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

Esophageal Carcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1F47N1F

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 85 focal events and 8 molecular subtypes across 184 patients, 91 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q42.3 cnv correlated to 'CN_CNMF'.
amp_3q26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
amp_8p23.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
amp_11q13.3 cnv correlated to 'CN_CNMF'.
amp_13q22.1 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_14q21.1 cnv correlated to 'CN_CNMF'.
amp_18q11.2 cnv correlated to 'MIRSEQ_CNMF'.
del_1p13.2 cnv correlated to 'CN_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q26.31 cnv correlated to 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF'.
del_4q34.3 cnv correlated to 'MRNASEQ_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF'.
del_8p12 cnv correlated to 'CN_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF'.
del_10p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q25 cnv correlated to 'CN_CNMF'.
del_13q12.11 cnv correlated to 'CN_CNMF'.
del_16p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q12.2 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF'.
del_22q11.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 85 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 91 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	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
amp 3q26 2	128 (70%)	56	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)	2e-05 (0.0126)	1e-05 (0.0068)	3e-05 (0.0188)
del 3p14 3	126 (68%)	58	1e-05 (0.0068)	1e-05 (0.0068)	0.00029 (0.173)	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)
del 16q23 1	84 (46%)	100	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)
del 2q22 1	59 (32%)	125	1e-05 (0.0068)	1e-05 (0.0068)	0.0001 (0.061)	0.00051 (0.299)	1e-05 (0.0068)	2e-05 (0.0126)	0.00013 (0.0792)	1e-05 (0.0068)
del 3p14 2	125 (68%)	59	1e-05 (0.0068)	2e-05 (0.0126)	0.00112 (0.634)	6e-05 (0.0369)	1e-05 (0.0068)	1e-05 (0.0068)	4e-05 (0.0248)	1e-05 (0.0068)
del 16p13 3	65 (35%)	119	2e-05 (0.0126)	4e-05 (0.0248)	0.00028 (0.168)	0.00059 (0.345)	3e-05 (0.0188)	1e-05 (0.0068)	4e-05 (0.0248)	1e-05 (0.0068)
del 10p11 21	52 (28%)	132	1e-05 (0.0068)	3e-05 (0.0188)	0.00134 (0.749)	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)	0.00047 (0.276)	3e-05 (0.0188)
del 22q11 1	79 (43%)	105	1e-05 (0.0068)	1e-05 (0.0068)	0.00244 (1.00)	0.0152 (1.00)	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)	1e-05 (0.0068)
del 3p26 2	111 (60%)	73	1e-05 (0.0068)	3e-05 (0.0188)	0.00059 (0.345)	0.00108 (0.613)	0.00019 (0.115)	0.00017 (0.103)	0.013 (1.00)	0.0003 (0.178)
