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

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 68 focal events and 12 molecular subtypes across 450 patients, 185 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 'MRNASEQ_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_7p21.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'CN_CNMF'.
amp_8p11.21 cnv correlated to 'CN_CNMF'.
amp_8q12.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_11p15.5 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_13q12.13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_13q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_16p11.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_16q12.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_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_20p12.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_20p11.21 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_20q11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_20q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_20q13.12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p13.1 cnv correlated to 'CN_CNMF'.
del_1q43 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_4p16.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4q35.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_5q21.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_5q22.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_8p23.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_8p22 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_10q21.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_10q25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_12p13.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_14q31.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q15.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q22.33 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_17p12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_18p11.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_18q12.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 68 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, 185 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 20q13 12	326 (72%)	124	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	0.00036 (0.227)	0.00033 (0.209)	1e-05 (0.00812)	1e-05 (0.00812)	0.789 (1.00)	0.00244 (1.00)	1 (1.00)	0.00547 (1.00)
del 14q31 1	150 (33%)	300	1e-05 (0.00812)	8e-05 (0.0526)	1e-05 (0.00812)	2e-05 (0.0136)	0.00038 (0.239)	0.0188 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.278 (1.00)	0.0207 (1.00)	0.266 (1.00)	0.0146 (1.00)
amp 11p15 5	94 (21%)	356	7e-05 (0.0461)	0.00549 (1.00)	1e-05 (0.00812)	2e-05 (0.0136)	0.00096 (0.567)	0.0335 (1.00)	2e-05 (0.0136)	1e-05 (0.00812)	0.106 (1.00)	1e-05 (0.00812)	0.941 (1.00)	0.277 (1.00)
amp 13q12 13	275 (61%)	175	2e-05 (0.0136)	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	0.00485 (1.00)	0.0197 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.574 (1.00)	0.812 (1.00)	0.398 (1.00)	0.0156 (1.00)
amp 13q22 1	277 (62%)	173	0.00013 (0.0842)	1e-05 (0.00812)	1e-05 (0.00812)	2e-05 (0.0136)	0.00885 (1.00)	0.0484 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.452 (1.00)	0.996 (1.00)	0.397 (1.00)	0.077 (1.00)
amp 20q11 21	323 (72%)	127	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	0.00085 (0.507)	0.00234 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.823 (1.00)	0.0016 (0.918)	1 (1.00)	0.00414 (1.00)
amp 20q12	324 (72%)	126	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	0.00048 (0.298)	0.0004 (0.251)	1e-05 (0.00812)	1e-05 (0.00812)	0.775 (1.00)	0.00132 (0.764)	1 (1.00)	0.00545 (1.00)
del 17p12	254 (56%)	196	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	0.0122 (1.00)	0.00124 (0.72)	1e-05 (0.00812)	1e-05 (0.00812)	0.668 (1.00)	0.0216 (1.00)	0.604 (1.00)	0.00141 (0.815)
del 18p11 31	246 (55%)	204	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	0.00071 (0.428)	0.01 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.834 (1.00)	0.0107 (1.00)	0.16 (1.00)	0.00303 (1.00)
del 18q12 2	274 (61%)	176	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	0.004 (1.00)	0.00128 (0.742)	1e-05 (0.00812)	1e-05 (0.00812)	0.916 (1.00)	0.0206 (1.00)	0.152 (1.00)	0.00503 (1.00)
del 18q21 2	287 (64%)	163	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	0.00072 (0.433)	0.0005 (0.31)	1e-05 (0.00812)	1e-05 (0.00812)	0.382 (1.00)	0.0351 (1.00)	0.0928 (1.00)	0.00777 (1.00)
amp 7p21 2	255 (57%)	195	0.00972 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.00013 (0.0842)	0.00118 (0.693)	0.00167 (0.957)	1e-05 (0.00812)	1e-05 (0.00812)	0.544 (1.00)	0.456 (1.00)	0.841 (1.00)	0.0341 (1.00)
amp 20p11 21	252 (56%)	198	0.00218 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	1e-05 (0.00812)	0.00362 (1.00)	0.103 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.166 (1.00)	0.0366 (1.00)	0.919 (1.00)	0.0493 (1.00)
del 1p36 11	168 (37%)	282	0.0001 (0.0652)	0.00798 (1.00)	1e-05 (0.00812)	2e-05 (0.0136)	0.0221 (1.00)	0.0183 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.664 (1.00)	0.0211 (1.00)	0.921 (1.00)	0.258 (1.00)
