e-06

Table S89. Gene #23: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 1(1P36.11) MUTATED	65	13	80
DEL PEAK 1(1P36.11) WILD-TYPE	99	85	81

Figure S89. Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.81e-05 (Fisher's exact test), Q value = 0.012

Table S90. Gene #23: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 1(1P36.11) MUTATED	39	13	28
DEL PEAK 1(1P36.11) WILD-TYPE	40	65	35

Figure S90. Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p33' versus 'CN_CNMF'

P value = 4.34e-13 (Fisher's exact test), Q value = 3.3e-10

Table S91. Gene #24: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 2(1P33) MUTATED	80	28	7
DEL PEAK 2(1P33) WILD-TYPE	91	167	54

Figure S91. Get High-res Image Gene #24: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p33' versus 'METHLYATION_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.079

Table S92. Gene #24: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 2(1P33) MUTATED	44	11	18
DEL PEAK 2(1P33) WILD-TYPE	70	77	50

Figure S92. Get High-res Image Gene #24: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.022

Table S93. Gene #24: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 2(1P33) MUTATED	45	11	58
DEL PEAK 2(1P33) WILD-TYPE	119	87	103

Figure S93. Get High-res Image Gene #24: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 5.97e-12 (Fisher's exact test), Q value = 4.4e-09

Table S94. Gene #25: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 3(1P13.1) MUTATED	75	31	4
DEL PEAK 3(1P13.1) WILD-TYPE	96	164	57

Figure S94. Get High-res Image Gene #25: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q43' versus 'CN_CNMF'

P value = 2.09e-06 (Fisher's exact test), Q value = 0.0014

Table S95. Gene #26: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 4(1Q43) MUTATED	36	8	7
DEL PEAK 4(1Q43) WILD-TYPE	135	187	54

Figure S95. Get High-res Image Gene #26: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.6e-06 (Fisher's exact test), Q value = 0.0064

Table S96. Gene #26: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 4(1Q43) MUTATED	15	2	33
DEL PEAK 4(1Q43) WILD-TYPE	149	96	128

Figure S96. Get High-res Image Gene #26: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.1' versus 'CN_CNMF'

P value = 2.58e-05 (Fisher's exact test), Q value = 0.017

Table S97. Gene #30: 'del_3p26.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 8(3P26.1) MUTATED	43	17	5
DEL PEAK 8(3P26.1) WILD-TYPE	128	178	56

Figure S97. Get High-res Image Gene #30: 'del_3p26.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q26.31' versus 'CN_CNMF'

P value = 0.000144 (Fisher's exact test), Q value = 0.088

Table S98. Gene #32: 'del_3q26.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 10(3Q26.31) MUTATED	30	13	1
DEL PEAK 10(3Q26.31) WILD-TYPE	141	182	60

Figure S98. Get High-res Image Gene #32: 'del_3q26.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.2' versus 'CN_CNMF'

P value = 6.15e-14 (Fisher's exact test), Q value = 4.7e-11

Table S99. Gene #33: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 11(4P16.2) MUTATED	87	28	13
DEL PEAK 11(4P16.2) WILD-TYPE	84	167	48

Figure S99. Get High-res Image Gene #33: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.2' versus 'MRNASEQ_CNMF'

P value = 5.77e-06 (Chi-square test), Q value = 0.0039

Table S100. Gene #33: 'del_4p16.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 11(4P16.2) MUTATED	8	44	25	7	43
DEL PEAK 11(4P16.2) WILD-TYPE	25	69	46	83	73

Figure S100. Get High-res Image Gene #33: 'del_4p16.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.82e-08 (Fisher's exact test), Q value = 2e-05

Table S101. Gene #33: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 11(4P16.2) MUTATED	56	8	63
DEL PEAK 11(4P16.2) WILD-TYPE	108	90	98

Figure S101. Get High-res Image Gene #33: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000138 (Fisher's exact test), Q value = 0.085

Table S102. Gene #33: 'del_4p16.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 11(4P16.2) MUTATED	27	8	23
DEL PEAK 11(4P16.2) WILD-TYPE	52	70	40

Figure S102. Get High-res Image Gene #33: 'del_4p16.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.000412 (Fisher's exact test), Q value = 0.24

Table S103. Gene #34: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 12(4Q22.1) MUTATED	9	27	2	11
DEL PEAK 12(4Q22.1) WILD-TYPE	26	34	27	10

Figure S103. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'CN_CNMF'

P value = 2.75e-14 (Fisher's exact test), Q value = 2.1e-11

Table S104. Gene #34: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 12(4Q22.1) MUTATED	92	32	13
DEL PEAK 12(4Q22.1) WILD-TYPE	79	163	48

Figure S104. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 1.05e-06 (Chi-square test), Q value = 0.00072

Table S105. Gene #34: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 12(4Q22.1) MUTATED	12	47	22	7	47
DEL PEAK 12(4Q22.1) WILD-TYPE	21	66	49	83	69