del 17p12	86 (47%)	98	9e-05 (0.0551)	1e-05 (0.0068)	0.0013 (0.728)	0.00063 (0.365)	1e-05 (0.0068)	1e-05 (0.0068)	0.01 (1.00)	2e-05 (0.0126)
del 3q26 31	16 (9%)	168	0.00227 (1.00)	3e-05 (0.0188)	0.0876 (1.00)	0.00353 (1.00)	0.0003 (0.178)	0.00035 (0.207)	0.00223 (1.00)	7e-05 (0.0429)
amp 5p15 33	98 (53%)	86	1e-05 (0.0068)	0.0153 (1.00)	0.0658 (1.00)	0.0113 (1.00)	0.00027 (0.163)	0.00386 (1.00)	0.0103 (1.00)	0.00226 (1.00)
amp 8p23 1	52 (28%)	132	4e-05 (0.0248)	0.00225 (1.00)	0.0445 (1.00)	0.0153 (1.00)	0.00406 (1.00)	0.0149 (1.00)	0.00028 (0.168)	0.00177 (0.979)
amp 13q22 1	65 (35%)	119	0.00173 (0.958)	0.00668 (1.00)	0.223 (1.00)	0.0108 (1.00)	0.00028 (0.168)	0.00223 (1.00)	0.012 (1.00)	0.00026 (0.157)
amp 1q42 3	96 (52%)	88	2e-05 (0.0126)	0.314 (1.00)	0.141 (1.00)	0.265 (1.00)	0.299 (1.00)	0.284 (1.00)	0.149 (1.00)	0.261 (1.00)
amp 11q13 3	104 (57%)	80	1e-05 (0.0068)	0.00321 (1.00)	0.114 (1.00)	0.00161 (0.897)	0.00112 (0.634)	0.0012 (0.676)	0.0921 (1.00)	0.00146 (0.815)
amp 14q21 1	61 (33%)	123	0.00023 (0.139)	0.00905 (1.00)	0.0664 (1.00)	0.0083 (1.00)	0.00368 (1.00)	0.004 (1.00)	0.0569 (1.00)	0.0126 (1.00)
amp 18q11 2	59 (32%)	125	0.0124 (1.00)	0.01 (1.00)	0.00111 (0.629)	0.00089 (0.507)	0.00031 (0.184)	0.00885 (1.00)	0.0148 (1.00)	0.00082 (0.471)
del 1p13 2	64 (35%)	120	6e-05 (0.0369)	0.0982 (1.00)	0.0144 (1.00)	0.545 (1.00)	0.755 (1.00)	0.104 (1.00)	0.172 (1.00)	0.902 (1.00)
del 4q22 1	105 (57%)	79	0.00019 (0.115)	0.11 (1.00)	0.00052 (0.304)	0.239 (1.00)	0.00299 (1.00)	0.143 (1.00)	0.0516 (1.00)	0.0362 (1.00)
del 4q34 3	99 (54%)	85	0.0005 (0.293)	0.00619 (1.00)	0.0004 (0.236)	0.0562 (1.00)	0.00083 (0.476)	0.00308 (1.00)	0.0196 (1.00)	0.00198 (1.00)
del 8p23 2	90 (49%)	94	9e-05 (0.0551)	0.028 (1.00)	0.194 (1.00)	0.185 (1.00)	0.0094 (1.00)	0.108 (1.00)	0.0368 (1.00)	0.146 (1.00)
del 8p12	75 (41%)	109	0.00029 (0.173)	0.411 (1.00)	0.758 (1.00)	0.526 (1.00)	0.227 (1.00)	0.805 (1.00)	0.553 (1.00)	0.494 (1.00)
del 9p21 3	141 (77%)	43	1e-05 (0.0068)	0.236 (1.00)	0.297 (1.00)	0.0296 (1.00)	0.034 (1.00)	0.104 (1.00)	0.306 (1.00)	0.106 (1.00)
del 11q25	81 (44%)	103	3e-05 (0.0188)	0.028 (1.00)	0.694 (1.00)	0.217 (1.00)	0.0574 (1.00)	0.0819 (1.00)	0.0277 (1.00)	0.0298 (1.00)
del 13q12 11	76 (41%)	108	0.00021 (0.127)	0.0134 (1.00)	0.00791 (1.00)	0.00232 (1.00)	0.00865 (1.00)	0.0092 (1.00)	0.0133 (1.00)	0.0158 (1.00)
del 18q12 2	111 (60%)	73	0.0943 (1.00)	0.0174 (1.00)	0.125 (1.00)	0.285 (1.00)	0.0445 (1.00)	0.0006 (0.349)	0.0355 (1.00)	0.00027 (0.163)
del 19p13 3	93 (51%)	91	0.0004 (0.236)	0.302 (1.00)	0.723 (1.00)	0.77 (1.00)	0.0358 (1.00)	0.0226 (1.00)	0.113 (1.00)	0.00665 (1.00)
