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

Colon Adenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1RJ4H6T

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 69 focal events and 12 molecular subtypes across 438 patients, 235 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_2q33.1 cnv correlated to 'CN_CNMF'.
amp_5p13.2 cnv correlated to 'CN_CNMF'.
amp_6p21.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'CN_CNMF'.
amp_8p11.21 cnv correlated to 'CN_CNMF'.
amp_8q12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_11p15.5 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q12.13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_13q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_16p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_16q12.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_17q24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF'.
amp_19q13.11 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_20p11.23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_20q11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_1p33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p13.1 cnv correlated to 'CN_CNMF'.
del_1q43 cnv correlated to 'CN_CNMF'.
del_3p26.1 cnv correlated to 'CN_CNMF'.
del_3q26.31 cnv correlated to 'CN_CNMF'.
del_4p16.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_4q22.1 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_4q35.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_5q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_5q21.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_5q23.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_8p23.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_8p22 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_8p11.21 cnv correlated to 'CN_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF'.
del_10p15.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_10q21.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_10q25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_12p13.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_14q31.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_15q15.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_15q21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_15q22.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18p11.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'CN_CNMF'.
del_20p12.1 cnv correlated to 'CN_CNMF'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_22q13.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 69 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, 235 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
amp 20q12	315 (72%)	123	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00047 (0.279)	0.00039 (0.233)	1e-05 (0.00828)	1e-05 (0.00828)	0.775 (1.00)	0.00127 (0.693)	1e-05 (0.00828)	3e-05 (0.0198)
amp 20q13 32	317 (72%)	121	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00058 (0.339)	0.00034 (0.204)	1e-05 (0.00828)	1e-05 (0.00828)	0.789 (1.00)	0.00272 (1.00)	1e-05 (0.00828)	2e-05 (0.0135)
del 18q22 1	277 (63%)	161	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00238 (1.00)	0.00039 (0.233)	1e-05 (0.00828)	1e-05 (0.00828)	0.582 (1.00)	0.0727 (1.00)	1e-05 (0.00828)	0.00032 (0.193)
amp 20q11 21	314 (72%)	124	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00068 (0.392)	0.00206 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.821 (1.00)	0.0012 (0.656)	1e-05 (0.00828)	2e-05 (0.0135)
del 14q31 1	145 (33%)	293	1e-05 (0.00828)	8e-05 (0.0517)	1e-05 (0.00828)	2e-05 (0.0135)	0.00032 (0.193)	0.0192 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.334 (1.00)	0.0218 (1.00)	5e-05 (0.0325)	0.0156 (1.00)
del 15q22 33	158 (36%)	280	0.00017 (0.106)	0.00035 (0.21)	1e-05 (0.00828)	3e-05 (0.0198)	0.0437 (1.00)	0.0592 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.664 (1.00)	0.729 (1.00)	5e-05 (0.0325)	0.00027 (0.164)
del 17p12	246 (56%)	192	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.0127 (1.00)	0.00115 (0.634)	1e-05 (0.00828)	1e-05 (0.00828)	0.667 (1.00)	0.0221 (1.00)	1e-05 (0.00828)	2e-05 (0.0135)
del 18p11 31	237 (54%)	201	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00091 (0.511)	0.0103 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.838 (1.00)	0.0108 (1.00)	1e-05 (0.00828)	5e-05 (0.0325)
del 18q12 2	263 (60%)	175	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00234 (1.00)	0.00197 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.942 (1.00)	0.0184 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)
del 18q21 2	277 (63%)	161	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00102 (0.568)	0.00053 (0.312)	1e-05 (0.00828)	1e-05 (0.00828)	0.444 (1.00)	0.0344 (1.00)	1e-05 (0.00828)	0.00016 (0.0998)
amp 11p15 5	91 (21%)	347	4e-05 (0.0262)	0.00628 (1.00)	1e-05 (0.00828)	2e-05 (0.0135)	0.0009 (0.508)	0.0326 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.106 (1.00)	1e-05 (0.00828)	0.00218 (1.00)	1e-05 (0.00828)
amp 13q12 13	267 (61%)	171	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00503 (1.00)	0.0196 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.574 (1.00)	0.809 (1.00)	1e-05 (0.00828)	0.00097 (0.541)
amp 13q22 1	270 (62%)	168	0.00012 (0.0767)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00845 (1.00)	0.0471 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.456 (1.00)	0.996 (1.00)	1e-05 (0.00828)	0.00388 (1.00)
amp 16q12 1	107 (24%)	331	2e-05 (0.0135)	1e-05 (0.00828)	1e-05 (0.00828)	0.0569 (1.00)	0.109 (1.00)	0.19 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.975 (1.00)	0.0818 (1.00)	0.00014 (0.0886)	0.00019 (0.118)
del 1p36 11	165 (38%)	273	0.00016 (0.0998)	0.00795 (1.00)	1e-05 (0.00828)	2e-05 (0.0135)	0.0232 (1.00)	0.0177 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.662 (1.00)	0.0203 (1.00)	2e-05 (0.0135)	0.00066 (0.381)
del 4q22 1	144 (33%)	294	0.0004 (0.238)	0.00361 (1.00)	1e-05 (0.00828)	0.0001 (0.0644)	0.104 (1.00)	0.155 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.388 (1.00)	0.173 (1.00)	0.00019 (0.118)	0.00764 (1.00)
del 8p23 3	182 (42%)	256	0.0113 (1.00)	0.00019 (0.118)	1e-05 (0.00828)	2e-05 (0.0135)	0.00465 (1.00)	0.00798 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.217 (1.00)	0.0517 (1.00)	1e-05 (0.00828)	0.0197 (1.00)
del 8p22	197 (45%)	241	0.00259 (1.00)	0.00014 (0.0886)	1e-05 (0.00828)	2e-05 (0.0135)	0.00741 (1.00)	0.00077 (0.44)	1e-05 (0.00828)	1e-05 (0.00828)	0.483 (1.00)	0.0178 (1.00)	1e-05 (0.00828)	0.0129 (1.00)
del 22q13 32	154 (35%)	284	0.0004 (0.238)	0.00031 (0.188)	1e-05 (0.00828)	0.0008 (0.454)	0.118 (1.00)	0.245 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.345 (1.00)	0.751 (1.00)	1e-05 (0.00828)	0.0085 (1.00)
amp 16p11 2	121 (28%)	317	0.00042 (0.249)	1e-05 (0.00828)	1e-05 (0.00828)	0.0256 (1.00)	0.0298 (1.00)	0.125 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.894 (1.00)	0.142 (1.00)	0.00051 (0.301)	0.00135 (0.734)
del 1p33	121 (28%)	317	0.0153 (1.00)	0.558 (1.00)	1e-05 (0.00828)	0.00022 (0.136)	0.83 (1.00)	0.489 (1.00)	0.00025 (0.153)	0.00036 (0.216)	0.716 (1.00)	0.153 (1.00)	0.00107 (0.595)	7e-05 (0.0454)
del 4q35 1	152 (35%)	286	0.00096 (0.537)	0.00735 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.013 (1.00)	0.3 (1.00)	4e-05 (0.0262)	1e-05 (0.00828)	0.362 (1.00)	0.415 (1.00)	1e-05 (0.00828)	0.0178 (1.00)
del 15q15 2	166 (38%)	272	0.00187 (1.00)	0.00061 (0.356)	1e-05 (0.00828)	0.0003 (0.182)	0.00937 (1.00)	0.0259 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.923 (1.00)	0.555 (1.00)	0.0001 (0.0644)	0.00261 (1.00)
amp 8q12 1	228 (52%)	210	0.489 (1.00)	0.00572 (1.00)	1e-05 (0.00828)	0.00726 (1.00)	0.00992 (1.00)	0.00324 (1.00)	0.00025 (0.153)	4e-05 (0.0262)	0.387 (1.00)	0.039 (1.00)	0.00026 (0.159)	0.056 (1.00)
amp 17q24 1	102 (23%)	336	0.0163 (1.00)	0.00771 (1.00)	1e-05 (0.00828)	0.00022 (0.136)	0.0609 (1.00)	0.00226 (1.00)	4e-05 (0.0262)	2e-05 (0.0135)	0.0116 (1.00)	0.0541 (1.00)	0.0547 (1.00)	0.00367 (1.00)
del 4p16 2	133 (30%)	305	0.00063 (0.366)	0.0018 (0.968)	1e-05 (0.00828)	0.00064 (0.371)	0.0271 (1.00)	0.16 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.356 (1.00)	0.448 (1.00)	0.00014 (0.0886)	0.0903 (1.00)