del 8p23 3	189 (42%)	261	0.0121 (1.00)	0.00018 (0.116)	1e-05 (0.00812)	2e-05 (0.0136)	0.00439 (1.00)	0.00829 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.219 (1.00)	0.0519 (1.00)	0.892 (1.00)	0.0441 (1.00)
del 8p22	203 (45%)	247	0.00489 (1.00)	0.00014 (0.0904)	1e-05 (0.00812)	1e-05 (0.00812)	0.00743 (1.00)	0.00115 (0.676)	1e-05 (0.00812)	1e-05 (0.00812)	0.453 (1.00)	0.0146 (1.00)	0.762 (1.00)	0.0484 (1.00)
del 15q22 33	161 (36%)	289	0.00032 (0.203)	0.00054 (0.332)	1e-05 (0.00812)	0.00024 (0.153)	0.0744 (1.00)	0.032 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.787 (1.00)	0.853 (1.00)	0.102 (1.00)	0.0802 (1.00)
amp 16q12 1	111 (25%)	339	5e-05 (0.0334)	1e-05 (0.00812)	1e-05 (0.00812)	0.0564 (1.00)	0.11 (1.00)	0.187 (1.00)	0.00088 (0.524)	1e-05 (0.00812)	0.975 (1.00)	0.0827 (1.00)	0.555 (1.00)	0.0236 (1.00)
amp 17q24 1	106 (24%)	344	0.0168 (1.00)	0.00763 (1.00)	1e-05 (0.00812)	0.00025 (0.159)	0.0627 (1.00)	0.00212 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.0122 (1.00)	0.0543 (1.00)	0.211 (1.00)	0.534 (1.00)
del 4q22 1	151 (34%)	299	0.00036 (0.227)	0.0044 (1.00)	1e-05 (0.00812)	5e-05 (0.0334)	0.104 (1.00)	0.155 (1.00)	0.00141 (0.815)	1e-05 (0.00812)	0.39 (1.00)	0.173 (1.00)	0.318 (1.00)	0.206 (1.00)
del 4q35 1	159 (35%)	291	0.00119 (0.697)	0.0076 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.0132 (1.00)	0.297 (1.00)	0.00015 (0.0964)	1e-05 (0.00812)	0.362 (1.00)	0.414 (1.00)	0.548 (1.00)	0.913 (1.00)
del 10q25 2	109 (24%)	341	0.124 (1.00)	0.0173 (1.00)	1e-05 (0.00812)	9e-05 (0.0589)	0.00626 (1.00)	0.0876 (1.00)	2e-05 (0.0136)	1e-05 (0.00812)	0.962 (1.00)	0.486 (1.00)	0.53 (1.00)	0.738 (1.00)
del 22q13 32	160 (36%)	290	0.00053 (0.326)	0.00024 (0.153)	1e-05 (0.00812)	0.00067 (0.405)	0.113 (1.00)	0.2 (1.00)	0.00021 (0.134)	1e-05 (0.00812)	0.417 (1.00)	0.792 (1.00)	0.732 (1.00)	0.544 (1.00)
amp 6p21 1	96 (21%)	354	0.266 (1.00)	5e-05 (0.0334)	1e-05 (0.00812)	0.0961 (1.00)	0.506 (1.00)	0.7 (1.00)	0.0094 (1.00)	9e-05 (0.0589)	0.706 (1.00)	0.774 (1.00)	0.309 (1.00)	0.397 (1.00)
amp 8q24 21	260 (58%)	190	0.561 (1.00)	0.0282 (1.00)	1e-05 (0.00812)	0.00059 (0.359)	0.0395 (1.00)	0.0132 (1.00)	0.00036 (0.227)	6e-05 (0.0397)	0.712 (1.00)	0.0384 (1.00)	0.265 (1.00)	0.0157 (1.00)
amp 16p11 2	126 (28%)	324	0.00041 (0.257)	1e-05 (0.00812)	1e-05 (0.00812)	0.0255 (1.00)	0.0305 (1.00)	0.124 (1.00)	0.00047 (0.292)	1e-05 (0.00812)	0.892 (1.00)	0.142 (1.00)	0.959 (1.00)	0.0611 (1.00)
del 1p33	123 (27%)	327	0.0155 (1.00)	0.56 (1.00)	1e-05 (0.00812)	0.00019 (0.122)	0.83 (1.00)	0.494 (1.00)	0.00061 (0.37)	0.0001 (0.0652)	0.717 (1.00)	0.152 (1.00)	1 (1.00)	0.351 (1.00)
del 5q12 1	105 (23%)	345	0.00106 (0.624)	0.00355 (1.00)	1e-05 (0.00812)	0.0107 (1.00)	0.00096 (0.567)	0.033 (1.00)	0.00028 (0.178)	6e-05 (0.0397)	0.705 (1.00)	0.566 (1.00)	1 (1.00)	0.139 (1.00)
del 12p13 2	60 (13%)	390	0.00922 (1.00)	0.00316 (1.00)	1e-05 (0.00812)	0.00794 (1.00)	0.308 (1.00)	0.918 (1.00)	2e-05 (0.0136)	1e-05 (0.00812)	0.794 (1.00)	0.354 (1.00)	0.224 (1.00)	0.00218 (1.00)
del 15q11 2	177 (39%)	273	0.00042 (0.262)	0.00071 (0.428)	1e-05 (0.00812)	0.0005 (0.31)	0.0208 (1.00)	0.0638 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.98 (1.00)	0.779 (1.00)	0.258 (1.00)	0.27 (1.00)
del 15q15 2	172 (38%)	278	0.00158 (0.908)	0.00065 (0.393)	1e-05 (0.00812)	0.00041 (0.257)	0.00927 (1.00)	0.025 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.923 (1.00)	0.555 (1.00)	0.154 (1.00)	0.167 (1.00)
del 15q21 1	169 (38%)	281	0.019 (1.00)	0.0148 (1.00)	1e-05 (0.00812)	0.00092 (0.545)	0.00943 (1.00)	0.0537 (1.00)	1e-05 (0.00812)	1e-05 (0.00812)	0.885 (1.00)	0.677 (1.00)	0.137 (1.00)	0.129 (1.00)
del 20p12 1	86 (19%)	364	0.0492 (1.00)	0.0288 (1.00)	2e-05 (0.0136)	0.00081 (0.484)	0.727 (1.00)	0.197 (1.00)	1e-05 (0.00812)	2e-05 (0.0136)	0.104 (1.00)	0.0106 (1.00)	0.802 (1.00)	0.0475 (1.00)
amp 8q12 1	236 (52%)	214	0.49 (1.00)	0.00576 (1.00)	1e-05 (0.00812)	0.00698 (1.00)	0.00994 (1.00)	0.00346 (1.00)	0.00192 (1.00)	0.00014 (0.0904)	0.383 (1.00)	0.0372 (1.00)	0.275 (1.00)	0.0128 (1.00)
amp 17q12	114 (25%)	336	0.0257 (1.00)	0.0143 (1.00)	1e-05 (0.00812)	0.00054 (0.332)	0.14 (1.00)	0.00245 (1.00)	5e-05 (0.0334)	0.00089 (0.529)	0.0375 (1.00)	0.0141 (1.00)	0.533 (1.00)	0.56 (1.00)
amp 19q13 11	95 (21%)	355	0.183 (1.00)	0.0313 (1.00)	8e-05 (0.0526)	0.0945 (1.00)	0.0341 (1.00)	0.313 (1.00)	0.0458 (1.00)	0.00014 (0.0904)	0.46 (1.00)	0.557 (1.00)	0.0177 (1.00)	0.00156 (0.899)
amp 20p12 1	208 (46%)	242	0.0468 (1.00)	0.00088 (0.524)	1e-05 (0.00812)	0.128 (1.00)	0.00927 (1.00)	0.265 (1.00)	0.00325 (1.00)	1e-05 (0.00812)	0.262 (1.00)	0.34 (1.00)	0.278 (1.00)	0.522 (1.00)
del 1q43	54 (12%)	396	0.0616 (1.00)	0.501 (1.00)	1e-05 (0.00812)	0.031 (1.00)	0.473 (1.00)	0.717 (1.00)	0.0005 (0.31)	6e-05 (0.0397)	0.139 (1.00)	0.00057 (0.348)	0.0277 (1.00)	0.961 (1.00)
del 4p16 2	139 (31%)	311	0.00073 (0.438)	0.00173 (0.99)	1e-05 (0.00812)	0.00058 (0.354)	0.0262 (1.00)	0.16 (1.00)	0.00194 (1.00)	1e-05 (0.00812)	0.354 (1.00)	0.447 (1.00)	0.147 (1.00)	0.235 (1.00)
del 5q21 1	127 (28%)	323	0.276 (1.00)	0.0442 (1.00)	1e-05 (0.00812)	0.0127 (1.00)	0.0247 (1.00)	0.4 (1.00)	0.00122 (0.711)	2e-05 (0.0136)	0.944 (1.00)	0.89 (1.00)	0.87 (1.00)	0.497 (1.00)