Figure S105. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.3e-07 (Fisher's exact test), Q value = 0.00016

Table S106. Gene #34: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 12(4Q22.1) MUTATED	56	11	68
DEL PEAK 12(4Q22.1) WILD-TYPE	108	87	93

Figure S106. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.11

Table S107. Gene #34: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 12(4Q22.1) MUTATED	34	11	22
DEL PEAK 12(4Q22.1) WILD-TYPE	45	67	41

Figure S107. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'CN_CNMF'

P value = 3.65e-15 (Fisher's exact test), Q value = 2.8e-12

Table S108. Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 13(4Q35.1) MUTATED	96	32	17
DEL PEAK 13(4Q35.1) WILD-TYPE	75	163	44

Figure S108. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 3.67e-06 (Fisher's exact test), Q value = 0.0025

Table S109. Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 13(4Q35.1) MUTATED	52	12	24
DEL PEAK 13(4Q35.1) WILD-TYPE	62	76	44

Figure S109. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 4.39e-05 (Chi-square test), Q value = 0.028

Table S110. Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 13(4Q35.1) MUTATED	13	48	25	11	47
DEL PEAK 13(4Q35.1) WILD-TYPE	20	65	46	79	69

Figure S110. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.19e-07 (Fisher's exact test), Q value = 0.00056

Table S111. Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 13(4Q35.1) MUTATED	62	13	69
DEL PEAK 13(4Q35.1) WILD-TYPE	102	85	92

Figure S111. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.43e-06 (Fisher's exact test), Q value = 0.00098

Table S112. Gene #35: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 13(4Q35.1) MUTATED	35	8	25
DEL PEAK 13(4Q35.1) WILD-TYPE	44	70	38

Figure S112. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'CN_CNMF'

P value = 2.32e-10 (Fisher's exact test), Q value = 1.7e-07

Table S113. Gene #36: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 14(5Q11.2) MUTATED	62	17	18
DEL PEAK 14(5Q11.2) WILD-TYPE	109	178	43

Figure S113. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q11.2' versus 'MRNASEQ_CNMF'

P value = 0.000151 (Chi-square test), Q value = 0.092

Table S114. Gene #36: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 14(5Q11.2) MUTATED	10	31	18	4	34
DEL PEAK 14(5Q11.2) WILD-TYPE	23	82	53	86	82

Figure S114. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.27e-06 (Fisher's exact test), Q value = 0.00087

Table S115. Gene #36: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 14(5Q11.2) MUTATED	39	6	52
DEL PEAK 14(5Q11.2) WILD-TYPE	125	92	109

Figure S115. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.16e-05 (Fisher's exact test), Q value = 0.058

Table S116. Gene #36: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 14(5Q11.2) MUTATED	25	5	17
DEL PEAK 14(5Q11.2) WILD-TYPE	54	73	46

Figure S116. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q21.3' versus 'CN_CNMF'

P value = 1.22e-11 (Fisher's exact test), Q value = 9.1e-09

Table S117. Gene #37: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 15(5Q21.3) MUTATED	75	24	23
DEL PEAK 15(5Q21.3) WILD-TYPE	96	171	38

Figure S117. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000142 (Fisher's exact test), Q value = 0.087

Table S118. Gene #37: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 15(5Q21.3) MUTATED	49	13	59
DEL PEAK 15(5Q21.3) WILD-TYPE	115	85	102

Figure S118. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q23.1' versus 'CN_CNMF'

P value = 1.31e-10 (Fisher's exact test), Q value = 9.6e-08

Table S119. Gene #38: 'del_5q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 16(5Q23.1) MUTATED	68	22	23
DEL PEAK 16(5Q23.1) WILD-TYPE	103	173	38

Figure S119. Get High-res Image Gene #38: 'del_5q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q23.1' versus 'MRNASEQ_CNMF'

P value = 0.000318 (Chi-square test), Q value = 0.19

Table S120. Gene #38: 'del_5q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 16(5Q23.1) MUTATED	10	41	18	8	35
DEL PEAK 16(5Q23.1) WILD-TYPE	23	72	53	82	81

Figure S120. Get High-res Image Gene #38: 'del_5q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.43e-05 (Fisher's exact test), Q value = 0.022

Table S121. Gene #38: 'del_5q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 16(5Q23.1) MUTATED	43	11	58
DEL PEAK 16(5Q23.1) WILD-TYPE	121	87	103

Figure S121. Get High-res Image Gene #38: 'del_5q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MRNA_CHIERARCHICAL'

P value = 6.46e-05 (Fisher's exact test), Q value = 0.041

Table S122. Gene #42: 'del_8p23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 20(8P23.3) MUTATED	19	11	32
DEL PEAK 20(8P23.3) WILD-TYPE	37	32	15