del 5q11 2	100 (23%)	338	0.00116 (0.637)	0.00358 (1.00)	1e-05 (0.00828)	0.0106 (1.00)	0.00079 (0.45)	0.0337 (1.00)	2e-05 (0.0135)	0.00015 (0.0942)	0.707 (1.00)	0.565 (1.00)	0.00013 (0.0827)	0.315 (1.00)
del 10q25 2	105 (24%)	333	0.125 (1.00)	0.0182 (1.00)	1e-05 (0.00828)	0.0001 (0.0644)	0.00699 (1.00)	0.0872 (1.00)	0.00051 (0.301)	2e-05 (0.0135)	0.962 (1.00)	0.49 (1.00)	1e-05 (0.00828)	0.00194 (1.00)
del 15q11 2	171 (39%)	267	0.00051 (0.301)	0.0009 (0.508)	1e-05 (0.00828)	0.00061 (0.356)	0.0223 (1.00)	0.0631 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.981 (1.00)	0.776 (1.00)	2e-05 (0.0135)	0.00704 (1.00)
del 15q21 1	163 (37%)	275	0.0189 (1.00)	0.0147 (1.00)	1e-05 (0.00828)	0.00114 (0.632)	0.00936 (1.00)	0.0549 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.886 (1.00)	0.677 (1.00)	0.00014 (0.0886)	0.00361 (1.00)
del 21q11 2	137 (31%)	301	0.0158 (1.00)	0.0689 (1.00)	1e-05 (0.00828)	0.0509 (1.00)	0.161 (1.00)	0.819 (1.00)	0.00014 (0.0886)	0.00011 (0.0704)	0.935 (1.00)	0.128 (1.00)	0.00013 (0.0827)	0.0633 (1.00)
amp 6p21 1	94 (21%)	344	0.264 (1.00)	2e-05 (0.0135)	1e-05 (0.00828)	0.0967 (1.00)	0.503 (1.00)	0.7 (1.00)	0.0034 (1.00)	0.00029 (0.176)	0.706 (1.00)	0.776 (1.00)	0.00082 (0.465)	0.254 (1.00)
amp 20p11 23	215 (49%)	223	0.0787 (1.00)	0.00056 (0.328)	1e-05 (0.00828)	0.0292 (1.00)	0.00647 (1.00)	0.203 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.423 (1.00)	0.125 (1.00)	0.00203 (1.00)	0.0284 (1.00)
del 5q21 3	125 (29%)	313	0.0667 (1.00)	0.0192 (1.00)	1e-05 (0.00828)	0.0139 (1.00)	0.0458 (1.00)	0.26 (1.00)	0.00026 (0.159)	7e-05 (0.0454)	0.966 (1.00)	0.932 (1.00)	0.0183 (1.00)	0.34 (1.00)
del 5q23 1	116 (26%)	322	0.0499 (1.00)	0.0121 (1.00)	1e-05 (0.00828)	0.0203 (1.00)	0.0247 (1.00)	0.348 (1.00)	8e-05 (0.0517)	0.00012 (0.0767)	0.865 (1.00)	0.394 (1.00)	0.00229 (1.00)	0.216 (1.00)
del 10q23 31	105 (24%)	333	0.0991 (1.00)	0.0633 (1.00)	1e-05 (0.00828)	0.00328 (1.00)	0.147 (1.00)	0.473 (1.00)	0.00366 (1.00)	0.00015 (0.0942)	0.58 (1.00)	0.135 (1.00)	0.00022 (0.136)	0.0005 (0.296)
amp 8q24 21	251 (57%)	187	0.567 (1.00)	0.0285 (1.00)	1e-05 (0.00828)	0.00055 (0.323)	0.0372 (1.00)	0.0132 (1.00)	0.00089 (0.503)	2e-05 (0.0135)	0.711 (1.00)	0.0365 (1.00)	0.00059 (0.345)	0.0446 (1.00)
amp 17q12	109 (25%)	329	0.0266 (1.00)	0.0136 (1.00)	1e-05 (0.00828)	0.00065 (0.376)	0.14 (1.00)	0.00244 (1.00)	0.00022 (0.136)	0.00135 (0.734)	0.0372 (1.00)	0.0148 (1.00)	0.0391 (1.00)	0.0346 (1.00)
amp 19q13 11	90 (21%)	348	0.184 (1.00)	0.0313 (1.00)	1e-05 (0.00828)	0.0958 (1.00)	0.0338 (1.00)	0.313 (1.00)	0.0693 (1.00)	0.00015 (0.0942)	0.46 (1.00)	0.558 (1.00)	0.0289 (1.00)	0.0792 (1.00)
del 10p15 3	77 (18%)	361	0.115 (1.00)	0.104 (1.00)	1e-05 (0.00828)	0.00065 (0.376)	0.0222 (1.00)	0.143 (1.00)	0.0404 (1.00)	0.00019 (0.118)	0.455 (1.00)	0.18 (1.00)	0.00131 (0.714)	0.00718 (1.00)
del 10q21 1	92 (21%)	346	0.00317 (1.00)	0.0278 (1.00)	1e-05 (0.00828)	0.00996 (1.00)	0.071 (1.00)	0.259 (1.00)	0.00078 (0.445)	0.0001 (0.0644)	0.752 (1.00)	0.491 (1.00)	0.00114 (0.632)	0.0579 (1.00)
del 12p13 2	58 (13%)	380	0.0103 (1.00)	0.00339 (1.00)	1e-05 (0.00828)	0.00894 (1.00)	0.31 (1.00)	0.918 (1.00)	0.00082 (0.465)	4e-05 (0.0262)	0.793 (1.00)	0.355 (1.00)	0.00516 (1.00)	0.00892 (1.00)
del 19p13 3	63 (14%)	375	0.13 (1.00)	0.125 (1.00)	0.00033 (0.199)	0.11 (1.00)	0.981 (1.00)	0.209 (1.00)	0.00371 (1.00)	0.00018 (0.112)	0.651 (1.00)	0.00855 (1.00)	0.0266 (1.00)	0.427 (1.00)
amp 2q33 1	87 (20%)	351	0.165 (1.00)	0.114 (1.00)	0.00013 (0.0827)	0.00469 (1.00)	0.0425 (1.00)	0.0485 (1.00)	0.00092 (0.516)	0.0124 (1.00)	0.293 (1.00)	0.105 (1.00)	0.185 (1.00)	0.0674 (1.00)
amp 5p13 2	84 (19%)	354	0.379 (1.00)	0.191 (1.00)	0.00012 (0.0767)	0.548 (1.00)	0.00471 (1.00)	0.914 (1.00)	0.0234 (1.00)	0.00355 (1.00)	0.727 (1.00)	0.665 (1.00)	0.0708 (1.00)	0.617 (1.00)
amp 8p11 23	154 (35%)	284	0.303 (1.00)	0.11 (1.00)	1e-05 (0.00828)	0.389 (1.00)	0.764 (1.00)	0.626 (1.00)	0.0958 (1.00)	0.0133 (1.00)	0.362 (1.00)	0.267 (1.00)	0.255 (1.00)	0.984 (1.00)
amp 8p11 21	183 (42%)	255	0.443 (1.00)	0.0188 (1.00)	1e-05 (0.00828)	0.288 (1.00)	0.243 (1.00)	0.0238 (1.00)	0.213 (1.00)	0.00692 (1.00)	0.718 (1.00)	0.321 (1.00)	0.266 (1.00)	0.842 (1.00)
amp 19p13 2	71 (16%)	367	0.0669 (1.00)	0.0548 (1.00)	3e-05 (0.0198)	0.0123 (1.00)	0.672 (1.00)	0.381 (1.00)	0.693 (1.00)	0.00266 (1.00)	0.35 (1.00)	0.436 (1.00)	0.0109 (1.00)	0.0308 (1.00)
del 1p13 1	116 (26%)	322	0.0869 (1.00)	0.545 (1.00)	1e-05 (0.00828)	0.0125 (1.00)	0.681 (1.00)	0.892 (1.00)	0.00114 (0.632)	0.00143 (0.775)	0.801 (1.00)	0.166 (1.00)	0.044 (1.00)	0.00115 (0.634)
del 1q43	54 (12%)	384	0.0621 (1.00)	0.498 (1.00)	1e-05 (0.00828)	0.0302 (1.00)	0.467 (1.00)	0.718 (1.00)	0.00117 (0.641)	0.00074 (0.424)	0.142 (1.00)	0.00072 (0.413)	0.00111 (0.616)	0.118 (1.00)
del 3p26 1	68 (16%)	370	0.121 (1.00)	0.38 (1.00)	1e-05 (0.00828)	0.134 (1.00)	0.75 (1.00)	0.556 (1.00)	0.0189 (1.00)	0.0632 (1.00)	0.834 (1.00)	0.897 (1.00)	0.00174 (0.938)	0.135 (1.00)
del 3q26 31	46 (11%)	392	0.706 (1.00)	0.933 (1.00)	1e-05 (0.00828)	0.168 (1.00)	0.506 (1.00)	0.799 (1.00)	0.0807 (1.00)	0.202 (1.00)	0.451 (1.00)	0.57 (1.00)	0.00685 (1.00)	0.0253 (1.00)
del 8p11 21	46 (11%)	392	0.0252 (1.00)	0.118 (1.00)	1e-05 (0.00828)	0.156 (1.00)	0.0435 (1.00)	0.167 (1.00)	0.0669 (1.00)	0.00609 (1.00)	0.358 (1.00)	0.0476 (1.00)	0.0661 (1.00)	0.123 (1.00)
del 9p21 3	60 (14%)	378	0.452 (1.00)	0.0888 (1.00)	0.00015 (0.0942)	0.0717 (1.00)	0.821 (1.00)	0.408 (1.00)	0.0224 (1.00)	0.0055 (1.00)	0.618 (1.00)	0.255 (1.00)	0.0477 (1.00)	0.849 (1.00)
del 20p12 1	124 (28%)	314	0.0178 (1.00)	0.0314 (1.00)	1e-05 (0.00828)	0.00143 (0.775)	0.686 (1.00)	0.0789 (1.00)	0.00272 (1.00)	0.00093 (0.521)	0.452 (1.00)	0.0705 (1.00)	0.0647 (1.00)	0.0789 (1.00)
del 20p12 1	124 (28%)	314	0.018 (1.00)	0.0311 (1.00)	1e-05 (0.00828)	0.00159 (0.859)	0.685 (1.00)	0.0793 (1.00)	0.00235 (1.00)	0.00076 (0.435)	0.455 (1.00)	0.0694 (1.00)	0.067 (1.00)	0.0786 (1.00)
amp 5q22 3	43 (10%)	395	0.924 (1.00)	1 (1.00)	0.00661 (1.00)	0.805 (1.00)	0.324 (1.00)	0.642 (1.00)	0.299 (1.00)	0.0436 (1.00)	0.949 (1.00)	0.702 (1.00)	0.227 (1.00)	0.434 (1.00)
amp 12p13 33	108 (25%)	330	0.657 (1.00)	0.791 (1.00)	0.0508 (1.00)	0.0495 (1.00)	0.423 (1.00)	0.874 (1.00)	0.956 (1.00)	0.558 (1.00)	0.512 (1.00)	0.797 (1.00)	0.673 (1.00)	0.694 (1.00)
amp 17p11 2	43 (10%)	395	0.264 (1.00)	0.00403 (1.00)	0.0169 (1.00)	0.0865 (1.00)	0.00431 (1.00)	0.0605 (1.00)	0.253 (1.00)	0.638 (1.00)	0.546 (1.00)	0.804 (1.00)	0.261 (1.00)	0.215 (1.00)
del 2p21	16 (4%)	422	0.592 (1.00)	0.865 (1.00)	0.618 (1.00)	0.767 (1.00)	0.81 (1.00)	0.714 (1.00)	0.657 (1.00)	0.246 (1.00)	0.092 (1.00)	0.35 (1.00)	0.269 (1.00)	0.652 (1.00)
del 2q32 1	14 (3%)	424	0.959 (1.00)	0.668 (1.00)	0.157 (1.00)	0.264 (1.00)	0.65 (1.00)	0.986 (1.00)	0.0338 (1.00)	0.319 (1.00)	0.194 (1.00)	0.204 (1.00)	1 (1.00)	0.557 (1.00)
del 3p14 2	83 (19%)	355	0.553 (1.00)	0.84 (1.00)	0.0191 (1.00)	0.272 (1.00)	0.525 (1.00)	0.0416 (1.00)	0.118 (1.00)	0.0952 (1.00)	0.652 (1.00)	0.698 (1.00)	0.00434 (1.00)	0.805 (1.00)
del 6p25 3	55 (13%)	383	0.851 (1.00)	0.736 (1.00)	0.00223 (1.00)	0.0305 (1.00)	0.0432 (1.00)	0.574 (1.00)	0.938 (1.00)	0.797 (1.00)	0.668 (1.00)	0.939 (1.00)	0.174 (1.00)	0.809 (1.00)
del 6q26	60 (14%)	378	0.585 (1.00)	0.401 (1.00)	0.0373 (1.00)	0.474 (1.00)	0.0818 (1.00)	0.223 (1.00)	0.0864 (1.00)	0.382 (1.00)	0.699 (1.00)	0.939 (1.00)	0.447 (1.00)	0.384 (1.00)
del 7q31 1	12 (3%)	426	1 (1.00)	0.599 (1.00)	0.321 (1.00)	0.599 (1.00)	0.164 (1.00)	0.462 (1.00)	0.201 (1.00)	0.223 (1.00)	0.796 (1.00)	0.829 (1.00)	0.628 (1.00)	0.166 (1.00)
del 13q14 13	19 (4%)	419	0.276 (1.00)	0.864 (1.00)	0.0253 (1.00)	0.222 (1.00)	0.24 (1.00)	0.252 (1.00)	0.571 (1.00)	0.661 (1.00)	0.688 (1.00)	0.943 (1.00)	0.635 (1.00)	0.926 (1.00)
del 16p13 3	55 (13%)	383	0.23 (1.00)	0.063 (1.00)	0.0221 (1.00)	0.0603 (1.00)	0.394 (1.00)	0.516 (1.00)	0.237 (1.00)	0.258 (1.00)	0.852 (1.00)	0.698 (1.00)	0.149 (1.00)	0.689 (1.00)
del 16q23 1	59 (13%)	379	0.27 (1.00)	0.00541 (1.00)	0.172 (1.00)	0.851 (1.00)	0.139 (1.00)	0.613 (1.00)	0.207 (1.00)	0.0134 (1.00)	0.525 (1.00)	0.464 (1.00)	0.861 (1.00)	0.916 (1.00)
del 17q24 3	65 (15%)	373	0.0947 (1.00)	0.513 (1.00)	0.0171 (1.00)	0.0109 (1.00)	0.827 (1.00)	0.314 (1.00)	0.00071 (0.408)	0.055 (1.00)	0.708 (1.00)	0.97 (1.00)	0.0111 (1.00)	0.138 (1.00)