del 5q22 2	130 (29%)	320	0.0142 (1.00)	0.00924 (1.00)	1e-05 (0.00812)	0.0316 (1.00)	0.0477 (1.00)	0.343 (1.00)	0.00058 (0.354)	2e-05 (0.0136)	0.913 (1.00)	0.277 (1.00)	0.616 (1.00)	0.455 (1.00)
del 10p15 3	80 (18%)	370	0.115 (1.00)	0.105 (1.00)	1e-05 (0.00812)	0.00074 (0.443)	0.0222 (1.00)	0.141 (1.00)	0.00123 (0.716)	8e-05 (0.0526)	0.454 (1.00)	0.177 (1.00)	0.52 (1.00)	0.0218 (1.00)
del 10q21 1	98 (22%)	352	0.00356 (1.00)	0.0289 (1.00)	1e-05 (0.00812)	0.00982 (1.00)	0.0696 (1.00)	0.259 (1.00)	0.0018 (1.00)	0.0001 (0.0652)	0.753 (1.00)	0.49 (1.00)	0.754 (1.00)	0.732 (1.00)
del 10q23 31	109 (24%)	341	0.0969 (1.00)	0.0623 (1.00)	1e-05 (0.00812)	0.00344 (1.00)	0.146 (1.00)	0.47 (1.00)	0.00044 (0.274)	9e-05 (0.0589)	0.58 (1.00)	0.136 (1.00)	0.35 (1.00)	0.399 (1.00)
del 19p13 3	63 (14%)	387	0.132 (1.00)	0.125 (1.00)	4e-05 (0.0268)	0.11 (1.00)	0.981 (1.00)	0.21 (1.00)	0.0794 (1.00)	0.00021 (0.134)	0.654 (1.00)	0.00853 (1.00)	0.486 (1.00)	0.283 (1.00)
del 21q11 2	141 (31%)	309	0.0159 (1.00)	0.0692 (1.00)	1e-05 (0.00812)	0.0511 (1.00)	0.161 (1.00)	0.821 (1.00)	0.00064 (0.388)	0.0001 (0.0652)	0.936 (1.00)	0.126 (1.00)	0.67 (1.00)	0.35 (1.00)
amp 2q33 1	92 (20%)	358	0.165 (1.00)	0.114 (1.00)	5e-05 (0.0334)	0.00459 (1.00)	0.0431 (1.00)	0.0495 (1.00)	0.0219 (1.00)	0.00089 (0.529)	0.293 (1.00)	0.108 (1.00)	0.951 (1.00)	0.673 (1.00)
amp 5p13 2	88 (20%)	362	0.379 (1.00)	0.193 (1.00)	0.0012 (0.702)	0.546 (1.00)	0.00458 (1.00)	0.914 (1.00)	0.243 (1.00)	0.00027 (0.171)	0.73 (1.00)	0.664 (1.00)	0.754 (1.00)	0.584 (1.00)
amp 8p11 23	158 (35%)	292	0.302 (1.00)	0.109 (1.00)	1e-05 (0.00812)	0.386 (1.00)	0.765 (1.00)	0.625 (1.00)	0.00832 (1.00)	0.0312 (1.00)	0.358 (1.00)	0.266 (1.00)	0.505 (1.00)	0.127 (1.00)
amp 8p11 21	188 (42%)	262	0.445 (1.00)	0.0186 (1.00)	1e-05 (0.00812)	0.289 (1.00)	0.242 (1.00)	0.0245 (1.00)	0.0182 (1.00)	0.00507 (1.00)	0.718 (1.00)	0.323 (1.00)	0.538 (1.00)	0.104 (1.00)
amp 19p13 2	75 (17%)	375	0.0679 (1.00)	0.0543 (1.00)	5e-05 (0.0334)	0.0128 (1.00)	0.675 (1.00)	0.383 (1.00)	0.254 (1.00)	0.00181 (1.00)	0.348 (1.00)	0.436 (1.00)	0.104 (1.00)	0.0229 (1.00)
del 1p13 1	119 (26%)	331	0.0852 (1.00)	0.546 (1.00)	1e-05 (0.00812)	0.0118 (1.00)	0.679 (1.00)	0.893 (1.00)	0.00812 (1.00)	0.0005 (0.31)	0.799 (1.00)	0.166 (1.00)	0.953 (1.00)	0.643 (1.00)
amp 5q22 3	46 (10%)	404	0.922 (1.00)	1 (1.00)	0.0121 (1.00)	0.805 (1.00)	0.327 (1.00)	0.641 (1.00)	0.29 (1.00)	0.123 (1.00)	0.95 (1.00)	0.701 (1.00)	0.356 (1.00)	0.333 (1.00)
amp 12p13 33	111 (25%)	339	0.656 (1.00)	0.796 (1.00)	0.0162 (1.00)	0.0489 (1.00)	0.428 (1.00)	0.875 (1.00)	0.374 (1.00)	0.82 (1.00)	0.512 (1.00)	0.796 (1.00)	0.629 (1.00)	0.848 (1.00)
amp 17p11 2	44 (10%)	406	0.265 (1.00)	0.00394 (1.00)	0.041 (1.00)	0.0868 (1.00)	0.00407 (1.00)	0.0609 (1.00)	0.00653 (1.00)	0.16 (1.00)	0.545 (1.00)	0.803 (1.00)	0.173 (1.00)	0.0649 (1.00)
del 2p21	17 (4%)	433	0.593 (1.00)	0.865 (1.00)	1 (1.00)	0.765 (1.00)	0.808 (1.00)	0.714 (1.00)	0.161 (1.00)	0.207 (1.00)	0.0921 (1.00)	0.347 (1.00)
del 2q22 1	24 (5%)	426	0.973 (1.00)	0.538 (1.00)	0.482 (1.00)	0.724 (1.00)	0.0858 (1.00)	0.363 (1.00)	0.121 (1.00)	0.311 (1.00)	0.249 (1.00)	0.166 (1.00)	1 (1.00)	0.849 (1.00)
del 3p26 2	72 (16%)	378	0.221 (1.00)	0.234 (1.00)	0.00054 (0.332)	0.134 (1.00)	0.729 (1.00)	0.501 (1.00)	0.212 (1.00)	0.0542 (1.00)	0.739 (1.00)	0.789 (1.00)	0.536 (1.00)	0.41 (1.00)
del 3p14 2	88 (20%)	362	0.554 (1.00)	0.835 (1.00)	0.0446 (1.00)	0.274 (1.00)	0.528 (1.00)	0.0413 (1.00)	0.0964 (1.00)	0.135 (1.00)	0.652 (1.00)	0.699 (1.00)	0.127 (1.00)	0.706 (1.00)
del 3q26 31	46 (10%)	404	0.642 (1.00)	0.539 (1.00)	0.0645 (1.00)	0.662 (1.00)	0.601 (1.00)	0.835 (1.00)	0.696 (1.00)	0.15 (1.00)	0.157 (1.00)	0.818 (1.00)	0.0918 (1.00)	0.704 (1.00)
del 6p25 3	56 (12%)	394	0.85 (1.00)	0.735 (1.00)	0.197 (1.00)	0.0302 (1.00)	0.0416 (1.00)	0.572 (1.00)	1 (1.00)	0.827 (1.00)	0.667 (1.00)	0.939 (1.00)	0.0552 (1.00)	0.0435 (1.00)
del 6q26	62 (14%)	388	0.586 (1.00)	0.4 (1.00)	0.635 (1.00)	0.477 (1.00)	0.0829 (1.00)	0.22 (1.00)	0.166 (1.00)	0.431 (1.00)	0.696 (1.00)	0.938 (1.00)	0.441 (1.00)	0.0613 (1.00)
del 7q31 1	13 (3%)	437	1 (1.00)	0.601 (1.00)	0.0896 (1.00)	0.601 (1.00)	0.165 (1.00)	0.465 (1.00)	0.385 (1.00)	0.792 (1.00)	0.794 (1.00)	0.829 (1.00)
del 8q11 1	30 (7%)	420	0.261 (1.00)	0.0969 (1.00)	0.0467 (1.00)	0.628 (1.00)	0.268 (1.00)	0.166 (1.00)	0.318 (1.00)	0.0197 (1.00)	0.2 (1.00)	0.295 (1.00)	0.662 (1.00)	0.891 (1.00)
del 9p21 3	62 (14%)	388	0.455 (1.00)	0.0893 (1.00)	0.00121 (0.707)	0.0729 (1.00)	0.823 (1.00)	0.41 (1.00)	0.16 (1.00)	0.00279 (1.00)	0.618 (1.00)	0.258 (1.00)	0.202 (1.00)	0.582 (1.00)
del 16p13 3	56 (12%)	394	0.228 (1.00)	0.0618 (1.00)	0.0427 (1.00)	0.0584 (1.00)	0.393 (1.00)	0.514 (1.00)	0.0419 (1.00)	0.0841 (1.00)	0.848 (1.00)	0.701 (1.00)	0.617 (1.00)	1 (1.00)
del 16q23 1	61 (14%)	389	0.27 (1.00)	0.00566 (1.00)	0.241 (1.00)	0.852 (1.00)	0.14 (1.00)	0.614 (1.00)	0.628 (1.00)	0.0297 (1.00)	0.528 (1.00)	0.463 (1.00)	0.723 (1.00)	0.481 (1.00)
del 17q24 3	69 (15%)	381	0.0952 (1.00)	0.515 (1.00)	0.00053 (0.326)	0.0204 (1.00)	0.867 (1.00)	0.18 (1.00)	0.296 (1.00)	0.0386 (1.00)	0.724 (1.00)	0.97 (1.00)	0.81 (1.00)	0.433 (1.00)

