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

Colorectal Adenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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/C19P30HM

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 73 focal events and 12 molecular subtypes across 615 patients, 211 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q31.1 cnv correlated to 'CN_CNMF'.
amp_2q33.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_5p12 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_7p21.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_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', and 'MRNASEQ_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_11p15.5 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_13q12.13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_13q12.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_13q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_16p11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_17q24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_19p13.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'CN_CNMF'.
amp_20p12.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_20p11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_20q11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_20q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_20q13.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_1p13.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_2p12 cnv correlated to 'CN_CNMF'.
del_4p16.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4q35.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_5q21.2 cnv correlated to 'CN_CNMF'.
del_5q22.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_8p22 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_8q11.1 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_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_10q25.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_12p13.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_12q21.33 cnv correlated to 'CN_CNMF'.
del_14q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_14q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q15.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q22.33 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_17p12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF'.
del_20p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_22q13.32 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 73 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, 211 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	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 18q21 2	432 (70%)	183	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	0.012 (1.00)	0.0242 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	6e-05 (0.0425)	0.0309 (1.00)	1e-05 (0.00876)	5e-05 (0.0356)
del 18q12 2	416 (68%)	199	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	0.05 (1.00)	0.0605 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.00074 (0.477)	0.00783 (1.00)	1e-05 (0.00876)	7e-05 (0.0495)
del 18q22 1	427 (69%)	188	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	0.0305 (1.00)	0.0377 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	7e-05 (0.0495)	0.0883 (1.00)	2e-05 (0.0147)	0.00067 (0.433)
amp 13q12 13	401 (65%)	214	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	0.0168 (1.00)	0.0159 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.00026 (0.175)	0.483 (1.00)	0.00172 (1.00)	0.0507 (1.00)
amp 20q11 21	469 (76%)	146	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	0.00699 (1.00)	0.0134 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.0173 (1.00)	0.00034 (0.227)	0.0031 (1.00)	0.0169 (1.00)
amp 20q12	471 (77%)	144	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	0.0107 (1.00)	0.00697 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.00757 (1.00)	8e-05 (0.056)	0.00153 (0.964)	0.0288 (1.00)
amp 20q13 31	473 (77%)	142	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	0.0142 (1.00)	0.00547 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.0158 (1.00)	0.00034 (0.227)	0.00441 (1.00)	0.0332 (1.00)
del 18p11 31	370 (60%)	245	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	0.0575 (1.00)	0.116 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.0035 (1.00)	0.00708 (1.00)	3e-05 (0.0217)	0.00041 (0.271)
amp 13q12 2	396 (64%)	219	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	0.0201 (1.00)	0.04 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.00053 (0.346)	0.709 (1.00)	0.00331 (1.00)	0.0452 (1.00)
amp 13q22 1	397 (65%)	218	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	0.0836 (1.00)	0.096 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.00148 (0.934)	0.343 (1.00)	0.0395 (1.00)	0.179 (1.00)
amp 20p11 21	363 (59%)	252	0.00012 (0.0827)	2e-05 (0.0147)	1e-05 (0.00876)	2e-05 (0.0147)	0.00547 (1.00)	0.139 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.0194 (1.00)	0.00789 (1.00)	0.125 (1.00)	0.128 (1.00)
del 14q11 2	212 (34%)	403	1e-05 (0.00876)	7e-05 (0.0495)	1e-05 (0.00876)	2e-05 (0.0147)	0.00749 (1.00)	0.14 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.0576 (1.00)	0.12 (1.00)	0.0403 (1.00)	0.0438 (1.00)
del 17p12	370 (60%)	245	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	0.0178 (1.00)	0.00691 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.0128 (1.00)	0.012 (1.00)	0.0362 (1.00)	0.162 (1.00)
amp 7p21 3	363 (59%)	252	0.00099 (0.633)	1e-05 (0.00876)	1e-05 (0.00876)	1e-05 (0.00876)	0.025 (1.00)	0.00248 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.00899 (1.00)	0.167 (1.00)	0.0245 (1.00)	0.0998 (1.00)