'amp_2q33.1' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 1(2Q33.1) MUTATED	13	42	21	11
AMP PEAK 1(2Q33.1) WILD-TYPE	24	113	171	43

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

'amp_5p13.2' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.077

Table S2. Gene #2: 'amp_5p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 2(5P13.2) MUTATED	12	42	20	10
AMP PEAK 2(5P13.2) WILD-TYPE	25	113	172	44

Figure S2. Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S3. Gene #4: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 4(6P21.1) MUTATED	3	10	16
AMP PEAK 4(6P21.1) WILD-TYPE	39	62	16

Figure S3. Get High-res Image Gene #4: '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 = 0.0083

Table S4. Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 4(6P21.1) MUTATED	10	57	14	13
AMP PEAK 4(6P21.1) WILD-TYPE	27	98	178	41

Figure S4. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.18

Table S5. Gene #4: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 4(6P21.1) MUTATED	27	20	9	33	3
AMP PEAK 4(6P21.1) WILD-TYPE	48	76	79	95	33

Figure S5. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S6. Gene #5: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 5(8P11.23) MUTATED	23	43	43	45
AMP PEAK 5(8P11.23) WILD-TYPE	14	112	149	9

Figure S6. Get High-res Image Gene #5: '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 = 0.0083

Table S7. Gene #6: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 6(8P11.21) MUTATED	25	62	47	49
AMP PEAK 6(8P11.21) WILD-TYPE	12	93	145	5

Figure S7. Get High-res Image Gene #6: '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 = 0.0083

Table S8. Gene #7: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 7(8Q12.1) MUTATED	29	88	59	52
AMP PEAK 7(8Q12.1) WILD-TYPE	8	67	133	2

Figure S8. Get High-res Image Gene #7: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q12.1' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.15

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

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

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

'amp_8q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S10. Gene #7: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 7(8Q12.1) MUTATED	50	58	34	70	9
AMP PEAK 7(8Q12.1) WILD-TYPE	25	38	54	58	27

Figure S10. Get High-res Image Gene #7: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.16

Table S11. Gene #7: 'amp_8q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S11. Get High-res Image Gene #7: 'amp_8q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S12. Gene #8: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 8(8Q24.21) MUTATED	29	101	68	53
AMP PEAK 8(8Q24.21) WILD-TYPE	8	54	124	1

Figure S12. Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 8(8Q24.21) MUTATED	54	62	40	79	10
AMP PEAK 8(8Q24.21) WILD-TYPE	21	34	48	49	26

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

'amp_11p15.5' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

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

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

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

'amp_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 9(11P15.5) MUTATED	15	46	19	11
AMP PEAK 9(11P15.5) WILD-TYPE	22	109	173	43