'amp_2q33.1' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 1(2Q33.1) MUTATED	25	56	11
AMP PEAK 1(2Q33.1) WILD-TYPE	178	126	54

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

'amp_5p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.17

Table S2. Gene #2: 'amp_5p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 2(5P13.2) MUTATED	15	24	8	33	4
AMP PEAK 2(5P13.2) WILD-TYPE	91	50	82	95	32

Figure S2. Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MRNA_CHIERARCHICAL'

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

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 = 0.0081

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 4(6P21.1) MUTATED	17	65	14
AMP PEAK 4(6P21.1) WILD-TYPE	186	117	51

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 = 9e-05 (Fisher's exact test), Q value = 0.059

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	106	74	90	128	36
AMP PEAK 4(6P21.1) MUTATED	25	26	7	33	3
AMP PEAK 4(6P21.1) WILD-TYPE	81	48	83	95	33

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

'amp_7p21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S6. Gene #5: 'amp_7p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 5(7P21.2) MUTATED	10	34	26
AMP PEAK 5(7P21.2) WILD-TYPE	32	38	6

Figure S6. Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S7. Gene #5: 'amp_7p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 5(7P21.2) MUTATED	73	135	47
AMP PEAK 5(7P21.2) WILD-TYPE	130	47	18

Figure S7. Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p21.2' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.084

Table S8. Gene #5: 'amp_7p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 5(7P21.2) MUTATED	87	44	37
AMP PEAK 5(7P21.2) WILD-TYPE	31	48	34

Figure S8. Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S9. Gene #5: 'amp_7p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
AMP PEAK 5(7P21.2) MUTATED	101	68	75
AMP PEAK 5(7P21.2) WILD-TYPE	39	83	68

Figure S9. Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S10. Gene #5: 'amp_7p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 5(7P21.2) MUTATED	72	56	31	76	9
AMP PEAK 5(7P21.2) WILD-TYPE	34	18	59	52	27

Figure S10. Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S11. Gene #6: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 6(8P11.23) MUTATED	49	59	50
AMP PEAK 6(8P11.23) WILD-TYPE	154	123	15

Figure S11. Get High-res Image Gene #6: '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 = 0.0081

Table S12. Gene #7: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 7(8P11.21) MUTATED	55	77	56
AMP PEAK 7(8P11.21) WILD-TYPE	148	105	9

Figure S12. Get High-res Image Gene #7: '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 = 0.0081

Table S13. Gene #8: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 8(8Q12.1) MUTATED	67	107	62
AMP PEAK 8(8Q12.1) WILD-TYPE	136	75	3

Figure S13. Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.09

Table S14. Gene #8: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 8(8Q12.1) MUTATED	63	48	36	70	9
AMP PEAK 8(8Q12.1) WILD-TYPE	43	26	54	58	27

Figure S14. Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S15. Gene #9: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 9(8Q24.21) MUTATED	75	121	64
AMP PEAK 9(8Q24.21) WILD-TYPE	128	61	1

Figure S15. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.23

Table S16. Gene #9: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
AMP PEAK 9(8Q24.21) MUTATED	99	75	75
AMP PEAK 9(8Q24.21) WILD-TYPE	41	76	68

Figure S16. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S17. Gene #9: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 9(8Q24.21) MUTATED	67	52	41	79	10
AMP PEAK 9(8Q24.21) WILD-TYPE	39	22	49	49	26

Figure S17. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.046

Table S18. Gene #10: '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 10(11P15.5) MUTATED	2	18	3	12
AMP PEAK 10(11P15.5) WILD-TYPE	33	43	26	9

Figure S18. Get High-res Image Gene #10: '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 = 0.0081

Table S19. Gene #10: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 10(11P15.5) MUTATED	22	55	17
AMP PEAK 10(11P15.5) WILD-TYPE	181	127	48

Figure S19. Get High-res Image Gene #10: '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 = 0.014

Table S20. Gene #10: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 10(11P15.5) MUTATED	36	6	11
AMP PEAK 10(11P15.5) WILD-TYPE	82	86	60

Figure S20. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S21. Gene #10: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
AMP PEAK 10(11P15.5) MUTATED	39	13	38
AMP PEAK 10(11P15.5) WILD-TYPE	101	138	105

Figure S21. Get High-res Image Gene #10: '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 = 0.0081

Table S22. Gene #10: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 10(11P15.5) MUTATED	24	20	4	42	0
AMP PEAK 10(11P15.5) WILD-TYPE	82	54	86	86	36

Figure S22. Get High-res Image Gene #10: '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 = 0.0081

Table S23. Gene #10: '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 10(11P15.5) MUTATED	8	12	46	18
AMP PEAK 10(11P15.5) WILD-TYPE	127	38	31	117

Figure S23. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S24. Gene #12: '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 12(13Q12.13) MUTATED	15	51	10	16
AMP PEAK 12(13Q12.13) WILD-TYPE	20	10	19	5

Figure S24. Get High-res Image Gene #12: '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 = 0.0081

Table S25. Gene #12: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 12(13Q12.13) MUTATED	13	49	30
AMP PEAK 12(13Q12.13) WILD-TYPE	29	23	2

Figure S25. Get High-res Image Gene #12: '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 = 0.0081

Table S26. Gene #12: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 12(13Q12.13) MUTATED	66	166	43
AMP PEAK 12(13Q12.13) WILD-TYPE	137	16	22

Figure S26. Get High-res Image Gene #12: '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 = 0.0081

Table S27. Gene #12: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 12(13Q12.13) MUTATED	93	42	37
AMP PEAK 12(13Q12.13) WILD-TYPE	25	50	34

Figure S27. Get High-res Image Gene #12: '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 = 0.0081

Table S28. Gene #12: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
AMP PEAK 12(13Q12.13) MUTATED	112	65	88
AMP PEAK 12(13Q12.13) WILD-TYPE	28	86	55

Figure S28. Get High-res Image Gene #12: '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 = 0.0081

Table S29. Gene #12: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 12(13Q12.13) MUTATED	75	62	25	94	9
AMP PEAK 12(13Q12.13) WILD-TYPE	31	12	65	34	27

Figure S29. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MRNA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.084

Table S30. Gene #13: '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 13(13Q22.1) MUTATED	15	49	12	15
AMP PEAK 13(13Q22.1) WILD-TYPE	20	12	17	6

Figure S30. Get High-res Image Gene #13: '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 = 0.0081

Table S31. Gene #13: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S31. Get High-res Image Gene #13: '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 = 0.0081

Table S32. Gene #13: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 13(13Q22.1) MUTATED	71	162	44
AMP PEAK 13(13Q22.1) WILD-TYPE	132	20	21

Figure S32. Get High-res Image Gene #13: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S33. Gene #13: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S33. Get High-res Image Gene #13: '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 = 0.0081

Table S34. Gene #13: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
AMP PEAK 13(13Q22.1) MUTATED	112	69	87
AMP PEAK 13(13Q22.1) WILD-TYPE	28	82	56

Figure S34. Get High-res Image Gene #13: '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 = 0.0081

Table S35. Gene #13: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 13(13Q22.1) MUTATED	76	61	29	92	10
AMP PEAK 13(13Q22.1) WILD-TYPE	30	13	61	36	26