amp 17q24 1	144 (23%)	471	0.00905 (1.00)	0.00787 (1.00)	1e-05 (0.00876)	0.00027 (0.181)	0.0914 (1.00)	0.0242 (1.00)	3e-05 (0.0217)	0.0002 (0.136)	0.00021 (0.143)	0.032 (1.00)	0.466 (1.00)	0.247 (1.00)
del 1p36 11	244 (40%)	371	0.00011 (0.076)	0.00054 (0.352)	1e-05 (0.00876)	3e-05 (0.0217)	0.11 (1.00)	0.104 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.4 (1.00)	0.01 (1.00)	0.223 (1.00)	0.537 (1.00)
del 8p23 2	290 (47%)	325	0.00018 (0.123)	0.00089 (0.57)	1e-05 (0.00876)	1e-05 (0.00876)	0.149 (1.00)	0.0308 (1.00)	2e-05 (0.0147)	1e-05 (0.00876)	0.162 (1.00)	0.0309 (1.00)	0.004 (1.00)	0.515 (1.00)
del 8p22	303 (49%)	312	0.00114 (0.726)	0.00032 (0.214)	1e-05 (0.00876)	1e-05 (0.00876)	0.147 (1.00)	0.00787 (1.00)	0.0001 (0.0693)	1e-05 (0.00876)	0.317 (1.00)	0.0614 (1.00)	0.00518 (1.00)	0.617 (1.00)
del 15q22 33	238 (39%)	377	3e-05 (0.0217)	0.00093 (0.595)	1e-05 (0.00876)	7e-05 (0.0495)	0.555 (1.00)	0.326 (1.00)	2e-05 (0.0147)	1e-05 (0.00876)	0.787 (1.00)	0.899 (1.00)	0.0835 (1.00)	0.145 (1.00)
amp 11p15 5	139 (23%)	476	0.0013 (0.823)	0.00187 (1.00)	0.00014 (0.0959)	0.0004 (0.265)	0.0302 (1.00)	0.0823 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.427 (1.00)	1e-05 (0.00876)	0.889 (1.00)	0.53 (1.00)
amp 17q12	160 (26%)	455	0.0249 (1.00)	0.00739 (1.00)	1e-05 (0.00876)	0.00024 (0.162)	0.16 (1.00)	0.088 (1.00)	5e-05 (0.0356)	9e-05 (0.0628)	0.00614 (1.00)	0.0223 (1.00)	0.379 (1.00)	0.331 (1.00)
del 4q22 1	224 (36%)	391	0.0167 (1.00)	0.0289 (1.00)	1e-05 (0.00876)	7e-05 (0.0495)	0.583 (1.00)	0.67 (1.00)	0.00024 (0.162)	2e-05 (0.0147)	0.0183 (1.00)	0.13 (1.00)	0.0393 (1.00)	0.208 (1.00)
del 14q31 1	218 (35%)	397	0.00056 (0.364)	0.00058 (0.376)	1e-05 (0.00876)	4e-05 (0.0286)	0.00127 (0.805)	0.14 (1.00)	1e-05 (0.00876)	1e-05 (0.00876)	0.243 (1.00)	0.1 (1.00)	0.357 (1.00)	0.0742 (1.00)
del 15q11 2	253 (41%)	362	0.00055 (0.358)	0.00384 (1.00)	1e-05 (0.00876)	0.00025 (0.168)	0.132 (1.00)	0.365 (1.00)	3e-05 (0.0217)	1e-05 (0.00876)	0.435 (1.00)	0.431 (1.00)	0.0453 (1.00)	0.0668 (1.00)
del 15q15 2	251 (41%)	364	2e-05 (0.0147)	0.00207 (1.00)	1e-05 (0.00876)	0.00039 (0.259)	0.0948 (1.00)	0.371 (1.00)	3e-05 (0.0217)	1e-05 (0.00876)	0.628 (1.00)	0.416 (1.00)	0.0566 (1.00)	0.416 (1.00)
del 20p12 1	135 (22%)	480	0.0563 (1.00)	0.0007 (0.452)	1e-05 (0.00876)	1e-05 (0.00876)	0.605 (1.00)	0.766 (1.00)	8e-05 (0.056)	1e-05 (0.00876)	0.0309 (1.00)	0.0126 (1.00)	0.871 (1.00)	0.128 (1.00)
amp 2q33 1	141 (23%)	474	0.067 (1.00)	0.00049 (0.322)	6e-05 (0.0425)	0.00083 (0.533)	0.242 (1.00)	0.655 (1.00)	9e-05 (0.0628)	0.00013 (0.0894)	0.0545 (1.00)	0.044 (1.00)	0.828 (1.00)	0.792 (1.00)
amp 6p21 1	154 (25%)	461	0.0306 (1.00)	0.00015 (0.103)	1e-05 (0.00876)	0.198 (1.00)	0.588 (1.00)	0.732 (1.00)	0.0674 (1.00)	0.0001 (0.0693)	0.183 (1.00)	0.706 (1.00)	0.0683 (1.00)	0.0155 (1.00)
amp 8q12 1	331 (54%)	284	0.143 (1.00)	0.0431 (1.00)	1e-05 (0.00876)	0.0304 (1.00)	0.0289 (1.00)	0.0229 (1.00)	0.00013 (0.0894)	3e-05 (0.0217)	0.112 (1.00)	0.015 (1.00)	0.0164 (1.00)	0.234 (1.00)
amp 8q24 21	368 (60%)	247	0.239 (1.00)	0.0492 (1.00)	1e-05 (0.00876)	0.00051 (0.334)	0.0256 (1.00)	0.0403 (1.00)	2e-05 (0.0147)	1e-05 (0.00876)	0.143 (1.00)	0.0337 (1.00)	0.0519 (1.00)	0.514 (1.00)
amp 16p11 2	173 (28%)	442	0.0181 (1.00)	0.0021 (1.00)	1e-05 (0.00876)	0.00038 (0.253)	0.0259 (1.00)	0.0543 (1.00)	3e-05 (0.0217)	2e-05 (0.0147)	0.448 (1.00)	0.718 (1.00)	0.0344 (1.00)	0.0834 (1.00)
del 1p33	176 (29%)	439	0.0204 (1.00)	0.0797 (1.00)	1e-05 (0.00876)	0.00031 (0.208)	0.829 (1.00)	0.557 (1.00)	9e-05 (0.0628)	0.00363 (1.00)	0.453 (1.00)	0.107 (1.00)	0.777 (1.00)	0.58 (1.00)
del 4q35 1	233 (38%)	382	0.0211 (1.00)	0.0574 (1.00)	1e-05 (0.00876)	4e-05 (0.0286)	0.35 (1.00)	0.762 (1.00)	0.00049 (0.322)	1e-05 (0.00876)	0.194 (1.00)	0.442 (1.00)	0.216 (1.00)	0.613 (1.00)
del 5q12 1	158 (26%)	457	0.00049 (0.322)	0.0002 (0.136)	1e-05 (0.00876)	0.00343 (1.00)	0.0448 (1.00)	0.171 (1.00)	0.00574 (1.00)	5e-05 (0.0356)	0.701 (1.00)	0.975 (1.00)	0.148 (1.00)	0.619 (1.00)
del 15q21 1	248 (40%)	367	0.00047 (0.31)	0.0236 (1.00)	1e-05 (0.00876)	0.00049 (0.322)	0.0956 (1.00)	0.347 (1.00)	7e-05 (0.0495)	1e-05 (0.00876)	0.673 (1.00)	0.466 (1.00)	0.0662 (1.00)	0.423 (1.00)
del 22q13 32	229 (37%)	386	0.00221 (1.00)	0.00013 (0.0894)	1e-05 (0.00876)	0.0162 (1.00)	0.476 (1.00)	0.542 (1.00)	0.00441 (1.00)	1e-05 (0.00876)	0.895 (1.00)	0.271 (1.00)	0.347 (1.00)	0.477 (1.00)
amp 5p12	119 (19%)	496	0.132 (1.00)	0.0213 (1.00)	1e-05 (0.00876)	0.697 (1.00)	0.00155 (0.973)	0.135 (1.00)	0.00183 (1.00)	3e-05 (0.0217)	0.915 (1.00)	0.343 (1.00)	0.0987 (1.00)	0.183 (1.00)
amp 19p13 2	111 (18%)	504	0.109 (1.00)	0.00789 (1.00)	1e-05 (0.00876)	0.0106 (1.00)	0.459 (1.00)	0.679 (1.00)	0.059 (1.00)	0.00024 (0.162)	0.116 (1.00)	0.67 (1.00)	0.564 (1.00)	0.0788 (1.00)
amp 20p12 1	278 (45%)	337	0.0176 (1.00)	0.00796 (1.00)	1e-05 (0.00876)	0.168 (1.00)	0.00116 (0.738)	0.111 (1.00)	0.0418 (1.00)	1e-05 (0.00876)	0.954 (1.00)	0.669 (1.00)	0.164 (1.00)	0.168 (1.00)
del 1p13 2	176 (29%)	439	0.265 (1.00)	0.401 (1.00)	1e-05 (0.00876)	0.0111 (1.00)	0.763 (1.00)	0.831 (1.00)	0.00121 (0.768)	0.00026 (0.175)	0.515 (1.00)	0.119 (1.00)	0.494 (1.00)	0.222 (1.00)
del 4p16 2	202 (33%)	413	0.0543 (1.00)	0.0348 (1.00)	1e-05 (0.00876)	0.00286 (1.00)	0.431 (1.00)	0.293 (1.00)	0.00945 (1.00)	9e-05 (0.0628)	0.379 (1.00)	0.238 (1.00)	0.0554 (1.00)	0.921 (1.00)
del 5q22 2	189 (31%)	426	0.00081 (0.521)	0.00073 (0.471)	1e-05 (0.00876)	0.0927 (1.00)	0.273 (1.00)	0.38 (1.00)	0.0785 (1.00)	0.00022 (0.149)	0.469 (1.00)	0.351 (1.00)	0.208 (1.00)	0.784 (1.00)