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

'amp_11p15.5' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 9(11P15.5) MUTATED	36	6	11
AMP PEAK 9(11P15.5) WILD-TYPE	82	86	60

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

'amp_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

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

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

'amp_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 9(11P15.5) MUTATED	22	20	4	42	0
AMP PEAK 9(11P15.5) WILD-TYPE	53	76	84	86	36

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

'amp_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
AMP PEAK 9(11P15.5) MUTATED	8	12	46	18
AMP PEAK 9(11P15.5) WILD-TYPE	127	38	31	117

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

'amp_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
AMP PEAK 9(11P15.5) MUTATED	8	3	16	12
AMP PEAK 9(11P15.5) WILD-TYPE	58	48	67	8

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

'amp_13q12.13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

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

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

'amp_13q12.13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 11(13Q12.13) MUTATED	13	49	30
AMP PEAK 11(13Q12.13) WILD-TYPE	29	23	2

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

'amp_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 11(13Q12.13) MUTATED	25	150	58	34
AMP PEAK 11(13Q12.13) WILD-TYPE	12	5	134	20

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

'amp_13q12.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 11(13Q12.13) MUTATED	93	42	37
AMP PEAK 11(13Q12.13) WILD-TYPE	25	50	34

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

'amp_13q12.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

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

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

'amp_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 11(13Q12.13) MUTATED	65	66	25	94	9
AMP PEAK 11(13Q12.13) WILD-TYPE	10	30	63	34	27

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

'amp_13q12.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

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

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

'amp_13q22.1' versus 'MRNA_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.077

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 12(13Q22.1) MUTATED	15	49	12	15
AMP PEAK 12(13Q22.1) WILD-TYPE	20	12	17	6

Figure S28. Get High-res Image Gene #12: '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 = 0.0083

Table S29. Gene #12: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 12(13Q22.1) MUTATED	13	48	30
AMP PEAK 12(13Q22.1) WILD-TYPE	29	24	2

Figure S29. Get High-res Image Gene #12: '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 = 0.0083

Table S30. Gene #12: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 12(13Q22.1) MUTATED	24	148	63	35
AMP PEAK 12(13Q22.1) WILD-TYPE	13	7	129	19

Figure S30. Get High-res Image Gene #12: '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 = 0.0083

Table S31. Gene #12: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 12(13Q22.1) MUTATED	93	45	37
AMP PEAK 12(13Q22.1) WILD-TYPE	25	47	34

Figure S31. Get High-res Image Gene #12: '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 = 0.0083

Table S32. Gene #12: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S32. Get High-res Image Gene #12: '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 = 0.0083

Table S33. Gene #12: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 12(13Q22.1) MUTATED	64	68	28	92	10
AMP PEAK 12(13Q22.1) WILD-TYPE	11	28	60	36	26

Figure S33. Get High-res Image Gene #12: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S34. Gene #12: 'amp_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S34. Get High-res Image Gene #12: 'amp_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_16p11.2' versus 'MRNA_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.25

Table S35. Gene #13: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 13(16P11.2) MUTATED	6	24	3	12
AMP PEAK 13(16P11.2) WILD-TYPE	29	37	26	9

Figure S35. Get High-res Image Gene #13: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 13(16P11.2) MUTATED	6	16	23
AMP PEAK 13(16P11.2) WILD-TYPE	36	56	9

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

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S37. Gene #13: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 13(16P11.2) MUTATED	12	84	16	9
AMP PEAK 13(16P11.2) WILD-TYPE	25	71	176	45

Figure S37. Get High-res Image Gene #13: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S38. Gene #13: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S38. Get High-res Image Gene #13: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S39. Gene #13: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 13(16P11.2) MUTATED	30	25	10	52	2
AMP PEAK 13(16P11.2) WILD-TYPE	45	71	78	76	34

Figure S39. Get High-res Image Gene #13: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16q12.1' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

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

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

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

'amp_16q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S41. Gene #14: 'amp_16q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 14(16Q12.1) MUTATED	3	17	20
AMP PEAK 14(16Q12.1) WILD-TYPE	39	55	12

Figure S41. Get High-res Image Gene #14: 'amp_16q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_16q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S42. Gene #14: 'amp_16q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 14(16Q12.1) MUTATED	11	75	12	9
AMP PEAK 14(16Q12.1) WILD-TYPE	26	80	180	45

Figure S42. Get High-res Image Gene #14: 'amp_16q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16q12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S43. Gene #14: 'amp_16q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S43. Get High-res Image Gene #14: 'amp_16q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S44. Gene #14: 'amp_16q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 14(16Q12.1) MUTATED	29	21	8	47	0
AMP PEAK 14(16Q12.1) WILD-TYPE	46	75	80	81	36

Figure S44. Get High-res Image Gene #14: 'amp_16q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.089

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

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

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

'amp_16q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S46. Gene #14: 'amp_16q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
AMP PEAK 14(16Q12.1) MUTATED	23	3	20	9
AMP PEAK 14(16Q12.1) WILD-TYPE	43	48	63	11

Figure S46. Get High-res Image Gene #14: 'amp_16q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S47. Gene #16: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 16(17Q12) MUTATED	11	57	22	19
AMP PEAK 16(17Q12) WILD-TYPE	26	98	170	35

Figure S47. Get High-res Image Gene #16: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S48. Gene #16: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 16(17Q12) MUTATED	9	44	12	11	29
AMP PEAK 16(17Q12) WILD-TYPE	24	69	59	79	87

Figure S48. Get High-res Image Gene #16: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S49. Gene #17: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 17(17Q24.1) MUTATED	10	57	17	18
AMP PEAK 17(17Q24.1) WILD-TYPE	27	98	175	36

Figure S49. Get High-res Image Gene #17: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.1' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S50. Gene #17: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 17(17Q24.1) MUTATED	43	18	8
AMP PEAK 17(17Q24.1) WILD-TYPE	75	74	63

Figure S50. Get High-res Image Gene #17: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S51. Gene #17: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S51. Get High-res Image Gene #17: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S52. Gene #17: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 17(17Q24.1) MUTATED	20	33	7	36	2
AMP PEAK 17(17Q24.1) WILD-TYPE	55	63	81	92	34

Figure S52. Get High-res Image Gene #17: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S53. Gene #18: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 18(19P13.2) MUTATED	11	37	14	9
AMP PEAK 18(19P13.2) WILD-TYPE	26	118	178	45

Figure S53. Get High-res Image Gene #18: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S54. Gene #19: 'amp_19q13.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 19(19Q13.11) MUTATED	16	42	22	10
AMP PEAK 19(19Q13.11) WILD-TYPE	21	113	170	44

Figure S54. Get High-res Image Gene #19: 'amp_19q13.11' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.094

Table S55. Gene #19: 'amp_19q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 19(19Q13.11) MUTATED	25	20	13	30	0
AMP PEAK 19(19Q13.11) WILD-TYPE	50	76	75	98	36

Figure S55. Get High-res Image Gene #19: 'amp_19q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S56. Gene #20: 'amp_20p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 20(20P11.23) MUTATED	37	88	58	32
AMP PEAK 20(20P11.23) WILD-TYPE	0	67	134	22

Figure S56. Get High-res Image Gene #20: 'amp_20p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S57. Gene #20: 'amp_20p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S57. Get High-res Image Gene #20: 'amp_20p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S58. Gene #20: 'amp_20p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 20(20P11.23) MUTATED	39	54	29	79	5
AMP PEAK 20(20P11.23) WILD-TYPE	36	42	59	49	31

Figure S58. Get High-res Image Gene #20: 'amp_20p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S59. Gene #21: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S59. Get High-res Image Gene #21: '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 = 0.0083

Table S60. Gene #21: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 21(20Q11.21) MUTATED	12	62	31
AMP PEAK 21(20Q11.21) WILD-TYPE	30	10	1

Figure S60. Get High-res Image Gene #21: '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 = 0.0083

Table S61. Gene #21: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 21(20Q11.21) MUTATED	37	152	77	48
AMP PEAK 21(20Q11.21) WILD-TYPE	0	3	115	6

Figure S61. Get High-res Image Gene #21: '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 = 0.0083

Table S62. Gene #21: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 21(20Q11.21) MUTATED	112	47	44
AMP PEAK 21(20Q11.21) WILD-TYPE	6	45	27

Figure S62. Get High-res Image Gene #21: '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 = 0.0083

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

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

Figure S63. Get High-res Image Gene #21: '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 = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 21(20Q11.21) MUTATED	69	83	33	112	6
AMP PEAK 21(20Q11.21) WILD-TYPE	6	13	55	16	30

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

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S65. Gene #21: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S65. Get High-res Image Gene #21: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S66. Gene #21: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
AMP PEAK 21(20Q11.21) MUTATED	58	24	58	19
AMP PEAK 21(20Q11.21) WILD-TYPE	8	27	25	1