Figure S35. Get High-res Image Gene #13: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S36. Gene #14: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 14(16P11.2) MUTATED	6	16	23
AMP PEAK 14(16P11.2) WILD-TYPE	36	56	9

Figure S36. Get High-res Image Gene #14: '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 = 0.0081

Table S37. Gene #14: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 14(16P11.2) MUTATED	20	92	14
AMP PEAK 14(16P11.2) WILD-TYPE	183	90	51

Figure S37. Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S38. Gene #14: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 14(16P11.2) MUTATED	26	31	10	52	2
AMP PEAK 14(16P11.2) WILD-TYPE	80	43	80	76	34

Figure S38. Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16q12.1' versus 'MRNA_CNMF'

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

Table S39. Gene #15: '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 15(16Q12.1) MUTATED	4	22	2	12
AMP PEAK 15(16Q12.1) WILD-TYPE	31	39	27	9

Figure S39. Get High-res Image Gene #15: '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 = 0.0081

Table S40. Gene #15: 'amp_16q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 15(16Q12.1) MUTATED	3	17	20
AMP PEAK 15(16Q12.1) WILD-TYPE	39	55	12

Figure S40. Get High-res Image Gene #15: '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 = 0.0081

Table S41. Gene #15: 'amp_16q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 15(16Q12.1) MUTATED	16	85	10
AMP PEAK 15(16Q12.1) WILD-TYPE	187	97	55

Figure S41. Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S42. Gene #15: 'amp_16q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 15(16Q12.1) MUTATED	22	30	8	47	0
AMP PEAK 15(16Q12.1) WILD-TYPE	84	44	82	81	36

Figure S42. Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S43. Gene #17: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 17(17Q12) MUTATED	24	67	23
AMP PEAK 17(17Q12) WILD-TYPE	179	115	42

Figure S43. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

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

Table S44. Gene #17: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
AMP PEAK 17(17Q12) MUTATED	53	22	33
AMP PEAK 17(17Q12) WILD-TYPE	87	129	110

Figure S44. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S45. Gene #18: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 18(17Q24.1) MUTATED	19	64	23
AMP PEAK 18(17Q24.1) WILD-TYPE	184	118	42

Figure S45. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.1' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.16

Table S46. Gene #18: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S46. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S47. Gene #18: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
AMP PEAK 18(17Q24.1) MUTATED	53	18	31
AMP PEAK 18(17Q24.1) WILD-TYPE	87	133	112

Figure S47. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S48. Gene #18: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 18(17Q24.1) MUTATED	38	18	8	36	2
AMP PEAK 18(17Q24.1) WILD-TYPE	68	56	82	92	34

Figure S48. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

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

Table S49. Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 19(19P13.2) MUTATED	18	48	9
AMP PEAK 19(19P13.2) WILD-TYPE	185	134	56

Figure S49. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.11' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.053

Table S50. Gene #20: 'amp_19q13.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 20(19Q13.11) MUTATED	29	57	9
AMP PEAK 20(19Q13.11) WILD-TYPE	174	125	56

Figure S50. Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.09

Table S51. Gene #20: 'amp_19q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 20(19Q13.11) MUTATED	22	25	13	30	0
AMP PEAK 20(19Q13.11) WILD-TYPE	84	49	77	98	36

Figure S51. Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S52. Gene #21: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 21(20P12.1) MUTATED	66	113	29
AMP PEAK 21(20P12.1) WILD-TYPE	137	69	36

Figure S52. Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S53. Gene #21: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 21(20P12.1) MUTATED	53	36	28	78	5
AMP PEAK 21(20P12.1) WILD-TYPE	53	38	62	50	31

Figure S53. Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S54. Gene #22: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 22(20P11.21) MUTATED	11	48	23
AMP PEAK 22(20P11.21) WILD-TYPE	31	24	9

Figure S54. Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S55. Gene #22: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 22(20P11.21) MUTATED	69	149	34
AMP PEAK 22(20P11.21) WILD-TYPE	134	33	31

Figure S55. Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S56. Gene #22: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 22(20P11.21) MUTATED	87	40	32
AMP PEAK 22(20P11.21) WILD-TYPE	31	52	39

Figure S56. Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S57. Gene #22: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
AMP PEAK 22(20P11.21) MUTATED	102	59	81
AMP PEAK 22(20P11.21) WILD-TYPE	38	92	62

Figure S57. Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S58. Gene #22: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 22(20P11.21) MUTATED	71	49	29	88	5
AMP PEAK 22(20P11.21) WILD-TYPE	35	25	61	40	31

Figure S58. Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S59. Gene #23: '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 23(20Q11.21) MUTATED	13	58	16	18
AMP PEAK 23(20Q11.21) WILD-TYPE	22	3	13	3

Figure S59. Get High-res Image Gene #23: '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 = 0.0081

Table S60. Gene #23: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 23(20Q11.21) MUTATED	12	62	31
AMP PEAK 23(20Q11.21) WILD-TYPE	30	10	1

Figure S60. Get High-res Image Gene #23: '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 = 0.0081

Table S61. Gene #23: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 23(20Q11.21) MUTATED	89	181	53
AMP PEAK 23(20Q11.21) WILD-TYPE	114	1	12

Figure S61. Get High-res Image Gene #23: '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 = 0.0081

Table S62. Gene #23: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 23(20Q11.21) MUTATED	112	47	44
AMP PEAK 23(20Q11.21) WILD-TYPE	6	45	27

Figure S62. Get High-res Image Gene #23: '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 = 0.0081

Table S63. Gene #23: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
AMP PEAK 23(20Q11.21) MUTATED	136	72	103
AMP PEAK 23(20Q11.21) WILD-TYPE	4	79	40

Figure S63. Get High-res Image Gene #23: '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 = 0.0081

Table S64. Gene #23: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 23(20Q11.21) MUTATED	92	68	33	112	6
AMP PEAK 23(20Q11.21) WILD-TYPE	14	6	57	16	30

Figure S64. Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S65. Gene #24: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 24(20Q12) MUTATED	12	58	15	18
AMP PEAK 24(20Q12) WILD-TYPE	23	3	14	3

Figure S65. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S66. Gene #24: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 24(20Q12) MUTATED	11	61	31
AMP PEAK 24(20Q12) WILD-TYPE	31	11	1

Figure S66. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S67. Gene #24: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 24(20Q12) MUTATED	88	181	55
AMP PEAK 24(20Q12) WILD-TYPE	115	1	10

Figure S67. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S68. Gene #24: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 24(20Q12) MUTATED	112	49	45
AMP PEAK 24(20Q12) WILD-TYPE	6	43	26

Figure S68. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S69. Gene #24: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
AMP PEAK 24(20Q12) MUTATED	136	75	101
AMP PEAK 24(20Q12) WILD-TYPE	4	76	42

Figure S69. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S70. Gene #24: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 24(20Q12) MUTATED	92	69	35	111	5
AMP PEAK 24(20Q12) WILD-TYPE	14	5	55	17	31

Figure S70. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S71. Gene #25: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 25(20Q13.12) MUTATED	13	58	16	18
AMP PEAK 25(20Q13.12) WILD-TYPE	22	3	13	3

Figure S71. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S72. Gene #25: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 25(20Q13.12) MUTATED	12	62	31
AMP PEAK 25(20Q13.12) WILD-TYPE	30	10	1

Figure S72. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S73. Gene #25: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
AMP PEAK 25(20Q13.12) MUTATED	88	181	57
AMP PEAK 25(20Q13.12) WILD-TYPE	115	1	8

Figure S73. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S74. Gene #25: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
AMP PEAK 25(20Q13.12) MUTATED	112	49	45
AMP PEAK 25(20Q13.12) WILD-TYPE	6	43	26