Figure S122. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 2.89e-22 (Fisher's exact test), Q value = 2.3e-19

Table S123. Gene #42: 'del_8p23.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 20(8P23.3) MUTATED	101	32	43
DEL PEAK 20(8P23.3) WILD-TYPE	70	163	18

Figure S123. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 3.4e-07 (Fisher's exact test), Q value = 0.00024

Table S124. Gene #42: 'del_8p23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 20(8P23.3) MUTATED	68	20	24
DEL PEAK 20(8P23.3) WILD-TYPE	46	68	44

Figure S124. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 4.67e-07 (Chi-square test), Q value = 0.00032

Table S125. Gene #42: 'del_8p23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 20(8P23.3) MUTATED	15	56	34	13	58
DEL PEAK 20(8P23.3) WILD-TYPE	18	57	37	77	58

Figure S125. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.06e-09 (Fisher's exact test), Q value = 2.2e-06

Table S126. Gene #42: 'del_8p23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 20(8P23.3) MUTATED	73	16	87
DEL PEAK 20(8P23.3) WILD-TYPE	91	82	74

Figure S126. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.22e-07 (Fisher's exact test), Q value = 0.00016

Table S127. Gene #42: 'del_8p23.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 20(8P23.3) MUTATED	46	14	32
DEL PEAK 20(8P23.3) WILD-TYPE	33	64	31

Figure S127. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p22' versus 'MRNA_CHIERARCHICAL'

P value = 0.000179 (Fisher's exact test), Q value = 0.11

Table S128. Gene #43: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 21(8P22) MUTATED	25	9	30
DEL PEAK 21(8P22) WILD-TYPE	31	34	17

Figure S128. Get High-res Image Gene #43: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 5.76e-28 (Fisher's exact test), Q value = 4.6e-25

Table S129. Gene #43: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 21(8P22) MUTATED	111	32	47
DEL PEAK 21(8P22) WILD-TYPE	60	163	14

Figure S129. Get High-res Image Gene #43: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p22' versus 'METHLYATION_CNMF'

P value = 3.92e-08 (Fisher's exact test), Q value = 2.8e-05

Table S130. Gene #43: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 21(8P22) MUTATED	75	23	26
DEL PEAK 21(8P22) WILD-TYPE	39	65	42

Figure S130. Get High-res Image Gene #43: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p22' versus 'RPPA_CHIERARCHICAL'

P value = 0.000135 (Fisher's exact test), Q value = 0.083

Table S131. Gene #43: 'del_8p22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 21(8P22) MUTATED	5	15	38	82
DEL PEAK 21(8P22) WILD-TYPE	21	41	25	98

Figure S131. Get High-res Image Gene #43: 'del_8p22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 2.22e-08 (Chi-square test), Q value = 1.6e-05

Table S132. Gene #43: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 21(8P22) MUTATED	16	65	36	14	59
DEL PEAK 21(8P22) WILD-TYPE	17	48	35	76	57

Figure S132. Get High-res Image Gene #43: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.66e-09 (Fisher's exact test), Q value = 3.3e-06

Table S133. Gene #43: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 21(8P22) MUTATED	75	20	95
DEL PEAK 21(8P22) WILD-TYPE	89	78	66

Figure S133. Get High-res Image Gene #43: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.42e-07 (Fisher's exact test), Q value = 0.00024

Table S134. Gene #43: 'del_8p22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 21(8P22) MUTATED	50	18	36
DEL PEAK 21(8P22) WILD-TYPE	29	60	27

Figure S134. Get High-res Image Gene #43: 'del_8p22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p11.21' versus 'CN_CNMF'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0086

Table S135. Gene #44: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 22(8P11.21) MUTATED	32	11	1
DEL PEAK 22(8P11.21) WILD-TYPE	139	184	60

Figure S135. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 4.85e-07 (Fisher's exact test), Q value = 0.00033

Table S136. Gene #46: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 24(10P15.3) MUTATED	46	14	15
DEL PEAK 24(10P15.3) WILD-TYPE	125	181	46

Figure S136. Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.068

Table S137. Gene #46: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 24(10P15.3) MUTATED	26	6	42
DEL PEAK 24(10P15.3) WILD-TYPE	138	92	119

Figure S137. Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 2.13e-10 (Fisher's exact test), Q value = 1.5e-07

Table S138. Gene #47: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 25(10Q21.1) MUTATED	60	15	15
DEL PEAK 25(10Q21.1) WILD-TYPE	111	180	46

Figure S138. Get High-res Image Gene #47: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000404 (Fisher's exact test), Q value = 0.24

Table S139. Gene #47: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 25(10Q21.1) MUTATED	33	9	47
DEL PEAK 25(10Q21.1) WILD-TYPE	131	89	114

Figure S139. Get High-res Image Gene #47: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1.72e-07 (Fisher's exact test), Q value = 0.00012