Figure S66. Get High-res Image Gene #21: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S67. Gene #22: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 22(20Q12) MUTATED	12	58	15	18
AMP PEAK 22(20Q12) WILD-TYPE	23	3	14	3

Figure S67. Get High-res Image Gene #22: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S68. Gene #22: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 22(20Q12) MUTATED	11	61	31
AMP PEAK 22(20Q12) WILD-TYPE	31	11	1

Figure S68. Get High-res Image Gene #22: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S69. Gene #22: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 22(20Q12) MUTATED	37	152	77	49
AMP PEAK 22(20Q12) WILD-TYPE	0	3	115	5

Figure S69. Get High-res Image Gene #22: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S70. Gene #22: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 22(20Q12) MUTATED	112	49	45
AMP PEAK 22(20Q12) WILD-TYPE	6	43	26

Figure S70. Get High-res Image Gene #22: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.23

Table S71. Gene #22: 'amp_20q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	59	48	56	68	68	26
AMP PEAK 22(20Q12) MUTATED	52	37	41	48	37	14
AMP PEAK 22(20Q12) WILD-TYPE	7	11	15	20	31	12

Figure S71. Get High-res Image Gene #22: 'amp_20q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S72. Gene #22: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 22(20Q12) MUTATED	26	110	52	29	87
AMP PEAK 22(20Q12) WILD-TYPE	7	3	19	61	29

Figure S72. Get High-res Image Gene #22: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S73. Gene #22: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 22(20Q12) MUTATED	70	83	35	111	5
AMP PEAK 22(20Q12) WILD-TYPE	5	13	53	17	31

Figure S73. Get High-res Image Gene #22: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S74. Gene #22: 'amp_20q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 22(20Q12) MUTATED	75	34	52
AMP PEAK 22(20Q12) WILD-TYPE	4	44	11

Figure S74. Get High-res Image Gene #22: 'amp_20q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S75. Gene #22: 'amp_20q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
AMP PEAK 22(20Q12) MUTATED	58	24	60	19
AMP PEAK 22(20Q12) WILD-TYPE	8	27	23	1

Figure S75. Get High-res Image Gene #22: 'amp_20q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.32' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S76. Gene #23: 'amp_20q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 23(20Q13.32) MUTATED	13	58	17	18
AMP PEAK 23(20Q13.32) WILD-TYPE	22	3	12	3

Figure S76. Get High-res Image Gene #23: 'amp_20q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S77. Gene #23: 'amp_20q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 23(20Q13.32) MUTATED	12	63	31
AMP PEAK 23(20Q13.32) WILD-TYPE	30	9	1

Figure S77. Get High-res Image Gene #23: 'amp_20q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S78. Gene #23: 'amp_20q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
AMP PEAK 23(20Q13.32) MUTATED	37	151	79	50
AMP PEAK 23(20Q13.32) WILD-TYPE	0	4	113	4

Figure S78. Get High-res Image Gene #23: 'amp_20q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S79. Gene #23: 'amp_20q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 23(20Q13.32) MUTATED	111	49	45
AMP PEAK 23(20Q13.32) WILD-TYPE	7	43	26

Figure S79. Get High-res Image Gene #23: 'amp_20q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.2

Table S80. Gene #23: 'amp_20q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	59	48	56	68	68	26
AMP PEAK 23(20Q13.32) MUTATED	52	38	41	50	37	14
AMP PEAK 23(20Q13.32) WILD-TYPE	7	10	15	18	31	12

Figure S80. Get High-res Image Gene #23: 'amp_20q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S81. Gene #23: 'amp_20q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
AMP PEAK 23(20Q13.32) MUTATED	26	110	52	30	89
AMP PEAK 23(20Q13.32) WILD-TYPE	7	3	19	60	27

Figure S81. Get High-res Image Gene #23: 'amp_20q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S82. Gene #23: 'amp_20q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
AMP PEAK 23(20Q13.32) MUTATED	70	83	35	112	7
AMP PEAK 23(20Q13.32) WILD-TYPE	5	13	53	16	29

Figure S82. Get High-res Image Gene #23: 'amp_20q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S83. Gene #23: 'amp_20q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 23(20Q13.32) MUTATED	75	35	52
AMP PEAK 23(20Q13.32) WILD-TYPE	4	43	11

Figure S83. Get High-res Image Gene #23: 'amp_20q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S84. Gene #23: 'amp_20q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
AMP PEAK 23(20Q13.32) MUTATED	58	25	60	19
AMP PEAK 23(20Q13.32) WILD-TYPE	8	26	23	1

Figure S84. Get High-res Image Gene #23: 'amp_20q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.1

Table S85. Gene #24: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S85. Get High-res Image Gene #24: '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 = 0.0083

Table S86. Gene #24: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 1(1P36.11) MUTATED	23	93	31	18
DEL PEAK 1(1P36.11) WILD-TYPE	14	62	161	36

Figure S86. Get High-res Image Gene #24: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S87. Gene #24: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 1(1P36.11) MUTATED	61	19	24
DEL PEAK 1(1P36.11) WILD-TYPE	57	73	47

Figure S87. Get High-res Image Gene #24: '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 = 0.0083

Table S88. Gene #24: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S88. Get High-res Image Gene #24: '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 = 0.0083

Table S89. Gene #24: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 1(1P36.11) MUTATED	38	43	12	61	4
DEL PEAK 1(1P36.11) WILD-TYPE	37	53	76	67	32

Figure S89. Get High-res Image Gene #24: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S90. Gene #24: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S90. Get High-res Image Gene #24: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S91. Gene #25: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 2(1P33) MUTATED	18	73	23	7
DEL PEAK 2(1P33) WILD-TYPE	19	82	169	47

Figure S91. Get High-res Image Gene #25: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p33' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S92. Gene #25: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 2(1P33) MUTATED	47	13	19
DEL PEAK 2(1P33) WILD-TYPE	71	79	52

Figure S92. Get High-res Image Gene #25: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p33' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.15

Table S93. Gene #25: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 2(1P33) MUTATED	7	41	20	9	37
DEL PEAK 2(1P33) WILD-TYPE	26	72	51	81	79

Figure S93. Get High-res Image Gene #25: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.22

Table S94. Gene #25: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 2(1P33) MUTATED	32	26	11	38	7
DEL PEAK 2(1P33) WILD-TYPE	43	70	77	90	29

Figure S94. Get High-res Image Gene #25: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S95. Gene #25: 'del_1p33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
DEL PEAK 2(1P33) MUTATED	18	5	24	13
DEL PEAK 2(1P33) WILD-TYPE	48	46	59	7

Figure S95. Get High-res Image Gene #25: 'del_1p33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S96. Gene #26: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 3(1P13.1) MUTATED	16	70	26	4
DEL PEAK 3(1P13.1) WILD-TYPE	21	85	166	50

Figure S96. Get High-res Image Gene #26: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S97. Gene #27: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 4(1Q43) MUTATED	6	33	7	8
DEL PEAK 4(1Q43) WILD-TYPE	31	122	185	46

Figure S97. Get High-res Image Gene #27: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S98. Gene #30: 'del_3p26.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 7(3P26.1) MUTATED	10	40	14	4
DEL PEAK 7(3P26.1) WILD-TYPE	27	115	178	50

Figure S98. Get High-res Image Gene #30: 'del_3p26.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S99. Gene #32: 'del_3q26.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 9(3Q26.31) MUTATED	8	26	12	0
DEL PEAK 9(3Q26.31) WILD-TYPE	29	129	180	54

Figure S99. Get High-res Image Gene #32: 'del_3q26.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S100. Gene #33: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 10(4P16.2) MUTATED	23	75	23	12
DEL PEAK 10(4P16.2) WILD-TYPE	14	80	169	42

Figure S100. Get High-res Image Gene #33: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S101. Gene #33: 'del_4p16.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 10(4P16.2) MUTATED	8	44	25	7	43
DEL PEAK 10(4P16.2) WILD-TYPE	25	69	46	83	73

Figure S101. Get High-res Image Gene #33: 'del_4p16.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S102. Gene #33: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 10(4P16.2) MUTATED	33	29	9	51	5
DEL PEAK 10(4P16.2) WILD-TYPE	42	67	79	77	31

Figure S102. Get High-res Image Gene #33: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.089

Table S103. Gene #33: 'del_4p16.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 10(4P16.2) MUTATED	27	8	23
DEL PEAK 10(4P16.2) WILD-TYPE	52	70	40

Figure S103. Get High-res Image Gene #33: 'del_4p16.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.24

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

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

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

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S105. Gene #34: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 11(4Q22.1) MUTATED	21	81	30	12
DEL PEAK 11(4Q22.1) WILD-TYPE	16	74	162	42