Figure S74. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.12' versus 'RPPA_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.23

Table S75. Gene #25: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	127	26	94
AMP PEAK 25(20Q13.12) MUTATED	64	96	21	51
AMP PEAK 25(20Q13.12) WILD-TYPE	14	31	5	43

Figure S75. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.21

Table S76. Gene #25: 'amp_20q13.12' 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 25(20Q13.12) MUTATED	52	38	42	49	37	14
AMP PEAK 25(20Q13.12) WILD-TYPE	7	10	14	19	31	12

Figure S76. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S77. Gene #25: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
AMP PEAK 25(20Q13.12) MUTATED	136	76	102
AMP PEAK 25(20Q13.12) WILD-TYPE	4	75	41

Figure S77. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S78. Gene #25: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
AMP PEAK 25(20Q13.12) MUTATED	92	69	35	112	6
AMP PEAK 25(20Q13.12) WILD-TYPE	14	5	55	16	30

Figure S78. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.065

Table S79. Gene #26: '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 S79. Get High-res Image Gene #26: '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 = 0.0081

Table S80. Gene #26: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 1(1P36.11) MUTATED	40	106	22
DEL PEAK 1(1P36.11) WILD-TYPE	163	76	43

Figure S80. Get High-res Image Gene #26: '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 = 0.014

Table S81. Gene #26: '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 S81. Get High-res Image Gene #26: '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 = 0.0081

Table S82. Gene #26: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 1(1P36.11) MUTATED	76	36	52
DEL PEAK 1(1P36.11) WILD-TYPE	64	115	91

Figure S82. Get High-res Image Gene #26: '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 = 0.0081

Table S83. Gene #26: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 1(1P36.11) MUTATED	48	39	12	61	4
DEL PEAK 1(1P36.11) WILD-TYPE	58	35	78	67	32

Figure S83. Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S84. Gene #27: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 2(1P33) MUTATED	32	83	8
DEL PEAK 2(1P33) WILD-TYPE	171	99	57

Figure S84. Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p33' versus 'METHLYATION_CNMF'

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

Table S85. Gene #27: '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 S85. Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.065

Table S86. Gene #27: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 2(1P33) MUTATED	34	31	10	38	7
DEL PEAK 2(1P33) WILD-TYPE	72	43	80	90	29

Figure S86. Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S87. Gene #28: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 3(1P13.1) MUTATED	35	78	6
DEL PEAK 3(1P13.1) WILD-TYPE	168	104	59

Figure S87. Get High-res Image Gene #28: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S88. Gene #29: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 4(1Q43) MUTATED	9	37	8
DEL PEAK 4(1Q43) WILD-TYPE	194	145	57

Figure S88. Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S89. Gene #29: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 4(1Q43) MUTATED	18	18	2	14	1
DEL PEAK 4(1Q43) WILD-TYPE	88	56	88	114	35

Figure S89. Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S90. Gene #35: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 10(4P16.2) MUTATED	31	91	17
DEL PEAK 10(4P16.2) WILD-TYPE	172	91	48

Figure S90. Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S91. Gene #35: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 10(4P16.2) MUTATED	34	35	7	51	5
DEL PEAK 10(4P16.2) WILD-TYPE	72	39	83	77	31

Figure S91. Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.23

Table S92. Gene #36: '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 S92. Get High-res Image Gene #36: '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 = 0.0081

Table S93. Gene #36: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 11(4Q22.1) MUTATED	34	102	15
DEL PEAK 11(4Q22.1) WILD-TYPE	169	80	50

Figure S93. Get High-res Image Gene #36: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

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

Table S94. Gene #36: '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 S94. Get High-res Image Gene #36: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S95. Gene #36: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 11(4Q22.1) MUTATED	40	37	9	51	5
DEL PEAK 11(4Q22.1) WILD-TYPE	66	37	81	77	31

Figure S95. Get High-res Image Gene #36: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S96. Gene #37: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 12(4Q35.1) MUTATED	34	105	20
DEL PEAK 12(4Q35.1) WILD-TYPE	169	77	45

Figure S96. Get High-res Image Gene #37: '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 = 0.0081

Table S97. Gene #37: '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 S97. Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.096

Table S98. Gene #37: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 12(4Q35.1) MUTATED	63	34	54
DEL PEAK 12(4Q35.1) WILD-TYPE	77	117	89

Figure S98. Get High-res Image Gene #37: '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 = 0.0081

Table S99. Gene #37: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 12(4Q35.1) MUTATED	41	37	11	56	6
DEL PEAK 12(4Q35.1) WILD-TYPE	65	37	79	72	30

Figure S99. Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S100. Gene #38: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 13(5Q12.1) MUTATED	19	65	21
DEL PEAK 13(5Q12.1) WILD-TYPE	184	117	44

Figure S100. Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.18

Table S101. Gene #38: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 13(5Q12.1) MUTATED	47	21	32
DEL PEAK 13(5Q12.1) WILD-TYPE	93	130	111

Figure S101. Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S102. Gene #38: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 13(5Q12.1) MUTATED	25	28	8	35	4
DEL PEAK 13(5Q12.1) WILD-TYPE	81	46	82	93	32

Figure S102. Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S103. Gene #39: 'del_5q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 14(5Q21.1) MUTATED	27	76	24
DEL PEAK 14(5Q21.1) WILD-TYPE	176	106	41

Figure S103. Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S104. Gene #39: 'del_5q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 14(5Q21.1) MUTATED	34	28	10	45	5
DEL PEAK 14(5Q21.1) WILD-TYPE	72	46	80	83	31

Figure S104. Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S105. Gene #40: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 15(5Q22.2) MUTATED	28	76	26
DEL PEAK 15(5Q22.2) WILD-TYPE	175	106	39

Figure S105. Get High-res Image Gene #40: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S106. Gene #40: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 15(5Q22.2) MUTATED	37	28	12	44	3
DEL PEAK 15(5Q22.2) WILD-TYPE	69	46	78	84	33

Figure S106. Get High-res Image Gene #40: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MRNA_CHIERARCHICAL'

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

Table S107. Gene #44: '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 S107. Get High-res Image Gene #44: '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 = 0.0081

Table S108. Gene #44: 'del_8p23.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 19(8P23.3) MUTATED	33	108	48
DEL PEAK 19(8P23.3) WILD-TYPE	170	74	17

Figure S108. Get High-res Image Gene #44: '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 = 0.014

Table S109. Gene #44: '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 S109. Get High-res Image Gene #44: '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 = 0.0081

Table S110. Gene #44: 'del_8p23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 19(8P23.3) MUTATED	79	42	61
DEL PEAK 19(8P23.3) WILD-TYPE	61	109	82

Figure S110. Get High-res Image Gene #44: '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 = 0.0081

Table S111. Gene #44: 'del_8p23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 19(8P23.3) MUTATED	47	45	17	68	5
DEL PEAK 19(8P23.3) WILD-TYPE	59	29	73	60	31

Figure S111. Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.09

Table S112. Gene #45: '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	34	21
DEL PEAK 20(8P22) WILD-TYPE	34	38	11

Figure S112. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S113. Gene #45: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 20(8P22) MUTATED	34	117	52
DEL PEAK 20(8P22) WILD-TYPE	169	65	13

Figure S113. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S114. Gene #45: '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 S114. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S115. Gene #45: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 20(8P22) MUTATED	86	45	65
DEL PEAK 20(8P22) WILD-TYPE	54	106	78

Figure S115. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S116. Gene #45: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 20(8P22) MUTATED	51	50	21	70	4
DEL PEAK 20(8P22) WILD-TYPE	55	24	69	58	32