del 10p15 3	115 (19%)	500	0.154 (1.00)	0.194 (1.00)	1e-05 (0.00876)	0.00404 (1.00)	0.0164 (1.00)	0.124 (1.00)	0.00318 (1.00)	4e-05 (0.0286)	0.637 (1.00)	0.498 (1.00)	0.0106 (1.00)	0.0438 (1.00)
del 10q21 1	139 (23%)	476	0.0327 (1.00)	0.118 (1.00)	1e-05 (0.00876)	0.0141 (1.00)	0.0448 (1.00)	0.073 (1.00)	3e-05 (0.0217)	0.0006 (0.389)	0.672 (1.00)	0.0956 (1.00)	0.352 (1.00)	0.483 (1.00)
del 10q23 31	161 (26%)	454	0.114 (1.00)	0.241 (1.00)	1e-05 (0.00876)	0.0399 (1.00)	0.0847 (1.00)	0.305 (1.00)	0.00153 (0.964)	0.00019 (0.13)	0.524 (1.00)	0.134 (1.00)	0.121 (1.00)	0.131 (1.00)
del 10q25 2	157 (26%)	458	0.223 (1.00)	0.299 (1.00)	1e-05 (0.00876)	0.0167 (1.00)	0.00602 (1.00)	0.15 (1.00)	0.00044 (0.291)	1e-05 (0.00876)	0.991 (1.00)	0.206 (1.00)	0.166 (1.00)	0.363 (1.00)
del 12p13 1	92 (15%)	523	0.00472 (1.00)	0.00177 (1.00)	1e-05 (0.00876)	0.046 (1.00)	0.91 (1.00)	0.473 (1.00)	0.0208 (1.00)	0.00011 (0.076)	0.709 (1.00)	0.757 (1.00)	0.0287 (1.00)	0.0265 (1.00)
del 21q11 2	214 (35%)	401	0.0203 (1.00)	0.00169 (1.00)	1e-05 (0.00876)	0.0206 (1.00)	0.456 (1.00)	0.708 (1.00)	7e-05 (0.0495)	0.00047 (0.31)	0.0385 (1.00)	0.317 (1.00)	0.667 (1.00)	0.346 (1.00)
amp 1q31 1	145 (24%)	470	0.585 (1.00)	0.547 (1.00)	9e-05 (0.0628)	0.524 (1.00)	0.366 (1.00)	0.125 (1.00)	0.926 (1.00)	0.396 (1.00)	0.343 (1.00)	0.257 (1.00)	0.389 (1.00)	0.29 (1.00)
amp 8p11 23	211 (34%)	404	0.394 (1.00)	0.209 (1.00)	1e-05 (0.00876)	0.363 (1.00)	0.769 (1.00)	0.988 (1.00)	0.0177 (1.00)	0.00299 (1.00)	0.0128 (1.00)	0.0825 (1.00)	0.693 (1.00)	0.421 (1.00)
amp 8p11 21	256 (42%)	359	0.174 (1.00)	0.109 (1.00)	1e-05 (0.00876)	0.221 (1.00)	0.725 (1.00)	0.356 (1.00)	0.0181 (1.00)	0.00769 (1.00)	0.0799 (1.00)	0.248 (1.00)	0.65 (1.00)	0.778 (1.00)
amp 19q12	139 (23%)	476	0.0289 (1.00)	0.00143 (0.904)	1e-05 (0.00876)	0.22 (1.00)	0.0762 (1.00)	0.431 (1.00)	0.158 (1.00)	0.00611 (1.00)	0.185 (1.00)	0.877 (1.00)	0.462 (1.00)	0.668 (1.00)
del 2p12	21 (3%)	594	1 (1.00)	0.962 (1.00)	0.00031 (0.208)	0.0063 (1.00)	0.367 (1.00)	1 (1.00)	0.0493 (1.00)	0.0211 (1.00)	0.00646 (1.00)	0.0914 (1.00)	0.127 (1.00)	0.0761 (1.00)
del 5q21 2	187 (30%)	428	0.0547 (1.00)	0.0134 (1.00)	1e-05 (0.00876)	0.0628 (1.00)	0.0773 (1.00)	0.076 (1.00)	0.205 (1.00)	0.00106 (0.676)	0.633 (1.00)	0.836 (1.00)	0.153 (1.00)	0.876 (1.00)
del 8q11 1	47 (8%)	568	0.582 (1.00)	0.181 (1.00)	2e-05 (0.0147)	0.394 (1.00)	0.284 (1.00)	0.304 (1.00)	0.321 (1.00)	0.0366 (1.00)	0.165 (1.00)	0.0936 (1.00)	0.598 (1.00)	0.652 (1.00)
del 12q21 33	90 (15%)	525	0.0347 (1.00)	0.0343 (1.00)	1e-05 (0.00876)	0.0301 (1.00)	0.539 (1.00)	0.891 (1.00)	0.066 (1.00)	0.00319 (1.00)	0.831 (1.00)	0.771 (1.00)	0.477 (1.00)	0.2 (1.00)
del 19p13 3	97 (16%)	518	0.118 (1.00)	0.465 (1.00)	2e-05 (0.0147)	0.404 (1.00)	0.881 (1.00)	0.102 (1.00)	0.198 (1.00)	0.0203 (1.00)	0.649 (1.00)	0.00502 (1.00)	0.036 (1.00)	0.191 (1.00)
amp 5q22 3	66 (11%)	549	0.601 (1.00)	0.575 (1.00)	0.00469 (1.00)	0.534 (1.00)	0.467 (1.00)	0.31 (1.00)	0.494 (1.00)	0.0113 (1.00)	0.62 (1.00)	0.126 (1.00)	0.889 (1.00)	0.109 (1.00)
amp 10q22 3	40 (7%)	575	1 (1.00)	0.861 (1.00)	0.169 (1.00)	0.648 (1.00)	0.296 (1.00)	0.688 (1.00)	0.606 (1.00)	0.625 (1.00)	0.435 (1.00)	0.974 (1.00)	0.348 (1.00)	0.481 (1.00)
amp 12p13 32	150 (24%)	465	0.649 (1.00)	0.594 (1.00)	0.0303 (1.00)	0.0151 (1.00)	0.476 (1.00)	0.304 (1.00)	0.723 (1.00)	0.428 (1.00)	0.718 (1.00)	1 (1.00)	0.513 (1.00)	0.176 (1.00)
amp 15q26 1	42 (7%)	573	0.711 (1.00)	0.663 (1.00)	0.0927 (1.00)	0.629 (1.00)	0.237 (1.00)	0.467 (1.00)	0.456 (1.00)	0.327 (1.00)	0.715 (1.00)	0.828 (1.00)	0.655 (1.00)	0.742 (1.00)
del 2q22 1	35 (6%)	580	0.927 (1.00)	0.61 (1.00)	0.0996 (1.00)	0.602 (1.00)	0.34 (1.00)	0.353 (1.00)	0.14 (1.00)	0.0897 (1.00)	0.578 (1.00)	0.112 (1.00)	0.706 (1.00)	0.681 (1.00)
del 3p26 3	93 (15%)	522	0.361 (1.00)	0.493 (1.00)	0.142 (1.00)	0.889 (1.00)	0.648 (1.00)	0.979 (1.00)	0.171 (1.00)	0.544 (1.00)	0.475 (1.00)	0.577 (1.00)	0.387 (1.00)	0.579 (1.00)
del 3p14 2	119 (19%)	496	0.62 (1.00)	0.467 (1.00)	0.454 (1.00)	0.9 (1.00)	0.47 (1.00)	0.246 (1.00)	0.339 (1.00)	0.332 (1.00)	0.385 (1.00)	0.309 (1.00)	0.994 (1.00)	0.672 (1.00)
del 3q26 31	64 (10%)	551	0.642 (1.00)	0.883 (1.00)	0.381 (1.00)	0.698 (1.00)	0.77 (1.00)	0.55 (1.00)	0.778 (1.00)	0.647 (1.00)	0.723 (1.00)	0.261 (1.00)	0.161 (1.00)	0.924 (1.00)
del 6p25 3	80 (13%)	535	0.908 (1.00)	0.346 (1.00)	0.369 (1.00)	0.261 (1.00)	0.0356 (1.00)	0.629 (1.00)	0.548 (1.00)	0.759 (1.00)	0.585 (1.00)	0.724 (1.00)	0.622 (1.00)	0.828 (1.00)
del 6q26	92 (15%)	523	0.801 (1.00)	0.85 (1.00)	0.771 (1.00)	0.921 (1.00)	0.0442 (1.00)	0.127 (1.00)	0.0879 (1.00)	0.0857 (1.00)	0.375 (1.00)	0.36 (1.00)	0.215 (1.00)	0.585 (1.00)
del 7q31 1	17 (3%)	598	0.292 (1.00)	0.687 (1.00)	0.636 (1.00)	1 (1.00)	0.686 (1.00)	0.217 (1.00)	0.726 (1.00)	0.833 (1.00)	0.109 (1.00)	0.947 (1.00)	0.253 (1.00)	1 (1.00)
del 9p24 2	84 (14%)	531	0.218 (1.00)	0.298 (1.00)	0.00458 (1.00)	0.112 (1.00)	0.598 (1.00)	1 (1.00)	0.00962 (1.00)	0.00783 (1.00)	0.211 (1.00)	0.0225 (1.00)	0.679 (1.00)	0.566 (1.00)
del 11q22 3	111 (18%)	504	0.381 (1.00)	0.231 (1.00)	0.00693 (1.00)	0.125 (1.00)	0.408 (1.00)	1 (1.00)	0.636 (1.00)	0.114 (1.00)	0.818 (1.00)	0.491 (1.00)	0.37 (1.00)	0.374 (1.00)
del 16p13 3	69 (11%)	546	0.0926 (1.00)	0.0769 (1.00)	0.22 (1.00)	0.387 (1.00)	0.541 (1.00)	0.971 (1.00)	0.522 (1.00)	0.56 (1.00)	0.67 (1.00)	0.134 (1.00)	0.278 (1.00)	0.929 (1.00)
del 16q23 1	84 (14%)	531	0.0447 (1.00)	0.00356 (1.00)	0.168 (1.00)	0.333 (1.00)	0.251 (1.00)	0.802 (1.00)	0.466 (1.00)	0.0452 (1.00)	0.607 (1.00)	0.273 (1.00)	0.939 (1.00)	0.399 (1.00)
del 17q24 3	95 (15%)	520	0.976 (1.00)	0.729 (1.00)	0.00565 (1.00)	1 (1.00)	0.906 (1.00)	0.231 (1.00)	0.481 (1.00)	0.144 (1.00)	0.644 (1.00)	0.468 (1.00)	0.306 (1.00)	0.552 (1.00)