Figure S105. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.064

Table S106. Gene #34: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 11(4Q22.1) MUTATED	53	16	25
DEL PEAK 11(4Q22.1) WILD-TYPE	65	76	46

Figure S106. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S107. Gene #34: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 11(4Q22.1) MUTATED	12	47	22	7	47
DEL PEAK 11(4Q22.1) WILD-TYPE	21	66	49	83	69

Figure S107. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S108. Gene #34: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 11(4Q22.1) MUTATED	38	32	9	51	5
DEL PEAK 11(4Q22.1) WILD-TYPE	37	64	79	77	31

Figure S108. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S109. Gene #34: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S109. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S110. Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 12(4Q35.1) MUTATED	20	87	29	16
DEL PEAK 12(4Q35.1) WILD-TYPE	17	68	163	38

Figure S110. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S111. Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 12(4Q35.1) MUTATED	56	13	26
DEL PEAK 12(4Q35.1) WILD-TYPE	62	79	45

Figure S111. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S112. Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 12(4Q35.1) MUTATED	13	48	25	11	47
DEL PEAK 12(4Q35.1) WILD-TYPE	20	65	46	79	69

Figure S112. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S113. Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 12(4Q35.1) MUTATED	38	32	12	56	6
DEL PEAK 12(4Q35.1) WILD-TYPE	37	64	76	72	30

Figure S113. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S114. Gene #35: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 12(4Q35.1) MUTATED	35	8	25
DEL PEAK 12(4Q35.1) WILD-TYPE	44	70	38

Figure S114. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S115. Gene #36: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 13(5Q11.2) MUTATED	12	54	17	17
DEL PEAK 13(5Q11.2) WILD-TYPE	25	101	175	37

Figure S115. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q11.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S116. Gene #36: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 13(5Q11.2) MUTATED	10	31	18	4	34
DEL PEAK 13(5Q11.2) WILD-TYPE	23	82	53	86	82

Figure S116. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.094

Table S117. Gene #36: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 13(5Q11.2) MUTATED	27	23	8	35	4
DEL PEAK 13(5Q11.2) WILD-TYPE	48	73	80	93	32

Figure S117. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.083

Table S118. Gene #36: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 13(5Q11.2) MUTATED	25	5	17
DEL PEAK 13(5Q11.2) WILD-TYPE	54	73	46

Figure S118. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S119. Gene #37: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 14(5Q21.3) MUTATED	16	62	26	21
DEL PEAK 14(5Q21.3) WILD-TYPE	21	93	166	33

Figure S119. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.16

Table S120. Gene #37: 'del_5q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 14(5Q21.3) MUTATED	11	41	18	10	41
DEL PEAK 14(5Q21.3) WILD-TYPE	22	72	53	80	75

Figure S120. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S121. Gene #37: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 14(5Q21.3) MUTATED	28	33	11	45	4
DEL PEAK 14(5Q21.3) WILD-TYPE	47	63	77	83	32

Figure S121. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S122. Gene #38: 'del_5q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 15(5Q23.1) MUTATED	14	58	23	21
DEL PEAK 15(5Q23.1) WILD-TYPE	23	97	169	33

Figure S122. Get High-res Image Gene #38: 'del_5q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q23.1' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.052

Table S123. Gene #38: 'del_5q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 15(5Q23.1) MUTATED	10	41	18	8	35
DEL PEAK 15(5Q23.1) WILD-TYPE	23	72	53	82	81

Figure S123. Get High-res Image Gene #38: 'del_5q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.077

Table S124. Gene #38: 'del_5q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 15(5Q23.1) MUTATED	27	31	11	40	3
DEL PEAK 15(5Q23.1) WILD-TYPE	48	65	77	88	33

Figure S124. Get High-res Image Gene #38: 'del_5q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S125. Gene #42: 'del_8p23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 19(8P23.3) MUTATED	10	29	23
DEL PEAK 19(8P23.3) WILD-TYPE	32	43	9

Figure S125. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 19(8P23.3) MUTATED	7	105	30	40
DEL PEAK 19(8P23.3) WILD-TYPE	30	50	162	14

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

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S127. Gene #42: 'del_8p23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 19(8P23.3) MUTATED	69	24	25
DEL PEAK 19(8P23.3) WILD-TYPE	49	68	46

Figure S127. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S128. Gene #42: 'del_8p23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 19(8P23.3) MUTATED	15	56	34	13	58
DEL PEAK 19(8P23.3) WILD-TYPE	18	57	37	77	58

Figure S128. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S129. Gene #42: 'del_8p23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 19(8P23.3) MUTATED	46	41	16	68	5
DEL PEAK 19(8P23.3) WILD-TYPE	29	55	72	60	31

Figure S129. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S130. Gene #42: 'del_8p23.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 19(8P23.3) MUTATED	46	14	32
DEL PEAK 19(8P23.3) WILD-TYPE	33	64	31

Figure S130. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p22' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.089

Table S131. Gene #43: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 20(8P22) MUTATED	8	35	21
DEL PEAK 20(8P22) WILD-TYPE	34	37	11

Figure S131. Get High-res Image Gene #43: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S132. Gene #43: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 20(8P22) MUTATED	7	115	32	43
DEL PEAK 20(8P22) WILD-TYPE	30	40	160	11

Figure S132. Get High-res Image Gene #43: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p22' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S133. Gene #43: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 20(8P22) MUTATED	76	28	27
DEL PEAK 20(8P22) WILD-TYPE	42	64	44

Figure S133. Get High-res Image Gene #43: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S134. Gene #43: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 20(8P22) MUTATED	16	65	36	14	59
DEL PEAK 20(8P22) WILD-TYPE	17	48	35	76	57

Figure S134. Get High-res Image Gene #43: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S135. Gene #43: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 20(8P22) MUTATED	51	45	19	71	4
DEL PEAK 20(8P22) WILD-TYPE	24	51	69	57	32

Figure S135. Get High-res Image Gene #43: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S136. Gene #43: 'del_8p22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 20(8P22) MUTATED	50	18	36
DEL PEAK 20(8P22) WILD-TYPE	29	60	27

Figure S136. Get High-res Image Gene #43: 'del_8p22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S137. Gene #44: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 21(8P11.21) MUTATED	4	33	9	0
DEL PEAK 21(8P11.21) WILD-TYPE	33	122	183	54

Figure S137. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.094

Table S138. Gene #45: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 22(9P21.3) MUTATED	9	32	11	8
DEL PEAK 22(9P21.3) WILD-TYPE	28	123	181	46

Figure S138. Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S139. Gene #46: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 23(10P15.3) MUTATED	14	37	13	13
DEL PEAK 23(10P15.3) WILD-TYPE	23	118	179	41

Figure S139. Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S140. Gene #46: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 23(10P15.3) MUTATED	25	17	6	23	3
DEL PEAK 23(10P15.3) WILD-TYPE	50	79	82	105	33

Figure S140. Get High-res Image Gene #46: '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 = 0.0083

Table S141. Gene #47: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 24(10Q21.1) MUTATED	16	50	13	13
DEL PEAK 24(10Q21.1) WILD-TYPE	21	105	179	41

Figure S141. Get High-res Image Gene #47: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.064

Table S142. Gene #47: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 24(10Q21.1) MUTATED	25	22	9	32	1
DEL PEAK 24(10Q21.1) WILD-TYPE	50	74	79	96	35

Figure S142. Get High-res Image Gene #47: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S143. Gene #48: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 25(10Q23.31) MUTATED	19	51	20	15
DEL PEAK 25(10Q23.31) WILD-TYPE	18	104	172	39

Figure S143. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.094

Table S144. Gene #48: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 25(10Q23.31) MUTATED	26	28	12	34	1
DEL PEAK 25(10Q23.31) WILD-TYPE	49	68	76	94	35

Figure S144. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S145. Gene #48: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 25(10Q23.31) MUTATED	27	7	21
DEL PEAK 25(10Q23.31) WILD-TYPE	52	71	42

Figure S145. Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S146. Gene #49: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 26(10Q25.2) MUTATED	19	57	16	13
DEL PEAK 26(10Q25.2) WILD-TYPE	18	98	176	41

Figure S146. Get High-res Image Gene #49: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q25.2' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.064

Table S147. Gene #49: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 26(10Q25.2) MUTATED	45	12	14
DEL PEAK 26(10Q25.2) WILD-TYPE	73	80	57

Figure S147. Get High-res Image Gene #49: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S148. Gene #49: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 26(10Q25.2) MUTATED	27	26	7	39	1
DEL PEAK 26(10Q25.2) WILD-TYPE	48	70	81	89	35

Figure S148. Get High-res Image Gene #49: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S149. Gene #49: 'del_10q25.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 26(10Q25.2) MUTATED	29	4	18
DEL PEAK 26(10Q25.2) WILD-TYPE	50	74	45