Table S140. Gene #48: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 26(10Q23.31) MUTATED	61	23	18
DEL PEAK 26(10Q23.31) WILD-TYPE	110	172	43

Figure S140. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000106 (Fisher's exact test), Q value = 0.066

Table S141. Gene #48: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 26(10Q23.31) MUTATED	27	7	21
DEL PEAK 26(10Q23.31) WILD-TYPE	52	71	42

Figure S141. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q25.2' versus 'CN_CNMF'

P value = 7.14e-10 (Fisher's exact test), Q value = 5.1e-07

Table S142. Gene #49: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 27(10Q25.2) MUTATED	66	20	15
DEL PEAK 27(10Q25.2) WILD-TYPE	105	175	46

Figure S142. Get High-res Image Gene #49: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.15e-06 (Fisher's exact test), Q value = 0.0021

Table S143. Gene #49: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 27(10Q25.2) MUTATED	40	7	53
DEL PEAK 27(10Q25.2) WILD-TYPE	124	91	108

Figure S143. Get High-res Image Gene #49: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.51e-06 (Fisher's exact test), Q value = 0.001

Table S144. Gene #49: 'del_10q25.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 27(10Q25.2) MUTATED	29	4	18
DEL PEAK 27(10Q25.2) WILD-TYPE	50	74	45

Figure S144. Get High-res Image Gene #49: 'del_10q25.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12p13.2' versus 'CN_CNMF'

P value = 6.93e-11 (Fisher's exact test), Q value = 5.1e-08

Table S145. Gene #50: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 28(12P13.2) MUTATED	42	4	8
DEL PEAK 28(12P13.2) WILD-TYPE	129	191	53

Figure S145. Get High-res Image Gene #50: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q32.11' versus 'MRNA_CNMF'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00076

Table S146. Gene #52: 'del_14q32.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 30(14Q32.11) MUTATED	8	36	2	11
DEL PEAK 30(14Q32.11) WILD-TYPE	27	25	27	10

Figure S146. Get High-res Image Gene #52: 'del_14q32.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q32.11' versus 'MRNA_CHIERARCHICAL'

P value = 3.13e-05 (Fisher's exact test), Q value = 0.02

Table S147. Gene #52: 'del_14q32.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 30(14Q32.11) MUTATED	23	6	28
DEL PEAK 30(14Q32.11) WILD-TYPE	33	37	19

Figure S147. Get High-res Image Gene #52: 'del_14q32.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q32.11' versus 'CN_CNMF'

P value = 4.19e-25 (Fisher's exact test), Q value = 3.3e-22

Table S148. Gene #52: 'del_14q32.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 30(14Q32.11) MUTATED	106	26	8
DEL PEAK 30(14Q32.11) WILD-TYPE	65	169	53

Figure S148. Get High-res Image Gene #52: 'del_14q32.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q32.11' versus 'METHLYATION_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.073

Table S149. Gene #52: 'del_14q32.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 30(14Q32.11) MUTATED	50	15	17
DEL PEAK 30(14Q32.11) WILD-TYPE	64	73	51

Figure S149. Get High-res Image Gene #52: 'del_14q32.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q32.11' versus 'MRNASEQ_CNMF'

P value = 4.38e-07 (Chi-square test), Q value = 3e-04

Table S150. Gene #52: 'del_14q32.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 30(14Q32.11) MUTATED	9	49	19	10	53
DEL PEAK 30(14Q32.11) WILD-TYPE	24	64	52	80	63

Figure S150. Get High-res Image Gene #52: 'del_14q32.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q32.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.85e-07 (Fisher's exact test), Q value = 0.00013

Table S151. Gene #52: 'del_14q32.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 30(14Q32.11) MUTATED	65	11	64
DEL PEAK 30(14Q32.11) WILD-TYPE	99	87	97

Figure S151. Get High-res Image Gene #52: 'del_14q32.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000245 (Fisher's exact test), Q value = 0.15

Table S152. Gene #52: 'del_14q32.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
DEL PEAK 30(14Q32.11) MUTATED	12	68	52
DEL PEAK 30(14Q32.11) WILD-TYPE	68	106	91

Figure S152. Get High-res Image Gene #52: 'del_14q32.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.014

Table S153. Gene #52: 'del_14q32.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 30(14Q32.11) MUTATED	34	9	22
DEL PEAK 30(14Q32.11) WILD-TYPE	45	69	41

Figure S153. Get High-res Image Gene #52: 'del_14q32.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q11.2' versus 'CN_CNMF'

P value = 3.99e-22 (Fisher's exact test), Q value = 3.1e-19

Table S154. Gene #53: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 31(15Q11.2) MUTATED	114	34	18
DEL PEAK 31(15Q11.2) WILD-TYPE	57	161	43

Figure S154. Get High-res Image Gene #53: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 2.65e-07 (Chi-square test), Q value = 0.00018