'amp_1q31.1' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.063

Table S1. Gene #1: 'amp_1q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 1(1Q31.1) MUTATED	39	67	39
AMP PEAK 1(1Q31.1) WILD-TYPE	214	142	114

Figure S1. Get High-res Image Gene #1: 'amp_1q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q33.1' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S2. Gene #2: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 2(2Q33.1) MUTATED	36	64	41
AMP PEAK 2(2Q33.1) WILD-TYPE	217	145	112

Figure S2. Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.063

Table S3. Gene #2: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 2(2Q33.1) MUTATED	48	32	15	38
AMP PEAK 2(2Q33.1) WILD-TYPE	91	98	120	153

Figure S3. Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.089

Table S4. Gene #2: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 2(2Q33.1) MUTATED	26	24	32	7	37	3	4
AMP PEAK 2(2Q33.1) WILD-TYPE	52	100	64	56	113	33	44

Figure S4. Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S5. Gene #3: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 3(5P12) MUTATED	25	58	36
AMP PEAK 3(5P12) WILD-TYPE	228	151	117

Figure S5. Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S6. Gene #3: 'amp_5p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 3(5P12) MUTATED	19	8	29	6	40	4	6
AMP PEAK 3(5P12) WILD-TYPE	59	116	67	57	110	32	42

Figure S6. Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S7. Gene #5: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
AMP PEAK 5(6P21.1) MUTATED	4	12	13	22
AMP PEAK 5(6P21.1) WILD-TYPE	45	29	63	27

Figure S7. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S8. Gene #5: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 5(6P21.1) MUTATED	23	82	49
AMP PEAK 5(6P21.1) WILD-TYPE	230	127	104

Figure S8. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.069

Table S9. Gene #5: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 5(6P21.1) MUTATED	21	31	35	7	48	4	5
AMP PEAK 5(6P21.1) WILD-TYPE	57	93	61	56	102	32	43

Figure S9. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S10. Gene #6: 'amp_7p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
AMP PEAK 6(7P21.3) MUTATED	13	27	33	37
AMP PEAK 6(7P21.3) WILD-TYPE	36	14	43	12

Figure S10. Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S11. Gene #6: 'amp_7p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 6(7P21.3) MUTATED	92	164	107
AMP PEAK 6(7P21.3) WILD-TYPE	161	45	46

Figure S11. Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S12. Gene #6: 'amp_7p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
AMP PEAK 6(7P21.3) MUTATED	55	123	59
AMP PEAK 6(7P21.3) WILD-TYPE	43	35	62

Figure S12. Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S13. Gene #6: 'amp_7p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 6(7P21.3) MUTATED	105	80	59	105
AMP PEAK 6(7P21.3) WILD-TYPE	34	50	76	86

Figure S13. Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S14. Gene #6: 'amp_7p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 6(7P21.3) MUTATED	53	76	80	15	97	10	18
AMP PEAK 6(7P21.3) WILD-TYPE	25	48	16	48	53	26	30

Figure S14. Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S15. Gene #7: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 7(8P11.23) MUTATED	51	60	100
AMP PEAK 7(8P11.23) WILD-TYPE	202	149	53

Figure S15. Get High-res Image Gene #7: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S16. Gene #8: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 8(8P11.21) MUTATED	57	74	125
AMP PEAK 8(8P11.21) WILD-TYPE	196	135	28

Figure S16. Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S17. Gene #9: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 9(8Q12.1) MUTATED	78	104	149
AMP PEAK 9(8Q12.1) WILD-TYPE	175	105	4

Figure S17. Get High-res Image Gene #9: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q12.1' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.089

Table S18. Gene #9: 'amp_8q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 9(8Q12.1) MUTATED	90	79	52	98
AMP PEAK 9(8Q12.1) WILD-TYPE	49	51	83	93

Figure S18. Get High-res Image Gene #9: 'amp_8q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S19. Gene #9: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 9(8Q12.1) MUTATED	53	57	66	26	85	12	20
AMP PEAK 9(8Q12.1) WILD-TYPE	25	67	30	37	65	24	28

Figure S19. Get High-res Image Gene #9: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S20. Gene #10: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 10(8Q24.21) MUTATED	89	127	152
AMP PEAK 10(8Q24.21) WILD-TYPE	164	82	1

Figure S20. Get High-res Image Gene #10: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S21. Gene #10: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 10(8Q24.21) MUTATED	100	84	59	111
AMP PEAK 10(8Q24.21) WILD-TYPE	39	46	76	80

Figure S21. Get High-res Image Gene #10: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S22. Gene #10: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 10(8Q24.21) MUTATED	56	63	72	29	95	13	26
AMP PEAK 10(8Q24.21) WILD-TYPE	22	61	24	34	55	23	22

Figure S22. Get High-res Image Gene #10: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.096

Table S23. Gene #12: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 12(11P15.5) MUTATED	36	58	45
AMP PEAK 12(11P15.5) WILD-TYPE	217	151	108

Figure S23. Get High-res Image Gene #12: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S24. Gene #12: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 12(11P15.5) MUTATED	49	24	12	48
AMP PEAK 12(11P15.5) WILD-TYPE	90	106	123	143

Figure S24. Get High-res Image Gene #12: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S25. Gene #12: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 12(11P15.5) MUTATED	29	17	24	4	49	1	9
AMP PEAK 12(11P15.5) WILD-TYPE	49	107	72	59	101	35	39

Figure S25. Get High-res Image Gene #12: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S26. Gene #12: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	228	139	171
AMP PEAK 12(11P15.5) MUTATED	35	67	22
AMP PEAK 12(11P15.5) WILD-TYPE	193	72	149

Figure S26. Get High-res Image Gene #12: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S27. Gene #14: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 14(13Q12.13) MUTATED	19	48	57	16
AMP PEAK 14(13Q12.13) WILD-TYPE	24	14	12	25

Figure S27. Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q12.13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S28. Gene #14: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
AMP PEAK 14(13Q12.13) MUTATED	15	30	51	44
AMP PEAK 14(13Q12.13) WILD-TYPE	34	11	25	5

Figure S28. Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S29. Gene #14: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 14(13Q12.13) MUTATED	94	199	108
AMP PEAK 14(13Q12.13) WILD-TYPE	159	10	45

Figure S29. Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S30. Gene #14: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
AMP PEAK 14(13Q12.13) MUTATED	57	135	58
AMP PEAK 14(13Q12.13) WILD-TYPE	41	23	63

Figure S30. Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S31. Gene #14: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 14(13Q12.13) MUTATED	111	81	62	133
AMP PEAK 14(13Q12.13) WILD-TYPE	28	49	73	58

Figure S31. Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S32. Gene #14: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 14(13Q12.13) MUTATED	60	82	81	15	121	9	19
AMP PEAK 14(13Q12.13) WILD-TYPE	18	42	15	48	29	27	29

Figure S32. Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.17

Table S33. Gene #14: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	211	95	232
AMP PEAK 14(13Q12.13) MUTATED	159	52	141
AMP PEAK 14(13Q12.13) WILD-TYPE	52	43	91

Figure S33. Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q12.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S34. Gene #15: 'amp_13q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 15(13Q12.2) MUTATED	19	47	55	17
AMP PEAK 15(13Q12.2) WILD-TYPE	24	15	14	24

Figure S34. Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q12.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S35. Gene #15: 'amp_13q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
AMP PEAK 15(13Q12.2) MUTATED	16	29	50	43
AMP PEAK 15(13Q12.2) WILD-TYPE	33	12	26	6

Figure S35. Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S36. Gene #15: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 15(13Q12.2) MUTATED	90	200	106
AMP PEAK 15(13Q12.2) WILD-TYPE	163	9	47

Figure S36. Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S37. Gene #15: 'amp_13q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
AMP PEAK 15(13Q12.2) MUTATED	57	135	56
AMP PEAK 15(13Q12.2) WILD-TYPE	41	23	65

Figure S37. Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S38. Gene #15: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 15(13Q12.2) MUTATED	110	80	61	131
AMP PEAK 15(13Q12.2) WILD-TYPE	29	50	74	60

Figure S38. Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S39. Gene #15: 'amp_13q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 15(13Q12.2) MUTATED	59	81	81	14	119	9	19
AMP PEAK 15(13Q12.2) WILD-TYPE	19	43	15	49	31	27	29

Figure S39. Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S40. Gene #16: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 16(13Q22.1) MUTATED	18	48	54	17
AMP PEAK 16(13Q22.1) WILD-TYPE	25	14	15	24

Figure S40. Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S41. Gene #16: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
AMP PEAK 16(13Q22.1) MUTATED	14	29	52	42
AMP PEAK 16(13Q22.1) WILD-TYPE	35	12	24	7

Figure S41. Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S42. Gene #16: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 16(13Q22.1) MUTATED	95	195	107
AMP PEAK 16(13Q22.1) WILD-TYPE	158	14	46

Figure S42. Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S43. Gene #16: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
AMP PEAK 16(13Q22.1) MUTATED	57	133	60
AMP PEAK 16(13Q22.1) WILD-TYPE	41	25	61

Figure S43. Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S44. Gene #16: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 16(13Q22.1) MUTATED	110	81	61	132
AMP PEAK 16(13Q22.1) WILD-TYPE	29	49	74	59

Figure S44. Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S45. Gene #16: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 16(13Q22.1) MUTATED	59	79	79	19	121	10	17
AMP PEAK 16(13Q22.1) WILD-TYPE	19	45	17	44	29	26	31