Figure S116. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S117. Gene #48: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 23(10P15.3) MUTATED	16	48	16
DEL PEAK 23(10P15.3) WILD-TYPE	187	134	49

Figure S117. Get High-res Image Gene #48: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.053

Table S118. Gene #48: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 23(10P15.3) MUTATED	18	26	6	23	3
DEL PEAK 23(10P15.3) WILD-TYPE	88	48	84	105	33

Figure S118. Get High-res Image Gene #48: '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 = 0.0081

Table S119. Gene #49: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 24(10Q21.1) MUTATED	17	63	18
DEL PEAK 24(10Q21.1) WILD-TYPE	186	119	47

Figure S119. Get High-res Image Gene #49: '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 = 0.065

Table S120. Gene #49: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 24(10Q21.1) MUTATED	24	25	9	32	1
DEL PEAK 24(10Q21.1) WILD-TYPE	82	49	81	96	35

Figure S120. Get High-res Image Gene #49: '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 = 0.0081

Table S121. Gene #50: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 25(10Q23.31) MUTATED	23	66	20
DEL PEAK 25(10Q23.31) WILD-TYPE	180	116	45

Figure S121. Get High-res Image Gene #50: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.059

Table S122. Gene #50: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 25(10Q23.31) MUTATED	31	26	12	34	1
DEL PEAK 25(10Q23.31) WILD-TYPE	75	48	78	94	35

Figure S122. Get High-res Image Gene #50: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S123. Gene #51: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 26(10Q25.2) MUTATED	22	70	17
DEL PEAK 26(10Q25.2) WILD-TYPE	181	112	48

Figure S123. Get High-res Image Gene #51: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q25.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.059

Table S124. Gene #51: '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 S124. Get High-res Image Gene #51: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q25.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S125. Gene #51: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 26(10Q25.2) MUTATED	51	18	35
DEL PEAK 26(10Q25.2) WILD-TYPE	89	133	108

Figure S125. Get High-res Image Gene #51: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S126. Gene #51: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 26(10Q25.2) MUTATED	29	28	7	39	1
DEL PEAK 26(10Q25.2) WILD-TYPE	77	46	83	89	35

Figure S126. Get High-res Image Gene #51: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S127. Gene #52: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 27(12P13.2) MUTATED	5	45	10
DEL PEAK 27(12P13.2) WILD-TYPE	198	137	55

Figure S127. Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S128. Gene #52: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 27(12P13.2) MUTATED	34	8	16
DEL PEAK 27(12P13.2) WILD-TYPE	106	143	127

Figure S128. Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S129. Gene #52: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 27(12P13.2) MUTATED	20	15	2	21	0
DEL PEAK 27(12P13.2) WILD-TYPE	86	59	88	107	36

Figure S129. Get High-res Image Gene #52: '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 = 0.0081

Table S130. Gene #53: '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 28(14Q31.1) MUTATED	6	36	3	10
DEL PEAK 28(14Q31.1) WILD-TYPE	29	25	26	11

Figure S130. Get High-res Image Gene #53: '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 = 0.053

Table S131. Gene #53: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 28(14Q31.1) MUTATED	6	29	20
DEL PEAK 28(14Q31.1) WILD-TYPE	36	43	12

Figure S131. Get High-res Image Gene #53: '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 = 0.0081

Table S132. Gene #53: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 28(14Q31.1) MUTATED	24	114	12
DEL PEAK 28(14Q31.1) WILD-TYPE	179	68	53

Figure S132. Get High-res Image Gene #53: '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 = 0.014

Table S133. Gene #53: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 28(14Q31.1) MUTATED	54	16	17
DEL PEAK 28(14Q31.1) WILD-TYPE	64	76	54

Figure S133. Get High-res Image Gene #53: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.24

Table S134. Gene #53: '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 28(14Q31.1) MUTATED	28	53	9	15
DEL PEAK 28(14Q31.1) WILD-TYPE	50	74	17	79

Figure S134. Get High-res Image Gene #53: '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 = 0.0081

Table S135. Gene #53: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 28(14Q31.1) MUTATED	65	24	55
DEL PEAK 28(14Q31.1) WILD-TYPE	75	127	88

Figure S135. Get High-res Image Gene #53: '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 = 0.0081

Table S136. Gene #53: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 28(14Q31.1) MUTATED	42	31	9	60	2
DEL PEAK 28(14Q31.1) WILD-TYPE	64	43	81	68	34

Figure S136. Get High-res Image Gene #53: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S137. Gene #54: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 29(15Q11.2) MUTATED	33	125	19
DEL PEAK 29(15Q11.2) WILD-TYPE	170	57	46

Figure S137. Get High-res Image Gene #54: '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 = 0.0081

Table S138. Gene #54: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 29(15Q11.2) MUTATED	81	33	56
DEL PEAK 29(15Q11.2) WILD-TYPE	59	118	87

Figure S138. Get High-res Image Gene #54: '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 = 0.0081

Table S139. Gene #54: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 29(15Q11.2) MUTATED	50	42	9	65	4
DEL PEAK 29(15Q11.2) WILD-TYPE	56	32	81	63	32

Figure S139. Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S140. Gene #55: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 30(15Q15.2) MUTATED	34	120	18
DEL PEAK 30(15Q15.2) WILD-TYPE	169	62	47

Figure S140. Get High-res Image Gene #55: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S141. Gene #55: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 30(15Q15.2) MUTATED	79	30	56
DEL PEAK 30(15Q15.2) WILD-TYPE	61	121	87

Figure S141. Get High-res Image Gene #55: '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 = 0.0081

Table S142. Gene #55: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 30(15Q15.2) MUTATED	49	38	10	65	3
DEL PEAK 30(15Q15.2) WILD-TYPE	57	36	80	63	33

Figure S142. Get High-res Image Gene #55: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S143. Gene #56: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 31(15Q21.1) MUTATED	34	117	18
DEL PEAK 31(15Q21.1) WILD-TYPE	169	65	47

Figure S143. Get High-res Image Gene #56: '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 = 0.0081

Table S144. Gene #56: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 31(15Q21.1) MUTATED	76	30	56
DEL PEAK 31(15Q21.1) WILD-TYPE	64	121	87

Figure S144. Get High-res Image Gene #56: '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 = 0.0081

Table S145. Gene #56: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 31(15Q21.1) MUTATED	47	37	9	63	6
DEL PEAK 31(15Q21.1) WILD-TYPE	59	37	81	65	30

Figure S145. Get High-res Image Gene #56: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MRNA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.2

Table S146. Gene #57: '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 32(15Q22.33) MUTATED	8	31	3	10
DEL PEAK 32(15Q22.33) WILD-TYPE	27	30	26	11

Figure S146. Get High-res Image Gene #57: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q22.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S147. Gene #57: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 32(15Q22.33) MUTATED	28	117	16
DEL PEAK 32(15Q22.33) WILD-TYPE	175	65	49

Figure S147. Get High-res Image Gene #57: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q22.33' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.15

Table S148. Gene #57: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 32(15Q22.33) MUTATED	58	20	24
DEL PEAK 32(15Q22.33) WILD-TYPE	60	72	47

Figure S148. Get High-res Image Gene #57: '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 = 0.0081

Table S149. Gene #57: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 32(15Q22.33) MUTATED	77	29	48
DEL PEAK 32(15Q22.33) WILD-TYPE	63	122	95

Figure S149. Get High-res Image Gene #57: '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 = 0.0081

Table S150. Gene #57: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 32(15Q22.33) MUTATED	45	39	9	59	2
DEL PEAK 32(15Q22.33) WILD-TYPE	61	35	81	69	34