Table S155. Gene #53: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 31(15Q11.2) MUTATED	10	54	31	12	58
DEL PEAK 31(15Q11.2) WILD-TYPE	23	59	40	78	58

Figure S155. Get High-res Image Gene #53: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.27e-09 (Fisher's exact test), Q value = 3e-06

Table S156. Gene #53: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 31(15Q11.2) MUTATED	69	14	82
DEL PEAK 31(15Q11.2) WILD-TYPE	95	84	79

Figure S156. Get High-res Image Gene #53: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.84e-05 (Fisher's exact test), Q value = 0.018

Table S157. Gene #53: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 31(15Q11.2) MUTATED	40	15	31
DEL PEAK 31(15Q11.2) WILD-TYPE	39	63	32

Figure S157. Get High-res Image Gene #53: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q21.1' versus 'CN_CNMF'

P value = 5.66e-19 (Fisher's exact test), Q value = 4.4e-16

Table S158. Gene #54: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 32(15Q21.1) MUTATED	107	34	17
DEL PEAK 32(15Q21.1) WILD-TYPE	64	161	44

Figure S158. Get High-res Image Gene #54: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'MRNASEQ_CNMF'

P value = 7.84e-08 (Chi-square test), Q value = 5.5e-05

Table S159. Gene #54: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 32(15Q21.1) MUTATED	10	50	28	10	59
DEL PEAK 32(15Q21.1) WILD-TYPE	23	63	43	80	57

Figure S159. Get High-res Image Gene #54: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.02e-09 (Fisher's exact test), Q value = 2.9e-06

Table S160. Gene #54: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 32(15Q21.1) MUTATED	69	12	76
DEL PEAK 32(15Q21.1) WILD-TYPE	95	86	85

Figure S160. Get High-res Image Gene #54: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000132 (Fisher's exact test), Q value = 0.081

Table S161. Gene #54: 'del_15q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 32(15Q21.1) MUTATED	36	14	29
DEL PEAK 32(15Q21.1) WILD-TYPE	43	64	34

Figure S161. Get High-res Image Gene #54: 'del_15q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q22.33' versus 'MRNA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.097

Table S162. Gene #55: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 33(15Q22.33) MUTATED	8	32	3	10
DEL PEAK 33(15Q22.33) WILD-TYPE	27	29	26	11

Figure S162. Get High-res Image Gene #55: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q22.33' versus 'CN_CNMF'

P value = 2.5e-22 (Fisher's exact test), Q value = 2e-19

Table S163. Gene #55: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 33(15Q22.33) MUTATED	108	28	17
DEL PEAK 33(15Q22.33) WILD-TYPE	63	167	44

Figure S163. Get High-res Image Gene #55: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q22.33' versus 'METHLYATION_CNMF'

P value = 2.99e-05 (Fisher's exact test), Q value = 0.019

Table S164. Gene #55: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 33(15Q22.33) MUTATED	57	17	24
DEL PEAK 33(15Q22.33) WILD-TYPE	57	71	44

Figure S164. Get High-res Image Gene #55: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q22.33' versus 'MRNASEQ_CNMF'

P value = 4.13e-08 (Chi-square test), Q value = 2.9e-05

Table S165. Gene #55: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 33(15Q22.33) MUTATED	10	52	28	8	54
DEL PEAK 33(15Q22.33) WILD-TYPE	23	61	43	82	62

Figure S165. Get High-res Image Gene #55: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q22.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.26e-10 (Fisher's exact test), Q value = 4.5e-07

Table S166. Gene #55: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 33(15Q22.33) MUTATED	62	11	79
DEL PEAK 33(15Q22.33) WILD-TYPE	102	87	82

Figure S166. Get High-res Image Gene #55: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000102 (Fisher's exact test), Q value = 0.064

Table S167. Gene #55: 'del_15q22.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
DEL PEAK 33(15Q22.33) MUTATED	14	62	65
DEL PEAK 33(15Q22.33) WILD-TYPE	66	112	78

Figure S167. Get High-res Image Gene #55: 'del_15q22.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.2e-05 (Fisher's exact test), Q value = 0.021

Table S168. Gene #55: 'del_15q22.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 33(15Q22.33) MUTATED	36	13	30
DEL PEAK 33(15Q22.33) WILD-TYPE	43	65	33

Figure S168. Get High-res Image Gene #55: 'del_15q22.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MRNA_CNMF'

P value = 2.85e-08 (Fisher's exact test), Q value = 2e-05

Table S169. Gene #58: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 36(17P12) MUTATED	10	49	8	15
DEL PEAK 36(17P12) WILD-TYPE	25	12	21	6

Figure S169. Get High-res Image Gene #58: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 5.25e-07 (Fisher's exact test), Q value = 0.00036

Table S170. Gene #58: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 36(17P12) MUTATED	36	10	36
DEL PEAK 36(17P12) WILD-TYPE	20	33	11