Figure S45. Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S46. Gene #18: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 18(16P11.2) MUTATED	24	98	51
AMP PEAK 18(16P11.2) WILD-TYPE	229	111	102

Figure S46. Get High-res Image Gene #18: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S47. Gene #18: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 18(16P11.2) MUTATED	53	33	18	61
AMP PEAK 18(16P11.2) WILD-TYPE	86	97	117	130

Figure S47. Get High-res Image Gene #18: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S48. Gene #18: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 18(16P11.2) MUTATED	21	26	40	6	57	3	12
AMP PEAK 18(16P11.2) WILD-TYPE	57	98	56	57	93	33	36

Figure S48. Get High-res Image Gene #18: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S49. Gene #19: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 19(17Q12) MUTATED	32	67	61
AMP PEAK 19(17Q12) WILD-TYPE	221	142	92

Figure S49. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.16

Table S50. Gene #19: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
AMP PEAK 19(17Q12) MUTATED	18	58	21
AMP PEAK 19(17Q12) WILD-TYPE	80	100	100

Figure S50. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.036

Table S51. Gene #19: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 19(17Q12) MUTATED	53	24	21	53
AMP PEAK 19(17Q12) WILD-TYPE	86	106	114	138

Figure S51. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.063

Table S52. Gene #19: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 19(17Q12) MUTATED	28	27	28	5	51	5	7
AMP PEAK 19(17Q12) WILD-TYPE	50	97	68	58	99	31	41

Figure S52. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S53. Gene #20: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 20(17Q24.1) MUTATED	27	66	51
AMP PEAK 20(17Q24.1) WILD-TYPE	226	143	102

Figure S53. Get High-res Image Gene #20: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.1' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.18

Table S54. Gene #20: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
AMP PEAK 20(17Q24.1) MUTATED	14	54	21
AMP PEAK 20(17Q24.1) WILD-TYPE	84	104	100

Figure S54. Get High-res Image Gene #20: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S55. Gene #20: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 20(17Q24.1) MUTATED	50	20	19	48
AMP PEAK 20(17Q24.1) WILD-TYPE	89	110	116	143

Figure S55. Get High-res Image Gene #20: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.14

Table S56. Gene #20: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 20(17Q24.1) MUTATED	27	26	25	4	44	4	7
AMP PEAK 20(17Q24.1) WILD-TYPE	51	98	71	59	106	32	41

Figure S56. Get High-res Image Gene #20: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S57. Gene #20: 'amp_17q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	211	95	232
AMP PEAK 20(17Q24.1) MUTATED	61	8	53
AMP PEAK 20(17Q24.1) WILD-TYPE	150	87	179

Figure S57. Get High-res Image Gene #20: 'amp_17q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S58. Gene #21: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 21(19P13.2) MUTATED	20	58	33
AMP PEAK 21(19P13.2) WILD-TYPE	233	151	120

Figure S58. Get High-res Image Gene #21: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.16

Table S59. Gene #21: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 21(19P13.2) MUTATED	13	23	28	3	32	1	5
AMP PEAK 21(19P13.2) WILD-TYPE	65	101	68	60	118	35	43

Figure S59. Get High-res Image Gene #21: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S60. Gene #22: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 22(19Q12) MUTATED	31	71	37
AMP PEAK 22(19Q12) WILD-TYPE	222	138	116

Figure S60. Get High-res Image Gene #22: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S61. Gene #23: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 23(20P12.1) MUTATED	89	119	70
AMP PEAK 23(20P12.1) WILD-TYPE	164	90	83

Figure S61. Get High-res Image Gene #23: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S62. Gene #23: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 23(20P12.1) MUTATED	40	59	46	15	84	5	22
AMP PEAK 23(20P12.1) WILD-TYPE	38	65	50	48	66	31	26

Figure S62. Get High-res Image Gene #23: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MRNA_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.083

Table S63. Gene #24: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 24(20P11.21) MUTATED	16	43	49	17
AMP PEAK 24(20P11.21) WILD-TYPE	27	19	20	24

Figure S63. Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S64. Gene #24: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
AMP PEAK 24(20P11.21) MUTATED	14	27	48	36
AMP PEAK 24(20P11.21) WILD-TYPE	35	14	28	13

Figure S64. Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S65. Gene #24: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 24(20P11.21) MUTATED	100	166	97
AMP PEAK 24(20P11.21) WILD-TYPE	153	43	56

Figure S65. Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.21' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S66. Gene #24: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
AMP PEAK 24(20P11.21) MUTATED	50	118	58
AMP PEAK 24(20P11.21) WILD-TYPE	48	40	63

Figure S66. Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S67. Gene #24: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 24(20P11.21) MUTATED	105	74	55	116
AMP PEAK 24(20P11.21) WILD-TYPE	34	56	80	75

Figure S67. Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S68. Gene #24: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 24(20P11.21) MUTATED	55	76	67	17	108	6	21
AMP PEAK 24(20P11.21) WILD-TYPE	23	48	29	46	42	30	27

Figure S68. Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S69. Gene #25: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 25(20Q11.21) MUTATED	18	60	63	23
AMP PEAK 25(20Q11.21) WILD-TYPE	25	2	6	18

Figure S69. Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S70. Gene #25: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
AMP PEAK 25(20Q11.21) MUTATED	15	39	62	48
AMP PEAK 25(20Q11.21) WILD-TYPE	34	2	14	1

Figure S70. Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S71. Gene #25: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 25(20Q11.21) MUTATED	130	208	131
AMP PEAK 25(20Q11.21) WILD-TYPE	123	1	22

Figure S71. Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S72. Gene #25: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
AMP PEAK 25(20Q11.21) MUTATED	68	154	68
AMP PEAK 25(20Q11.21) WILD-TYPE	30	4	53

Figure S72. Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S73. Gene #25: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 25(20Q11.21) MUTATED	135	95	72	151
AMP PEAK 25(20Q11.21) WILD-TYPE	4	35	63	40

Figure S73. Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S74. Gene #25: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 25(20Q11.21) MUTATED	72	94	90	19	143	7	28
AMP PEAK 25(20Q11.21) WILD-TYPE	6	30	6	44	7	29	20

Figure S74. Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.23

Table S75. Gene #25: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	228	139	171
AMP PEAK 25(20Q11.21) MUTATED	167	122	120
AMP PEAK 25(20Q11.21) WILD-TYPE	61	17	51

Figure S75. Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S76. Gene #26: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 26(20Q12) MUTATED	17	60	63	22
AMP PEAK 26(20Q12) WILD-TYPE	26	2	6	19

Figure S76. Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S77. Gene #26: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
AMP PEAK 26(20Q12) MUTATED	14	39	61	48
AMP PEAK 26(20Q12) WILD-TYPE	35	2	15	1

Figure S77. Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S78. Gene #26: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 26(20Q12) MUTATED	130	208	133
AMP PEAK 26(20Q12) WILD-TYPE	123	1	20

Figure S78. Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S79. Gene #26: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
AMP PEAK 26(20Q12) MUTATED	69	154	71
AMP PEAK 26(20Q12) WILD-TYPE	29	4	50

Figure S79. Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S80. Gene #26: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 26(20Q12) MUTATED	135	97	73	150
AMP PEAK 26(20Q12) WILD-TYPE	4	33	62	41

Figure S80. Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S81. Gene #26: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 26(20Q12) MUTATED	72	95	91	21	142	6	28
AMP PEAK 26(20Q12) WILD-TYPE	6	29	5	42	8	30	20

Figure S81. Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S82. Gene #26: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	228	139	171
AMP PEAK 26(20Q12) MUTATED	169	123	119
AMP PEAK 26(20Q12) WILD-TYPE	59	16	52

Figure S82. Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S83. Gene #27: 'amp_20q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 27(20Q13.31) MUTATED	18	60	64	24
AMP PEAK 27(20Q13.31) WILD-TYPE	25	2	5	17

Figure S83. Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S84. Gene #27: 'amp_20q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
AMP PEAK 27(20Q13.31) MUTATED	15	39	64	48
AMP PEAK 27(20Q13.31) WILD-TYPE	34	2	12	1

Figure S84. Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S85. Gene #27: 'amp_20q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
AMP PEAK 27(20Q13.31) MUTATED	131	208	134
AMP PEAK 27(20Q13.31) WILD-TYPE	122	1	19

Figure S85. Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S86. Gene #27: 'amp_20q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
AMP PEAK 27(20Q13.31) MUTATED	68	153	71
AMP PEAK 27(20Q13.31) WILD-TYPE	30	5	50

Figure S86. Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S87. Gene #27: 'amp_20q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
AMP PEAK 27(20Q13.31) MUTATED	133	97	75	152
AMP PEAK 27(20Q13.31) WILD-TYPE	6	33	60	39