Figure S149. Get High-res Image Gene #49: 'del_10q25.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S150. Gene #50: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 27(12P13.2) MUTATED	6	40	3	9
DEL PEAK 27(12P13.2) WILD-TYPE	31	115	189	45

Figure S150. Get High-res Image Gene #50: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S151. Gene #50: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 27(12P13.2) MUTATED	16	15	2	21	0
DEL PEAK 27(12P13.2) WILD-TYPE	59	81	86	107	36

Figure S151. Get High-res Image Gene #50: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S152. Gene #52: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 29(14Q31.1) MUTATED	6	36	3	10
DEL PEAK 29(14Q31.1) WILD-TYPE	29	25	26	11

Figure S152. Get High-res Image Gene #52: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.052

Table S153. Gene #52: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 29(14Q31.1) MUTATED	6	29	20
DEL PEAK 29(14Q31.1) WILD-TYPE	36	43	12

Figure S153. Get High-res Image Gene #52: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S154. Gene #52: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 29(14Q31.1) MUTATED	14	101	19	11
DEL PEAK 29(14Q31.1) WILD-TYPE	23	54	173	43

Figure S154. Get High-res Image Gene #52: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S155. Gene #52: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 29(14Q31.1) MUTATED	54	17	17
DEL PEAK 29(14Q31.1) WILD-TYPE	64	75	54

Figure S155. Get High-res Image Gene #52: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.19

Table S156. Gene #52: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	127	26	94
DEL PEAK 29(14Q31.1) MUTATED	28	53	9	15
DEL PEAK 29(14Q31.1) WILD-TYPE	50	74	17	79

Figure S156. Get High-res Image Gene #52: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S157. Gene #52: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 29(14Q31.1) MUTATED	9	50	19	8	53
DEL PEAK 29(14Q31.1) WILD-TYPE	24	63	52	82	63

Figure S157. Get High-res Image Gene #52: '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 = 0.0083

Table S158. Gene #52: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 29(14Q31.1) MUTATED	31	36	10	60	2
DEL PEAK 29(14Q31.1) WILD-TYPE	44	60	78	68	34

Figure S158. Get High-res Image Gene #52: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S159. Gene #52: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 29(14Q31.1) MUTATED	35	10	21
DEL PEAK 29(14Q31.1) WILD-TYPE	44	68	42

Figure S159. Get High-res Image Gene #52: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S160. Gene #53: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 30(15Q11.2) MUTATED	24	103	29	15
DEL PEAK 30(15Q11.2) WILD-TYPE	13	52	163	39

Figure S160. Get High-res Image Gene #53: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S161. Gene #53: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 30(15Q11.2) MUTATED	10	54	31	12	58
DEL PEAK 30(15Q11.2) WILD-TYPE	23	59	40	78	58

Figure S161. Get High-res Image Gene #53: '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 = 0.0083

Table S162. Gene #53: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 30(15Q11.2) MUTATED	43	42	11	65	4
DEL PEAK 30(15Q11.2) WILD-TYPE	32	54	77	63	32

Figure S162. Get High-res Image Gene #53: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S163. Gene #53: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 30(15Q11.2) MUTATED	40	15	31
DEL PEAK 30(15Q11.2) WILD-TYPE	39	63	32

Figure S163. Get High-res Image Gene #53: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S164. Gene #54: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 31(15Q15.2) MUTATED	24	101	27	14
DEL PEAK 31(15Q15.2) WILD-TYPE	13	54	165	40

Figure S164. Get High-res Image Gene #54: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.2' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.18

Table S165. Gene #54: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 31(15Q15.2) MUTATED	60	23	23
DEL PEAK 31(15Q15.2) WILD-TYPE	58	69	48

Figure S165. Get High-res Image Gene #54: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S166. Gene #54: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 31(15Q15.2) MUTATED	10	52	28	10	58
DEL PEAK 31(15Q15.2) WILD-TYPE	23	61	43	80	58

Figure S166. Get High-res Image Gene #54: '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 = 0.0083

Table S167. Gene #54: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 31(15Q15.2) MUTATED	39	41	10	65	3
DEL PEAK 31(15Q15.2) WILD-TYPE	36	55	78	63	33

Figure S167. Get High-res Image Gene #54: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.064

Table S168. Gene #54: 'del_15q15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 31(15Q15.2) MUTATED	37	14	29
DEL PEAK 31(15Q15.2) WILD-TYPE	42	64	34

Figure S168. Get High-res Image Gene #54: 'del_15q15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S169. Gene #55: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 32(15Q21.1) MUTATED	23	97	29	14
DEL PEAK 32(15Q21.1) WILD-TYPE	14	58	163	40

Figure S169. Get High-res Image Gene #55: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S170. Gene #55: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S170. Get High-res Image Gene #55: '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 = 0.0083

Table S171. Gene #55: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 32(15Q21.1) MUTATED	38	40	10	63	6
DEL PEAK 32(15Q21.1) WILD-TYPE	37	56	78	65	30

Figure S171. Get High-res Image Gene #55: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.089

Table S172. Gene #55: 'del_15q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S172. Get High-res Image Gene #55: 'del_15q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q22.33' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S173. Gene #56: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S173. Get High-res Image Gene #56: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q22.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.21

Table S174. Gene #56: 'del_15q22.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 33(15Q22.33) MUTATED	6	29	18
DEL PEAK 33(15Q22.33) WILD-TYPE	36	43	14

Figure S174. Get High-res Image Gene #56: 'del_15q22.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q22.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S175. Gene #56: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 33(15Q22.33) MUTATED	23	97	23	15
DEL PEAK 33(15Q22.33) WILD-TYPE	14	58	169	39

Figure S175. Get High-res Image Gene #56: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q22.33' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S176. Gene #56: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 33(15Q22.33) MUTATED	60	19	24
DEL PEAK 33(15Q22.33) WILD-TYPE	58	73	47

Figure S176. Get High-res Image Gene #56: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q22.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S177. Gene #56: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S177. Get High-res Image Gene #56: '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 = 0.0083

Table S178. Gene #56: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 33(15Q22.33) MUTATED	40	40	10	60	2
DEL PEAK 33(15Q22.33) WILD-TYPE	35	56	78	68	34

Figure S178. Get High-res Image Gene #56: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S179. Gene #56: 'del_15q22.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S179. Get High-res Image Gene #56: 'del_15q22.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q22.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.16

Table S180. Gene #56: 'del_15q22.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
DEL PEAK 33(15Q22.33) MUTATED	28	6	35	10
DEL PEAK 33(15Q22.33) WILD-TYPE	38	45	48	10

Figure S180. Get High-res Image Gene #56: 'del_15q22.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S181. Gene #59: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S181. Get High-res Image Gene #59: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S182. Gene #59: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 36(17P12) MUTATED	9	47	26
DEL PEAK 36(17P12) WILD-TYPE	33	25	6

Figure S182. Get High-res Image Gene #59: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S183. Gene #59: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 36(17P12) MUTATED	26	137	43	40
DEL PEAK 36(17P12) WILD-TYPE	11	18	149	14

Figure S183. Get High-res Image Gene #59: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S184. Gene #59: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 36(17P12) MUTATED	95	31	34
DEL PEAK 36(17P12) WILD-TYPE	23	61	37

Figure S184. Get High-res Image Gene #59: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S185. Gene #59: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S185. Get High-res Image Gene #59: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S186. Gene #59: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 36(17P12) MUTATED	53	70	18	91	4
DEL PEAK 36(17P12) WILD-TYPE	22	26	70	37	32

Figure S186. Get High-res Image Gene #59: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S187. Gene #59: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S187. Get High-res Image Gene #59: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S188. Gene #59: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
DEL PEAK 36(17P12) MUTATED	47	18	41	18
DEL PEAK 36(17P12) WILD-TYPE	19	33	42	2

Figure S188. Get High-res Image Gene #59: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18p11.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S189. Gene #61: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S189. Get High-res Image Gene #61: '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 = 0.0083

Table S190. Gene #61: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 38(18P11.31) MUTATED	5	47	26
DEL PEAK 38(18P11.31) WILD-TYPE	37	25	6

Figure S190. Get High-res Image Gene #61: '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 = 0.0083

Table S191. Gene #61: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 38(18P11.31) MUTATED	32	136	34	35
DEL PEAK 38(18P11.31) WILD-TYPE	5	19	158	19

Figure S191. Get High-res Image Gene #61: '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 = 0.0083

Table S192. Gene #61: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 38(18P11.31) MUTATED	98	23	35
DEL PEAK 38(18P11.31) WILD-TYPE	20	69	36

Figure S192. Get High-res Image Gene #61: '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 = 0.0083

Table S193. Gene #61: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S193. Get High-res Image Gene #61: '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 = 0.0083