Figure S170. Get High-res Image Gene #58: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 2.19e-34 (Fisher's exact test), Q value = 1.7e-31

Table S171. Gene #58: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 36(17P12) MUTATED	147	48	42
DEL PEAK 36(17P12) WILD-TYPE	24	147	19

Figure S171. Get High-res Image Gene #58: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1.25e-11 (Fisher's exact test), Q value = 9.3e-09

Table S172. Gene #58: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 36(17P12) MUTATED	91	29	31
DEL PEAK 36(17P12) WILD-TYPE	23	59	37

Figure S172. Get High-res Image Gene #58: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.000163 (Fisher's exact test), Q value = 0.099

Table S173. Gene #58: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 36(17P12) MUTATED	8	20	43	106
DEL PEAK 36(17P12) WILD-TYPE	18	36	20	74

Figure S173. Get High-res Image Gene #58: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 9.24e-19 (Chi-square test), Q value = 7.1e-16

Table S174. Gene #58: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 36(17P12) MUTATED	21	91	37	14	73
DEL PEAK 36(17P12) WILD-TYPE	12	22	34	76	43

Figure S174. Get High-res Image Gene #58: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.67e-14 (Fisher's exact test), Q value = 1.3e-11

Table S175. Gene #58: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 36(17P12) MUTATED	95	23	118
DEL PEAK 36(17P12) WILD-TYPE	69	75	43

Figure S175. Get High-res Image Gene #58: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.38e-11 (Fisher's exact test), Q value = 1.7e-08

Table S176. Gene #58: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 36(17P12) MUTATED	65	22	37
DEL PEAK 36(17P12) WILD-TYPE	14	56	26

Figure S176. Get High-res Image Gene #58: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18p11.31' versus 'MRNA_CNMF'

P value = 1.04e-11 (Fisher's exact test), Q value = 7.7e-09

Table S177. Gene #60: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 38(18P11.31) MUTATED	6	50	7	15
DEL PEAK 38(18P11.31) WILD-TYPE	29	11	22	6

Figure S177. Get High-res Image Gene #60: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18p11.31' versus 'MRNA_CHIERARCHICAL'

P value = 7.75e-10 (Fisher's exact test), Q value = 5.6e-07

Table S178. Gene #60: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 38(18P11.31) MUTATED	36	6	36
DEL PEAK 38(18P11.31) WILD-TYPE	20	37	11

Figure S178. Get High-res Image Gene #60: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18p11.31' versus 'CN_CNMF'

P value = 2.64e-42 (Fisher's exact test), Q value = 2.1e-39

Table S179. Gene #60: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 38(18P11.31) MUTATED	153	41	36
DEL PEAK 38(18P11.31) WILD-TYPE	18	154	25

Figure S179. Get High-res Image Gene #60: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_18p11.31' versus 'METHLYATION_CNMF'

P value = 1.19e-15 (Fisher's exact test), Q value = 9.1e-13

Table S180. Gene #60: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 38(18P11.31) MUTATED	93	22	34
DEL PEAK 38(18P11.31) WILD-TYPE	21	66	34

Figure S180. Get High-res Image Gene #60: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18p11.31' versus 'MRNASEQ_CNMF'

P value = 4.52e-26 (Chi-square test), Q value = 3.6e-23

Table S181. Gene #60: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 38(18P11.31) MUTATED	18	98	35	8	70
DEL PEAK 38(18P11.31) WILD-TYPE	15	15	36	82	46

Figure S181. Get High-res Image Gene #60: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.67e-24 (Fisher's exact test), Q value = 1.3e-21

Table S182. Gene #60: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 38(18P11.31) MUTATED	91	13	125
DEL PEAK 38(18P11.31) WILD-TYPE	73	85	36

Figure S182. Get High-res Image Gene #60: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.02e-14 (Fisher's exact test), Q value = 1.5e-11

Table S183. Gene #60: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 38(18P11.31) MUTATED	63	15	38
DEL PEAK 38(18P11.31) WILD-TYPE	16	63	25

Figure S183. Get High-res Image Gene #60: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MRNA_CNMF'

P value = 1.76e-11 (Fisher's exact test), Q value = 1.3e-08

Table S184. Gene #61: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 39(18Q12.2) MUTATED	8	53	9	16
DEL PEAK 39(18Q12.2) WILD-TYPE	27	8	20	5

Figure S184. Get High-res Image Gene #61: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q12.2' versus 'MRNA_CHIERARCHICAL'

P value = 2.8e-10 (Fisher's exact test), Q value = 2e-07

Table S185. Gene #61: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 39(18Q12.2) MUTATED	39	8	39
DEL PEAK 39(18Q12.2) WILD-TYPE	17	35	8

Figure S185. Get High-res Image Gene #61: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q12.2' versus 'CN_CNMF'