Figure S87. Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S88. Gene #27: 'amp_20q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
AMP PEAK 27(20Q13.31) MUTATED	71	95	91	20	144	8	28
AMP PEAK 27(20Q13.31) WILD-TYPE	7	29	5	43	6	28	20

Figure S88. Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.23

Table S89. Gene #27: 'amp_20q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	228	139	171
AMP PEAK 27(20Q13.31) MUTATED	170	123	121
AMP PEAK 27(20Q13.31) WILD-TYPE	58	16	50

Figure S89. Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.076

Table S90. Gene #28: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 1(1P36.11) MUTATED	14	36	36	7
DEL PEAK 1(1P36.11) WILD-TYPE	29	26	33	34

Figure S90. Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S91. Gene #28: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 1(1P36.11) MUTATED	61	121	62
DEL PEAK 1(1P36.11) WILD-TYPE	192	88	91

Figure S91. Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S92. Gene #28: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 1(1P36.11) MUTATED	34	84	29
DEL PEAK 1(1P36.11) WILD-TYPE	64	74	92

Figure S92. Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S93. Gene #28: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 1(1P36.11) MUTATED	72	53	28	84
DEL PEAK 1(1P36.11) WILD-TYPE	67	77	107	107

Figure S93. Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S94. Gene #28: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 1(1P36.11) MUTATED	38	43	47	8	79	8	14
DEL PEAK 1(1P36.11) WILD-TYPE	40	81	49	55	71	28	34

Figure S94. Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S95. Gene #29: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 2(1P33) MUTATED	44	95	37
DEL PEAK 2(1P33) WILD-TYPE	209	114	116

Figure S95. Get High-res Image Gene #29: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p33' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S96. Gene #29: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 2(1P33) MUTATED	29	63	21
DEL PEAK 2(1P33) WILD-TYPE	69	95	100

Figure S96. Get High-res Image Gene #29: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p33' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.063

Table S97. Gene #29: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 2(1P33) MUTATED	57	37	22	54
DEL PEAK 2(1P33) WILD-TYPE	82	93	113	137

Figure S97. Get High-res Image Gene #29: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S98. Gene #30: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 3(1P13.2) MUTATED	46	92	38
DEL PEAK 3(1P13.2) WILD-TYPE	207	117	115

Figure S98. Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.17

Table S99. Gene #30: 'del_1p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 3(1P13.2) MUTATED	32	27	37	9	49	5	11
DEL PEAK 3(1P13.2) WILD-TYPE	46	97	59	54	101	31	37

Figure S99. Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2p12' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S100. Gene #31: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 4(2P12) MUTATED	1	14	6
DEL PEAK 4(2P12) WILD-TYPE	252	195	147

Figure S100. Get High-res Image Gene #31: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S101. Gene #36: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 9(4P16.2) MUTATED	47	108	47
DEL PEAK 9(4P16.2) WILD-TYPE	206	101	106

Figure S101. Get High-res Image Gene #36: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.063

Table S102. Gene #36: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 9(4P16.2) MUTATED	29	37	40	6	60	8	14
DEL PEAK 9(4P16.2) WILD-TYPE	49	87	56	57	90	28	34

Figure S102. Get High-res Image Gene #36: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S103. Gene #37: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 10(4Q22.1) MUTATED	49	116	59
DEL PEAK 10(4Q22.1) WILD-TYPE	204	93	94

Figure S103. Get High-res Image Gene #37: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S104. Gene #37: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 10(4Q22.1) MUTATED	37	75	27
DEL PEAK 10(4Q22.1) WILD-TYPE	61	83	94

Figure S104. Get High-res Image Gene #37: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.16

Table S105. Gene #37: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 10(4Q22.1) MUTATED	63	46	29	76
DEL PEAK 10(4Q22.1) WILD-TYPE	76	84	106	115

Figure S105. Get High-res Image Gene #37: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S106. Gene #37: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 10(4Q22.1) MUTATED	37	40	43	7	65	8	14
DEL PEAK 10(4Q22.1) WILD-TYPE	41	84	53	56	85	28	34

Figure S106. Get High-res Image Gene #37: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S107. Gene #38: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 11(4Q35.1) MUTATED	52	120	61
DEL PEAK 11(4Q35.1) WILD-TYPE	201	89	92

Figure S107. Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S108. Gene #38: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 11(4Q35.1) MUTATED	39	76	28
DEL PEAK 11(4Q35.1) WILD-TYPE	59	82	93

Figure S108. Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S109. Gene #38: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 11(4Q35.1) MUTATED	39	40	46	9	67	9	14
DEL PEAK 11(4Q35.1) WILD-TYPE	39	84	50	54	83	27	34

Figure S109. Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.14

Table S110. Gene #39: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
DEL PEAK 12(5Q12.1) MUTATED	9	18	8	16
DEL PEAK 12(5Q12.1) WILD-TYPE	40	23	68	33

Figure S110. Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S111. Gene #39: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 12(5Q12.1) MUTATED	27	71	60
DEL PEAK 12(5Q12.1) WILD-TYPE	226	138	93

Figure S111. Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.036

Table S112. Gene #39: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 12(5Q12.1) MUTATED	23	29	37	5	46	6	6
DEL PEAK 12(5Q12.1) WILD-TYPE	55	95	59	58	104	30	42

Figure S112. Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S113. Gene #40: 'del_5q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 13(5Q21.2) MUTATED	37	81	69
DEL PEAK 13(5Q21.2) WILD-TYPE	216	128	84

Figure S113. Get High-res Image Gene #40: 'del_5q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S114. Gene #41: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 14(5Q22.2) MUTATED	41	81	67
DEL PEAK 14(5Q22.2) WILD-TYPE	212	128	86

Figure S114. Get High-res Image Gene #41: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.15

Table S115. Gene #41: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 14(5Q22.2) MUTATED	29	38	34	9	58	5	8
DEL PEAK 14(5Q22.2) WILD-TYPE	49	86	62	54	92	31	40

Figure S115. Get High-res Image Gene #41: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.12

Table S116. Gene #45: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 18(8P23.2) MUTATED	17	42	37	11
DEL PEAK 18(8P23.2) WILD-TYPE	26	20	32	30

Figure S116. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S117. Gene #45: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 18(8P23.2) MUTATED	45	124	121
DEL PEAK 18(8P23.2) WILD-TYPE	208	85	32

Figure S117. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S118. Gene #45: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 18(8P23.2) MUTATED	38	100	37
DEL PEAK 18(8P23.2) WILD-TYPE	60	58	84

Figure S118. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S119. Gene #45: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 18(8P23.2) MUTATED	79	65	38	99
DEL PEAK 18(8P23.2) WILD-TYPE	60	65	97	92

Figure S119. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S120. Gene #45: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 18(8P23.2) MUTATED	40	49	64	10	91	8	19
DEL PEAK 18(8P23.2) WILD-TYPE	38	75	32	53	59	28	29

Figure S120. Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MRNA_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.21

Table S121. Gene #46: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
DEL PEAK 19(8P22) MUTATED	13	28	39	29
DEL PEAK 19(8P22) WILD-TYPE	36	13	37	20

Figure S121. Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S122. Gene #46: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 19(8P22) MUTATED	50	128	125
DEL PEAK 19(8P22) WILD-TYPE	203	81	28

Figure S122. Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S123. Gene #46: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 19(8P22) MUTATED	39	105	42
DEL PEAK 19(8P22) WILD-TYPE	59	53	79

Figure S123. Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.069

Table S124. Gene #46: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 19(8P22) MUTATED	81	69	44	100
DEL PEAK 19(8P22) WILD-TYPE	58	61	91	91

Figure S124. Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S125. Gene #46: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 19(8P22) MUTATED	41	55	67	10	93	8	20
DEL PEAK 19(8P22) WILD-TYPE	37	69	29	53	57	28	28

Figure S125. Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8q11.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S126. Gene #47: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 20(8Q11.1) MUTATED	14	30	3
DEL PEAK 20(8Q11.1) WILD-TYPE	239	179	150

Figure S126. Get High-res Image Gene #47: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S127. Gene #49: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 22(10P15.3) MUTATED	24	52	39
DEL PEAK 22(10P15.3) WILD-TYPE	229	157	114

Figure S127. Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S128. Gene #49: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 22(10P15.3) MUTATED	16	16	34	3	32	4	5
DEL PEAK 22(10P15.3) WILD-TYPE	62	108	62	60	118	32	43

Figure S128. Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S129. Gene #50: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 23(10Q21.1) MUTATED	25	67	47
DEL PEAK 23(10Q21.1) WILD-TYPE	228	142	106