Table S194. Gene #61: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 38(18P11.31) MUTATED	57	69	12	90	1
DEL PEAK 38(18P11.31) WILD-TYPE	18	27	76	38	35

Figure S194. Get High-res Image Gene #61: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S195. Gene #61: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S195. Get High-res Image Gene #61: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S196. Gene #61: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
DEL PEAK 38(18P11.31) MUTATED	44	16	39	17
DEL PEAK 38(18P11.31) WILD-TYPE	22	35	44	3

Figure S196. Get High-res Image Gene #61: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q12.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S197. Gene #62: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S197. Get High-res Image Gene #62: '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 = 0.0083

Table S198. Gene #62: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 39(18Q12.2) MUTATED	7	51	28
DEL PEAK 39(18Q12.2) WILD-TYPE	35	21	4

Figure S198. Get High-res Image Gene #62: '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 = 0.0083

Table S199. Gene #62: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 39(18Q12.2) MUTATED	31	143	44	45
DEL PEAK 39(18Q12.2) WILD-TYPE	6	12	148	9

Figure S199. Get High-res Image Gene #62: '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 = 0.0083

Table S200. Gene #62: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 39(18Q12.2) MUTATED	106	30	36
DEL PEAK 39(18Q12.2) WILD-TYPE	12	62	35

Figure S200. Get High-res Image Gene #62: '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 = 0.0083

Table S201. Gene #62: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S201. Get High-res Image Gene #62: '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 = 0.0083

Table S202. Gene #62: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 39(18Q12.2) MUTATED	62	74	19	98	2
DEL PEAK 39(18Q12.2) WILD-TYPE	13	22	69	30	34

Figure S202. Get High-res Image Gene #62: '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 = 0.0083

Table S203. Gene #62: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S203. Get High-res Image Gene #62: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S204. Gene #62: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
DEL PEAK 39(18Q12.2) MUTATED	50	18	46	18
DEL PEAK 39(18Q12.2) WILD-TYPE	16	33	37	2

Figure S204. Get High-res Image Gene #62: '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 = 0.0083

Table S205. Gene #63: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S205. Get High-res Image Gene #63: '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 = 0.0083

Table S206. Gene #63: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 40(18Q21.2) MUTATED	7	52	28
DEL PEAK 40(18Q21.2) WILD-TYPE	35	20	4

Figure S206. Get High-res Image Gene #63: '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 = 0.0083

Table S207. Gene #63: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 40(18Q21.2) MUTATED	32	145	53	47
DEL PEAK 40(18Q21.2) WILD-TYPE	5	10	139	7

Figure S207. Get High-res Image Gene #63: '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 = 0.0083

Table S208. Gene #63: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 40(18Q21.2) MUTATED	107	40	38
DEL PEAK 40(18Q21.2) WILD-TYPE	11	52	33

Figure S208. Get High-res Image Gene #63: '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 = 0.0083

Table S209. Gene #63: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

Figure S209. Get High-res Image Gene #63: '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 = 0.0083

Table S210. Gene #63: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 40(18Q21.2) MUTATED	64	76	27	98	3
DEL PEAK 40(18Q21.2) WILD-TYPE	11	20	61	30	33

Figure S210. Get High-res Image Gene #63: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S211. Gene #63: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S211. Get High-res Image Gene #63: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.1

Table S212. Gene #63: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
DEL PEAK 40(18Q21.2) MUTATED	52	24	49	18
DEL PEAK 40(18Q21.2) WILD-TYPE	14	27	34	2

Figure S212. Get High-res Image Gene #63: '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 = 0.0083

Table S213. Gene #64: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 41(18Q22.1) MUTATED	8	53	11	16
DEL PEAK 41(18Q22.1) WILD-TYPE	27	8	18	5

Figure S213. Get High-res Image Gene #64: '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 = 0.0083

Table S214. Gene #64: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 41(18Q22.1) MUTATED	8	52	28
DEL PEAK 41(18Q22.1) WILD-TYPE	34	20	4

Figure S214. Get High-res Image Gene #64: '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 = 0.0083

Table S215. Gene #64: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 41(18Q22.1) MUTATED	33	146	52	46
DEL PEAK 41(18Q22.1) WILD-TYPE	4	9	140	8

Figure S215. Get High-res Image Gene #64: '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 = 0.0083

Table S216. Gene #64: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 41(18Q22.1) MUTATED	107	40	37
DEL PEAK 41(18Q22.1) WILD-TYPE	11	52	34

Figure S216. Get High-res Image Gene #64: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.23

Table S217. Gene #64: 'del_18q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	59	48	56	68	68	26
DEL PEAK 41(18Q22.1) MUTATED	42	35	41	43	29	11
DEL PEAK 41(18Q22.1) WILD-TYPE	17	13	15	25	39	15

Figure S217. Get High-res Image Gene #64: 'del_18q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S218. Gene #64: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 41(18Q22.1) MUTATED	20	100	46	23	79
DEL PEAK 41(18Q22.1) WILD-TYPE	13	13	25	67	37

Figure S218. Get High-res Image Gene #64: '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 = 0.0083

Table S219. Gene #64: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 41(18Q22.1) MUTATED	64	76	26	98	4
DEL PEAK 41(18Q22.1) WILD-TYPE	11	20	62	30	32

Figure S219. Get High-res Image Gene #64: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S220. Gene #64: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 41(18Q22.1) MUTATED	72	26	44
DEL PEAK 41(18Q22.1) WILD-TYPE	7	52	19

Figure S220. Get High-res Image Gene #64: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.19

Table S221. Gene #64: 'del_18q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
DEL PEAK 41(18Q22.1) MUTATED	51	24	49	18
DEL PEAK 41(18Q22.1) WILD-TYPE	15	27	34	2

Figure S221. Get High-res Image Gene #64: 'del_18q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.2

Table S222. Gene #65: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 42(19P13.3) MUTATED	6	34	13	10
DEL PEAK 42(19P13.3) WILD-TYPE	31	121	179	44

Figure S222. Get High-res Image Gene #65: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S223. Gene #65: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 42(19P13.3) MUTATED	9	17	5	28	0
DEL PEAK 42(19P13.3) WILD-TYPE	66	79	83	100	36

Figure S223. Get High-res Image Gene #65: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S224. Gene #66: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 43(20P12.1) MUTATED	0	75	32	17
DEL PEAK 43(20P12.1) WILD-TYPE	37	80	160	37

Figure S224. Get High-res Image Gene #66: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S225. Gene #67: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 44(20P12.1) MUTATED	0	75	32	17
DEL PEAK 44(20P12.1) WILD-TYPE	37	80	160	37

Figure S225. Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S226. Gene #68: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 45(21Q11.2) MUTATED	20	73	33	11
DEL PEAK 45(21Q11.2) WILD-TYPE	17	82	159	43

Figure S226. Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.089

Table S227. Gene #68: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 45(21Q11.2) MUTATED	6	48	23	13	42
DEL PEAK 45(21Q11.2) WILD-TYPE	27	65	48	77	74

Figure S227. Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.07

Table S228. Gene #68: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 45(21Q11.2) MUTATED	33	31	16	48	4
DEL PEAK 45(21Q11.2) WILD-TYPE	42	65	72	80	32

Figure S228. Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.083

Table S229. Gene #68: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 45(21Q11.2) MUTATED	35	11	22
DEL PEAK 45(21Q11.2) WILD-TYPE	44	67	41

Figure S229. Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.24

Table S230. Gene #69: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 46(22Q13.32) MUTATED	8	34	5	10
DEL PEAK 46(22Q13.32) WILD-TYPE	27	27	24	11

Figure S230. Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.19

Table S231. Gene #69: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 46(22Q13.32) MUTATED	6	35	16
DEL PEAK 46(22Q13.32) WILD-TYPE	36	37	16

Figure S231. Get High-res Image Gene #69: '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 = 0.0083

Table S232. Gene #69: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
DEL PEAK 46(22Q13.32) MUTATED	22	92	26	14
DEL PEAK 46(22Q13.32) WILD-TYPE	15	63	166	40

Figure S232. Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S233. Gene #69: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
DEL PEAK 46(22Q13.32) MUTATED	8	51	28	10	51
DEL PEAK 46(22Q13.32) WILD-TYPE	25	62	43	80	65

Figure S233. Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S234. Gene #69: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
DEL PEAK 46(22Q13.32) MUTATED	35	37	12	60	4
DEL PEAK 46(22Q13.32) WILD-TYPE	40	59	76	68	32

Figure S234. Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S235. Gene #69: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 46(22Q13.32) MUTATED	35	9	26
DEL PEAK 46(22Q13.32) WILD-TYPE	44	69	37

Figure S235. Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = COAD-TP.transferedmergedcluster.txt
Number of patients = 438
Number of significantly focal cnvs = 69
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)

Made with Nozzle