P value = 1.23e-43 (Fisher's exact test), Q value = 9.9e-41

Table S186. Gene #61: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 39(18Q12.2) MUTATED	158	50	48
DEL PEAK 39(18Q12.2) WILD-TYPE	13	145	13

Figure S186. Get High-res Image Gene #61: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 1.39e-17 (Fisher's exact test), Q value = 1.1e-14

Table S187. Gene #61: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 39(18Q12.2) MUTATED	102	29	34
DEL PEAK 39(18Q12.2) WILD-TYPE	12	59	34

Figure S187. Get High-res Image Gene #61: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 1.36e-23 (Chi-square test), Q value = 1.1e-20

Table S188. Gene #61: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 39(18Q12.2) MUTATED	20	99	43	14	79
DEL PEAK 39(18Q12.2) WILD-TYPE	13	14	28	76	37

Figure S188. Get High-res Image Gene #61: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.27e-24 (Fisher's exact test), Q value = 5e-21

Table S189. Gene #61: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 39(18Q12.2) MUTATED	100	20	135
DEL PEAK 39(18Q12.2) WILD-TYPE	64	78	26

Figure S189. Get High-res Image Gene #61: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.06e-14 (Fisher's exact test), Q value = 8.1e-12

Table S190. Gene #61: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 39(18Q12.2) MUTATED	69	21	42
DEL PEAK 39(18Q12.2) WILD-TYPE	10	57	21

Figure S190. Get High-res Image Gene #61: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MRNA_CNMF'

P value = 5.08e-11 (Fisher's exact test), Q value = 3.7e-08

Table S191. Gene #62: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 40(18Q21.2) MUTATED	8	53	10	16
DEL PEAK 40(18Q21.2) WILD-TYPE	27	8	19	5

Figure S191. Get High-res Image Gene #62: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1.75e-10 (Fisher's exact test), Q value = 1.3e-07

Table S192. Gene #62: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 40(18Q21.2) MUTATED	40	8	39
DEL PEAK 40(18Q21.2) WILD-TYPE	16	35	8

Figure S192. Get High-res Image Gene #62: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 2.05e-44 (Fisher's exact test), Q value = 1.6e-41

Table S193. Gene #62: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 40(18Q21.2) MUTATED	161	56	52
DEL PEAK 40(18Q21.2) WILD-TYPE	10	139	9

Figure S193. Get High-res Image Gene #62: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 6.96e-14 (Fisher's exact test), Q value = 5.3e-11

Table S194. Gene #62: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 40(18Q21.2) MUTATED	103	38	36
DEL PEAK 40(18Q21.2) WILD-TYPE	11	50	32

Figure S194. Get High-res Image Gene #62: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.000238 (Fisher's exact test), Q value = 0.14

Table S195. Gene #62: 'del_18q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 40(18Q21.2) MUTATED	10	24	46	120
DEL PEAK 40(18Q21.2) WILD-TYPE	16	32	17	60

Figure S195. Get High-res Image Gene #62: 'del_18q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 3.1e-19 (Chi-square test), Q value = 2.4e-16

Table S196. Gene #62: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 40(18Q21.2) MUTATED	20	101	46	22	79
DEL PEAK 40(18Q21.2) WILD-TYPE	13	12	25	68	37

Figure S196. Get High-res Image Gene #62: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.42e-19 (Fisher's exact test), Q value = 1.9e-16

Table S197. Gene #62: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 40(18Q21.2) MUTATED	101	29	138
DEL PEAK 40(18Q21.2) WILD-TYPE	63	69	23

Figure S197. Get High-res Image Gene #62: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.51e-13 (Fisher's exact test), Q value = 1.1e-10

Table S198. Gene #62: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 40(18Q21.2) MUTATED	72	27	44
DEL PEAK 40(18Q21.2) WILD-TYPE	7	51	19

Figure S198. Get High-res Image Gene #62: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q22.1' versus 'MRNA_CNMF'

P value = 1.3e-10 (Fisher's exact test), Q value = 9.5e-08

Table S199. Gene #63: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 41(18Q22.1) MUTATED	8	53	11	16
DEL PEAK 41(18Q22.1) WILD-TYPE	27	8	18	5

Figure S199. Get High-res Image Gene #63: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 9.95e-10 (Fisher's exact test), Q value = 7.1e-07

Table S200. Gene #63: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 41(18Q22.1) MUTATED	40	9	39
DEL PEAK 41(18Q22.1) WILD-TYPE	16	34	8

Figure S200. Get High-res Image Gene #63: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q22.1' versus 'CN_CNMF'

P value = 1.41e-46 (Fisher's exact test), Q value = 1.1e-43

Table S201. Gene #63: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 41(18Q22.1) MUTATED	163	55	51
DEL PEAK 41(18Q22.1) WILD-TYPE	8	140	10

Figure S201. Get High-res Image Gene #63: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q22.1' versus 'METHLYATION_CNMF'