Figure S129. Get High-res Image Gene #50: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S130. Gene #50: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 23(10Q21.1) MUTATED	48	24	15	44
DEL PEAK 23(10Q21.1) WILD-TYPE	91	106	120	147

Figure S130. Get High-res Image Gene #50: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S131. Gene #51: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 24(10Q23.31) MUTATED	38	68	55
DEL PEAK 24(10Q23.31) WILD-TYPE	215	141	98

Figure S131. Get High-res Image Gene #51: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.13

Table S132. Gene #51: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 24(10Q23.31) MUTATED	25	30	38	5	35	6	15
DEL PEAK 24(10Q23.31) WILD-TYPE	53	94	58	58	115	30	33

Figure S132. Get High-res Image Gene #51: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S133. Gene #52: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 25(10Q25.2) MUTATED	37	69	51
DEL PEAK 25(10Q25.2) WILD-TYPE	216	140	102

Figure S133. Get High-res Image Gene #52: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S134. Gene #52: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 25(10Q25.2) MUTATED	25	21	39	3	38	6	18
DEL PEAK 25(10Q25.2) WILD-TYPE	53	103	57	60	112	30	30

Figure S134. Get High-res Image Gene #52: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S135. Gene #54: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 27(12P13.1) MUTATED	11	53	28
DEL PEAK 27(12P13.1) WILD-TYPE	242	156	125

Figure S135. Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.076

Table S136. Gene #54: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 27(12P13.1) MUTATED	17	20	19	1	29	0	4
DEL PEAK 27(12P13.1) WILD-TYPE	61	104	77	62	121	36	44

Figure S136. Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S137. Gene #55: 'del_12q21.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 28(12Q21.33) MUTATED	13	48	29
DEL PEAK 28(12Q21.33) WILD-TYPE	240	161	124

Figure S137. Get High-res Image Gene #55: 'del_12q21.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S138. Gene #56: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 29(14Q11.2) MUTATED	8	31	34	6
DEL PEAK 29(14Q11.2) WILD-TYPE	35	31	35	35

Figure S138. Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S139. Gene #56: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
DEL PEAK 29(14Q11.2) MUTATED	5	21	28	25
DEL PEAK 29(14Q11.2) WILD-TYPE	44	20	48	24

Figure S139. Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S140. Gene #56: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 29(14Q11.2) MUTATED	35	144	33
DEL PEAK 29(14Q11.2) WILD-TYPE	218	65	120

Figure S140. Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S141. Gene #56: 'del_14q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 29(14Q11.2) MUTATED	29	73	24
DEL PEAK 29(14Q11.2) WILD-TYPE	69	85	97

Figure S141. Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S142. Gene #56: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 29(14Q11.2) MUTATED	73	28	23	79
DEL PEAK 29(14Q11.2) WILD-TYPE	66	102	112	112

Figure S142. Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S143. Gene #56: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 29(14Q11.2) MUTATED	35	40	40	3	73	3	9
DEL PEAK 29(14Q11.2) WILD-TYPE	43	84	56	60	77	33	39

Figure S143. Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S144. Gene #57: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 30(14Q31.1) MUTATED	40	144	34
DEL PEAK 30(14Q31.1) WILD-TYPE	213	65	119

Figure S144. Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S145. Gene #57: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 30(14Q31.1) MUTATED	28	74	27
DEL PEAK 30(14Q31.1) WILD-TYPE	70	84	94

Figure S145. Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S146. Gene #57: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 30(14Q31.1) MUTATED	73	30	24	82
DEL PEAK 30(14Q31.1) WILD-TYPE	66	100	111	109

Figure S146. Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S147. Gene #57: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 30(14Q31.1) MUTATED	34	42	38	6	75	4	10
DEL PEAK 30(14Q31.1) WILD-TYPE	44	82	58	57	75	32	38

Figure S147. Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S148. Gene #58: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 31(15Q11.2) MUTATED	47	136	70
DEL PEAK 31(15Q11.2) WILD-TYPE	206	73	83

Figure S148. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.17

Table S149. Gene #58: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 31(15Q11.2) MUTATED	37	83	35
DEL PEAK 31(15Q11.2) WILD-TYPE	61	75	86

Figure S149. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S150. Gene #58: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 31(15Q11.2) MUTATED	73	53	32	86
DEL PEAK 31(15Q11.2) WILD-TYPE	66	77	103	105

Figure S150. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S151. Gene #58: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 31(15Q11.2) MUTATED	39	44	55	5	75	9	17
DEL PEAK 31(15Q11.2) WILD-TYPE	39	80	41	58	75	27	31

Figure S151. Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.2' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S152. Gene #59: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 32(15Q15.2) MUTATED	11	34	39	8
DEL PEAK 32(15Q15.2) WILD-TYPE	32	28	30	33

Figure S152. Get High-res Image Gene #59: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S153. Gene #59: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 32(15Q15.2) MUTATED	48	134	69
DEL PEAK 32(15Q15.2) WILD-TYPE	205	75	84

Figure S153. Get High-res Image Gene #59: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S154. Gene #59: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 32(15Q15.2) MUTATED	74	49	35	84
DEL PEAK 32(15Q15.2) WILD-TYPE	65	81	100	107

Figure S154. Get High-res Image Gene #59: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S155. Gene #59: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 32(15Q15.2) MUTATED	40	44	51	5	74	8	20
DEL PEAK 32(15Q15.2) WILD-TYPE	38	80	45	58	76	28	28

Figure S155. Get High-res Image Gene #59: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S156. Gene #60: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 33(15Q21.1) MUTATED	48	131	69
DEL PEAK 33(15Q21.1) WILD-TYPE	205	78	84

Figure S156. Get High-res Image Gene #60: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S157. Gene #60: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 33(15Q21.1) MUTATED	72	48	35	84
DEL PEAK 33(15Q21.1) WILD-TYPE	67	82	100	107

Figure S157. Get High-res Image Gene #60: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S158. Gene #60: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 33(15Q21.1) MUTATED	38	43	50	5	73	11	19
DEL PEAK 33(15Q21.1) WILD-TYPE	40	81	46	58	77	25	29

Figure S158. Get High-res Image Gene #60: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S159. Gene #61: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 34(15Q22.33) MUTATED	12	31	36	6
DEL PEAK 34(15Q22.33) WILD-TYPE	31	31	33	35

Figure S159. Get High-res Image Gene #61: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q22.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S160. Gene #61: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 34(15Q22.33) MUTATED	41	129	68
DEL PEAK 34(15Q22.33) WILD-TYPE	212	80	85

Figure S160. Get High-res Image Gene #61: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q22.33' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S161. Gene #61: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 34(15Q22.33) MUTATED	35	80	31
DEL PEAK 34(15Q22.33) WILD-TYPE	63	78	90

Figure S161. Get High-res Image Gene #61: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q22.33' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S162. Gene #61: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 34(15Q22.33) MUTATED	69	51	29	81
DEL PEAK 34(15Q22.33) WILD-TYPE	70	79	106	110

Figure S162. Get High-res Image Gene #61: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q22.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S163. Gene #61: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 34(15Q22.33) MUTATED	37	40	54	4	71	8	16
DEL PEAK 34(15Q22.33) WILD-TYPE	41	84	42	59	79	28	32

Figure S163. Get High-res Image Gene #61: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S164. Gene #64: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 37(17P12) MUTATED	16	50	52	15
DEL PEAK 37(17P12) WILD-TYPE	27	12	17	26

Figure S164. Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S165. Gene #64: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
DEL PEAK 37(17P12) MUTATED	14	32	49	38
DEL PEAK 37(17P12) WILD-TYPE	35	9	27	11

Figure S165. Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S166. Gene #64: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 37(17P12) MUTATED	77	171	122
DEL PEAK 37(17P12) WILD-TYPE	176	38	31

Figure S166. Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S167. Gene #64: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 37(17P12) MUTATED	47	125	54
DEL PEAK 37(17P12) WILD-TYPE	51	33	67

Figure S167. Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S168. Gene #64: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 37(17P12) MUTATED	107	74	53	123
DEL PEAK 37(17P12) WILD-TYPE	32	56	82	68

Figure S168. Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S169. Gene #64: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 37(17P12) MUTATED	57	75	71	8	115	8	23
DEL PEAK 37(17P12) WILD-TYPE	21	49	25	55	35	28	25

Figure S169. Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S170. Gene #66: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 39(18P11.31) MUTATED	11	51	52	13
DEL PEAK 39(18P11.31) WILD-TYPE	32	11	17	28