Figure S150. Get High-res Image Gene #57: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S151. Gene #60: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S151. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S152. Gene #60: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 35(17P12) MUTATED	9	47	26
DEL PEAK 35(17P12) WILD-TYPE	33	25	6

Figure S152. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S153. Gene #60: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 35(17P12) MUTATED	51	158	45
DEL PEAK 35(17P12) WILD-TYPE	152	24	20

Figure S153. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S154. Gene #60: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 35(17P12) MUTATED	95	31	34
DEL PEAK 35(17P12) WILD-TYPE	23	61	37

Figure S154. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S155. Gene #60: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 35(17P12) MUTATED	110	52	83
DEL PEAK 35(17P12) WILD-TYPE	30	99	60

Figure S155. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S156. Gene #60: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 35(17P12) MUTATED	80	51	19	91	4
DEL PEAK 35(17P12) WILD-TYPE	26	23	71	37	32

Figure S156. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S157. Gene #62: '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 37(18P11.31) MUTATED	6	50	7	15
DEL PEAK 37(18P11.31) WILD-TYPE	29	11	22	6

Figure S157. Get High-res Image Gene #62: '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 = 0.0081

Table S158. Gene #62: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S158. Get High-res Image Gene #62: '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 = 0.0081

Table S159. Gene #62: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 37(18P11.31) MUTATED	43	163	40
DEL PEAK 37(18P11.31) WILD-TYPE	160	19	25

Figure S159. Get High-res Image Gene #62: '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 = 0.0081

Table S160. Gene #62: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 37(18P11.31) MUTATED	98	23	35
DEL PEAK 37(18P11.31) WILD-TYPE	20	69	36

Figure S160. Get High-res Image Gene #62: '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 = 0.0081

Table S161. Gene #62: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 37(18P11.31) MUTATED	121	38	77
DEL PEAK 37(18P11.31) WILD-TYPE	19	113	66

Figure S161. Get High-res Image Gene #62: '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 = 0.0081

Table S162. Gene #62: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 37(18P11.31) MUTATED	77	57	11	90	1
DEL PEAK 37(18P11.31) WILD-TYPE	29	17	79	38	35

Figure S162. Get High-res Image Gene #62: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S163. Gene #63: '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 38(18Q12.2) MUTATED	8	53	9	16
DEL PEAK 38(18Q12.2) WILD-TYPE	27	8	20	5

Figure S163. Get High-res Image Gene #63: '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 = 0.0081

Table S164. Gene #63: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 38(18Q12.2) MUTATED	7	51	28
DEL PEAK 38(18Q12.2) WILD-TYPE	35	21	4

Figure S164. Get High-res Image Gene #63: '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 = 0.0081

Table S165. Gene #63: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 38(18Q12.2) MUTATED	52	170	52
DEL PEAK 38(18Q12.2) WILD-TYPE	151	12	13

Figure S165. Get High-res Image Gene #63: '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 = 0.0081

Table S166. Gene #63: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 38(18Q12.2) MUTATED	106	31	36
DEL PEAK 38(18Q12.2) WILD-TYPE	12	61	35

Figure S166. Get High-res Image Gene #63: '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 = 0.0081

Table S167. Gene #63: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 38(18Q12.2) MUTATED	126	51	86
DEL PEAK 38(18Q12.2) WILD-TYPE	14	100	57

Figure S167. Get High-res Image Gene #63: '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 = 0.0081

Table S168. Gene #63: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 38(18Q12.2) MUTATED	83	62	18	98	2
DEL PEAK 38(18Q12.2) WILD-TYPE	23	12	72	30	34

Figure S168. Get High-res Image Gene #63: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S169. Gene #64: '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 39(18Q21.2) MUTATED	8	53	10	16
DEL PEAK 39(18Q21.2) WILD-TYPE	27	8	19	5

Figure S169. Get High-res Image Gene #64: '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 = 0.0081

Table S170. Gene #64: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 39(18Q21.2) MUTATED	7	52	28
DEL PEAK 39(18Q21.2) WILD-TYPE	35	20	4

Figure S170. Get High-res Image Gene #64: '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 = 0.0081

Table S171. Gene #64: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 39(18Q21.2) MUTATED	60	172	55
DEL PEAK 39(18Q21.2) WILD-TYPE	143	10	10

Figure S171. Get High-res Image Gene #64: '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 = 0.0081

Table S172. Gene #64: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
DEL PEAK 39(18Q21.2) MUTATED	107	41	38
DEL PEAK 39(18Q21.2) WILD-TYPE	11	51	33

Figure S172. Get High-res Image Gene #64: '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 = 0.0081

Table S173. Gene #64: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 39(18Q21.2) MUTATED	128	62	87
DEL PEAK 39(18Q21.2) WILD-TYPE	12	89	56

Figure S173. Get High-res Image Gene #64: '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 = 0.0081

Table S174. Gene #64: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 39(18Q21.2) MUTATED	86	64	26	98	3
DEL PEAK 39(18Q21.2) WILD-TYPE	20	10	64	30	33

Figure S174. Get High-res Image Gene #64: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.027

Table S175. Gene #65: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 40(19P13.3) MUTATED	13	38	12
DEL PEAK 40(19P13.3) WILD-TYPE	190	144	53

Figure S175. Get High-res Image Gene #65: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.13

Table S176. Gene #65: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 40(19P13.3) MUTATED	20	10	5	28	0
DEL PEAK 40(19P13.3) WILD-TYPE	86	64	85	100	36

Figure S176. Get High-res Image Gene #65: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S177. Gene #66: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 41(20P12.1) MUTATED	18	49	19
DEL PEAK 41(20P12.1) WILD-TYPE	185	133	46

Figure S177. Get High-res Image Gene #66: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S178. Gene #66: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 41(20P12.1) MUTATED	49	14	21
DEL PEAK 41(20P12.1) WILD-TYPE	91	137	122

Figure S178. Get High-res Image Gene #66: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S179. Gene #66: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 41(20P12.1) MUTATED	30	22	5	23	4
DEL PEAK 41(20P12.1) WILD-TYPE	76	52	85	105	32

Figure S179. Get High-res Image Gene #66: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S180. Gene #67: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 42(21Q11.2) MUTATED	39	89	13
DEL PEAK 42(21Q11.2) WILD-TYPE	164	93	52

Figure S180. Get High-res Image Gene #67: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.065

Table S181. Gene #67: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 42(21Q11.2) MUTATED	33	34	17	48	4
DEL PEAK 42(21Q11.2) WILD-TYPE	73	40	73	80	32

Figure S181. Get High-res Image Gene #67: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.15

Table S182. Gene #68: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 43(22Q13.32) MUTATED	6	35	16
DEL PEAK 43(22Q13.32) WILD-TYPE	36	37	16

Figure S182. Get High-res Image Gene #68: '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 = 0.0081

Table S183. Gene #68: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	182	65
DEL PEAK 43(22Q13.32) MUTATED	37	105	18
DEL PEAK 43(22Q13.32) WILD-TYPE	166	77	47

Figure S183. Get High-res Image Gene #68: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.13

Table S184. Gene #68: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	151	143
DEL PEAK 43(22Q13.32) MUTATED	66	36	52
DEL PEAK 43(22Q13.32) WILD-TYPE	74	115	91

Figure S184. Get High-res Image Gene #68: '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 = 0.0081

Table S185. Gene #68: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	106	74	90	128	36
DEL PEAK 43(22Q13.32) MUTATED	42	35	13	60	4
DEL PEAK 43(22Q13.32) WILD-TYPE	64	39	77	68	32

Figure S185. Get High-res Image Gene #68: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = COAD-TP.transferedmergedcluster.txt
Number of patients = 450
Number of significantly focal cnvs = 68
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.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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