P value = 4.09e-14 (Fisher's exact test), Q value = 3.1e-11

Table S202. Gene #63: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 41(18Q22.1) MUTATED	103	38	35
DEL PEAK 41(18Q22.1) WILD-TYPE	11	50	33

Figure S202. Get High-res Image Gene #63: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.000233 (Fisher's exact test), Q value = 0.14

Table S203. Gene #63: 'del_18q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 41(18Q22.1) MUTATED	10	24	45	122
DEL PEAK 41(18Q22.1) WILD-TYPE	16	32	18	58

Figure S203. Get High-res Image Gene #63: 'del_18q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q22.1' versus 'MRNASEQ_CNMF'

P value = 4.58e-18 (Chi-square test), Q value = 3.5e-15

Table S204. Gene #63: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 41(18Q22.1) MUTATED	20	100	46	23	79
DEL PEAK 41(18Q22.1) WILD-TYPE	13	13	25	67	37

Figure S204. Get High-res Image Gene #63: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.21e-19 (Fisher's exact test), Q value = 6.3e-16

Table S205. Gene #63: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 41(18Q22.1) MUTATED	102	29	137
DEL PEAK 41(18Q22.1) WILD-TYPE	62	69	24

Figure S205. Get High-res Image Gene #63: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.21e-14 (Fisher's exact test), Q value = 3.2e-11

Table S206. Gene #63: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 41(18Q22.1) MUTATED	72	26	44
DEL PEAK 41(18Q22.1) WILD-TYPE	7	52	19

Figure S206. Get High-res Image Gene #63: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_20p12.1' versus 'CN_CNMF'

P value = 1.91e-06 (Fisher's exact test), Q value = 0.0013

Table S207. Gene #65: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 43(20P12.1) MUTATED	47	17	17
DEL PEAK 43(20P12.1) WILD-TYPE	124	178	44

Figure S207. Get High-res Image Gene #65: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 6.19e-07 (Chi-square test), Q value = 0.00043

Table S208. Gene #65: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 43(20P12.1) MUTATED	4	42	11	7	17
DEL PEAK 43(20P12.1) WILD-TYPE	29	71	60	83	99

Figure S208. Get High-res Image Gene #65: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.71e-06 (Fisher's exact test), Q value = 0.0032

Table S209. Gene #65: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 43(20P12.1) MUTATED	27	6	48
DEL PEAK 43(20P12.1) WILD-TYPE	137	92	113

Figure S209. Get High-res Image Gene #65: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 2.16e-09 (Fisher's exact test), Q value = 1.5e-06

Table S210. Gene #66: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 44(21Q11.2) MUTATED	83	37	13
DEL PEAK 44(21Q11.2) WILD-TYPE	88	158	48

Figure S210. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.000161 (Chi-square test), Q value = 0.098

Table S211. Gene #66: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 44(21Q11.2) MUTATED	6	48	23	13	42
DEL PEAK 44(21Q11.2) WILD-TYPE	27	65	48	77	74

Figure S211. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.89e-05 (Fisher's exact test), Q value = 0.05

Table S212. Gene #66: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 44(21Q11.2) MUTATED	52	15	65
DEL PEAK 44(21Q11.2) WILD-TYPE	112	83	96

Figure S212. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.064

Table S213. Gene #66: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 44(21Q11.2) MUTATED	35	11	22
DEL PEAK 44(21Q11.2) WILD-TYPE	44	67	41

Figure S213. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.000134 (Fisher's exact test), Q value = 0.082

Table S214. Gene #67: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 45(22Q13.32) MUTATED	26	6	25
DEL PEAK 45(22Q13.32) WILD-TYPE	30	37	22

Figure S214. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 8.41e-18 (Fisher's exact test), Q value = 6.5e-15

Table S215. Gene #67: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	195	61
DEL PEAK 45(22Q13.32) MUTATED	102	33	14
DEL PEAK 45(22Q13.32) WILD-TYPE	69	162	47

Figure S215. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 7.2e-07 (Chi-square test), Q value = 0.00049

Table S216. Gene #67: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 45(22Q13.32) MUTATED	8	51	28	10	51
DEL PEAK 45(22Q13.32) WILD-TYPE	25	62	43	80	65

Figure S216. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.76e-07 (Fisher's exact test), Q value = 0.00019

Table S217. Gene #67: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	98	161
DEL PEAK 45(22Q13.32) MUTATED	64	13	71
DEL PEAK 45(22Q13.32) WILD-TYPE	100	85	90

Figure S217. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.42e-06 (Fisher's exact test), Q value = 0.0023

Table S218. Gene #67: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 45(22Q13.32) MUTATED	35	9	26
DEL PEAK 45(22Q13.32) WILD-TYPE	44	69	37

Figure S218. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = COAD-TP.transferedmergedcluster.txt
Number of patients = 427
Number of significantly focal cnvs = 67
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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