Figure S170. Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18p11.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S171. Gene #66: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
DEL PEAK 39(18P11.31) MUTATED	9	34	43	41
DEL PEAK 39(18P11.31) WILD-TYPE	40	7	33	8

Figure S171. Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S172. Gene #66: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 39(18P11.31) MUTATED	72	189	109
DEL PEAK 39(18P11.31) WILD-TYPE	181	20	44

Figure S172. Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_18p11.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S173. Gene #66: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 39(18P11.31) MUTATED	53	138	41
DEL PEAK 39(18P11.31) WILD-TYPE	45	20	80

Figure S173. Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18p11.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S174. Gene #66: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 39(18P11.31) MUTATED	126	73	37	120
DEL PEAK 39(18P11.31) WILD-TYPE	13	57	98	71

Figure S174. Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S175. Gene #66: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 39(18P11.31) MUTATED	65	68	76	7	116	4	20
DEL PEAK 39(18P11.31) WILD-TYPE	13	56	20	56	34	32	28

Figure S175. Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S176. Gene #66: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	20	28	28	18	17
DEL PEAK 39(18P11.31) MUTATED	21	9	24	21	13	4
DEL PEAK 39(18P11.31) WILD-TYPE	3	11	4	7	5	13

Figure S176. Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S177. Gene #67: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 40(18Q12.2) MUTATED	17	54	56	17
DEL PEAK 40(18Q12.2) WILD-TYPE	26	8	13	24

Figure S177. Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q12.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S178. Gene #67: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
DEL PEAK 40(18Q12.2) MUTATED	14	36	52	42
DEL PEAK 40(18Q12.2) WILD-TYPE	35	5	24	7

Figure S178. Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S179. Gene #67: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 40(18Q12.2) MUTATED	83	196	137
DEL PEAK 40(18Q12.2) WILD-TYPE	170	13	16

Figure S179. Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S180. Gene #67: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 40(18Q12.2) MUTATED	58	147	53
DEL PEAK 40(18Q12.2) WILD-TYPE	40	11	68

Figure S180. Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S181. Gene #67: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 40(18Q12.2) MUTATED	128	85	54	134
DEL PEAK 40(18Q12.2) WILD-TYPE	11	45	81	57

Figure S181. Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S182. Gene #67: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 40(18Q12.2) MUTATED	66	82	84	10	125	9	25
DEL PEAK 40(18Q12.2) WILD-TYPE	12	42	12	53	25	27	23

Figure S182. Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S183. Gene #67: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	20	28	28	18	17
DEL PEAK 40(18Q12.2) MUTATED	22	13	27	23	14	5
DEL PEAK 40(18Q12.2) WILD-TYPE	2	7	1	5	4	12

Figure S183. Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S184. Gene #67: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	15	34	31
DEL PEAK 40(18Q12.2) MUTATED	33	15	26	30
DEL PEAK 40(18Q12.2) WILD-TYPE	22	0	8	1

Figure S184. Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S185. Gene #68: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 41(18Q21.2) MUTATED	17	55	57	18
DEL PEAK 41(18Q21.2) WILD-TYPE	26	7	12	23

Figure S185. Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S186. Gene #68: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
DEL PEAK 41(18Q21.2) MUTATED	14	36	55	42
DEL PEAK 41(18Q21.2) WILD-TYPE	35	5	21	7

Figure S186. Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S187. Gene #68: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 41(18Q21.2) MUTATED	91	199	142
DEL PEAK 41(18Q21.2) WILD-TYPE	162	10	11

Figure S187. Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S188. Gene #68: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 41(18Q21.2) MUTATED	60	148	64
DEL PEAK 41(18Q21.2) WILD-TYPE	38	10	57

Figure S188. Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S189. Gene #68: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 41(18Q21.2) MUTATED	130	90	62	136
DEL PEAK 41(18Q21.2) WILD-TYPE	9	40	73	55

Figure S189. Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S190. Gene #68: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 41(18Q21.2) MUTATED	68	87	86	15	127	10	25
DEL PEAK 41(18Q21.2) WILD-TYPE	10	37	10	48	23	26	23

Figure S190. Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S191. Gene #68: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	211	95	232
DEL PEAK 41(18Q21.2) MUTATED	170	55	153
DEL PEAK 41(18Q21.2) WILD-TYPE	41	40	79

Figure S191. Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S192. Gene #68: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	20	28	28	18	17
DEL PEAK 41(18Q21.2) MUTATED	24	14	27	23	14	6
DEL PEAK 41(18Q21.2) WILD-TYPE	0	6	1	5	4	11

Figure S192. Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.036

Table S193. Gene #68: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	15	34	31
DEL PEAK 41(18Q21.2) MUTATED	34	15	29	30
DEL PEAK 41(18Q21.2) WILD-TYPE	21	0	5	1

Figure S193. Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q22.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S194. Gene #69: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 42(18Q22.1) MUTATED	17	55	56	19
DEL PEAK 42(18Q22.1) WILD-TYPE	26	7	13	22

Figure S194. Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S195. Gene #69: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
DEL PEAK 42(18Q22.1) MUTATED	15	36	54	42
DEL PEAK 42(18Q22.1) WILD-TYPE	34	5	22	7

Figure S195. Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S196. Gene #69: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 42(18Q22.1) MUTATED	87	199	141
DEL PEAK 42(18Q22.1) WILD-TYPE	166	10	12

Figure S196. Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S197. Gene #69: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 42(18Q22.1) MUTATED	58	148	61
DEL PEAK 42(18Q22.1) WILD-TYPE	40	10	60

Figure S197. Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S198. Gene #69: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 42(18Q22.1) MUTATED	129	87	62	135
DEL PEAK 42(18Q22.1) WILD-TYPE	10	43	73	56

Figure S198. Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S199. Gene #69: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 42(18Q22.1) MUTATED	67	84	85	15	126	10	26
DEL PEAK 42(18Q22.1) WILD-TYPE	11	40	11	48	24	26	22

Figure S199. Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q22.1' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S200. Gene #69: 'del_18q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	211	95	232
DEL PEAK 42(18Q22.1) MUTATED	167	53	153
DEL PEAK 42(18Q22.1) WILD-TYPE	44	42	79

Figure S200. Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S201. Gene #69: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	24	20	28	28	18	17
DEL PEAK 42(18Q22.1) MUTATED	24	14	26	22	14	6
DEL PEAK 42(18Q22.1) WILD-TYPE	0	6	2	6	4	11

Figure S201. Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S202. Gene #70: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 43(19P13.3) MUTATED	19	42	36
DEL PEAK 43(19P13.3) WILD-TYPE	234	167	117

Figure S202. Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S203. Gene #71: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 44(20P12.1) MUTATED	30	57	48
DEL PEAK 44(20P12.1) WILD-TYPE	223	152	105

Figure S203. Get High-res Image Gene #71: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S204. Gene #71: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	158	121
DEL PEAK 44(20P12.1) MUTATED	19	57	13
DEL PEAK 44(20P12.1) WILD-TYPE	79	101	108

Figure S204. Get High-res Image Gene #71: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S205. Gene #71: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 44(20P12.1) MUTATED	50	26	21	32
DEL PEAK 44(20P12.1) WILD-TYPE	89	104	114	159

Figure S205. Get High-res Image Gene #71: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S206. Gene #71: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 44(20P12.1) MUTATED	23	30	29	1	39	4	3
DEL PEAK 44(20P12.1) WILD-TYPE	55	94	67	62	111	32	45

Figure S206. Get High-res Image Gene #71: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S207. Gene #72: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 45(21Q11.2) MUTATED	59	105	50
DEL PEAK 45(21Q11.2) WILD-TYPE	194	104	103

Figure S207. Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S208. Gene #72: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	130	135	191
DEL PEAK 45(21Q11.2) MUTATED	69	40	31	66
DEL PEAK 45(21Q11.2) WILD-TYPE	70	90	104	125

Figure S208. Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.089

Table S209. Gene #73: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
DEL PEAK 46(22Q13.32) MUTATED	7	19	33	27
DEL PEAK 46(22Q13.32) WILD-TYPE	42	22	43	22

Figure S209. Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S210. Gene #73: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	253	209	153
DEL PEAK 46(22Q13.32) MUTATED	53	117	59
DEL PEAK 46(22Q13.32) WILD-TYPE	200	92	94

Figure S210. Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S211. Gene #73: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	78	124	96	63	150	36	48
DEL PEAK 46(22Q13.32) MUTATED	35	44	40	9	71	6	17
DEL PEAK 46(22Q13.32) WILD-TYPE	43	80	56	54	79	30	31

Figure S211. Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = COADREAD-TP.transferedmergedcluster.txt
Number of patients = 615
Number of significantly focal cnvs = 73
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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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