amp 1p34 2	40 (22%)	144	0.329 (1.00)	0.629 (1.00)	0.243 (1.00)	0.377 (1.00)	0.744 (1.00)	0.325 (1.00)	0.8 (1.00)	0.547 (1.00)
amp 1q23 3	93 (51%)	91	0.00182 (1.00)	0.125 (1.00)	0.0916 (1.00)	0.896 (1.00)	0.169 (1.00)	0.841 (1.00)	0.0195 (1.00)	0.809 (1.00)
amp 2q14 2	60 (33%)	124	0.353 (1.00)	0.307 (1.00)	0.58 (1.00)	0.0892 (1.00)	0.251 (1.00)	0.209 (1.00)	0.271 (1.00)	0.32 (1.00)
amp 2q31 1	60 (33%)	124	0.032 (1.00)	0.232 (1.00)	0.619 (1.00)	0.169 (1.00)	0.543 (1.00)	0.27 (1.00)	0.102 (1.00)	0.654 (1.00)
amp 4q21 1	34 (18%)	150	0.295 (1.00)	0.701 (1.00)	0.042 (1.00)	0.828 (1.00)	0.954 (1.00)	0.426 (1.00)	0.921 (1.00)	0.358 (1.00)
amp 6p21 1	69 (38%)	115	0.00305 (1.00)	0.123 (1.00)	0.31 (1.00)	0.203 (1.00)	0.00341 (1.00)	0.00188 (1.00)	0.00697 (1.00)	0.00125 (0.702)
amp 6q23 3	42 (23%)	142	0.0369 (1.00)	0.0698 (1.00)	0.223 (1.00)	0.307 (1.00)	0.0327 (1.00)	0.0309 (1.00)	0.00927 (1.00)	0.00672 (1.00)
amp 7p11 2	126 (68%)	58	0.331 (1.00)	0.111 (1.00)	0.483 (1.00)	0.0207 (1.00)	0.0375 (1.00)	0.268 (1.00)	0.67 (1.00)	0.128 (1.00)
amp 7q21 2	114 (62%)	70	0.477 (1.00)	0.158 (1.00)	0.595 (1.00)	0.755 (1.00)	0.346 (1.00)	0.608 (1.00)	0.771 (1.00)	0.141 (1.00)
amp 8p11 21	85 (46%)	99	0.493 (1.00)	0.174 (1.00)	0.0441 (1.00)	0.0742 (1.00)	0.387 (1.00)	0.966 (1.00)	0.734 (1.00)	0.687 (1.00)
amp 8q24 21	145 (79%)	39	0.0023 (1.00)	0.0221 (1.00)	0.0154 (1.00)	0.0864 (1.00)	0.00672 (1.00)	0.0987 (1.00)	0.353 (1.00)	0.147 (1.00)
amp 9p13 3	40 (22%)	144	0.0831 (1.00)	0.104 (1.00)	0.0297 (1.00)	0.849 (1.00)	0.715 (1.00)	0.132 (1.00)	0.535 (1.00)	0.553 (1.00)
amp 9q34 3	64 (35%)	120	0.0259 (1.00)	0.177 (1.00)	0.0294 (1.00)	0.959 (1.00)	0.271 (1.00)	0.113 (1.00)	0.115 (1.00)	0.678 (1.00)
amp 11p13	52 (28%)	132	0.142 (1.00)	0.461 (1.00)	0.459 (1.00)	0.512 (1.00)	0.204 (1.00)	0.126 (1.00)	0.582 (1.00)	0.254 (1.00)
amp 11p13	50 (27%)	134	0.0864 (1.00)	0.928 (1.00)	0.561 (1.00)	0.874 (1.00)	0.963 (1.00)	0.712 (1.00)	0.785 (1.00)	0.495 (1.00)
amp 12p12 1	79 (43%)	105	0.0336 (1.00)	0.128 (1.00)	0.183 (1.00)	0.0372 (1.00)	0.0604 (1.00)	0.0844 (1.00)	0.0578 (1.00)	0.0872 (1.00)
amp 12q15	51 (28%)	133	0.134 (1.00)	0.595 (1.00)	0.496 (1.00)	0.565 (1.00)	0.315 (1.00)	0.598 (1.00)	0.296 (1.00)	0.177 (1.00)
amp 15q26 1	58 (32%)	126	0.00821 (1.00)	0.0717 (1.00)	0.0276 (1.00)	0.00366 (1.00)	0.00662 (1.00)	0.0417 (1.00)	0.0364 (1.00)	0.015 (1.00)
amp 17q12	75 (41%)	109	0.00448 (1.00)	0.00418 (1.00)	0.125 (1.00)	0.265 (1.00)	0.00205 (1.00)	0.0198 (1.00)	0.0241 (1.00)	0.00166 (0.921)
amp 18p11 32	69 (38%)	115	0.059 (1.00)	0.108 (1.00)	0.237 (1.00)	0.445 (1.00)	0.017 (1.00)	0.56 (1.00)	0.365 (1.00)	0.511 (1.00)
amp 19p13 2	32 (17%)	152	0.406 (1.00)	0.083 (1.00)	0.822 (1.00)	0.396 (1.00)	0.121 (1.00)	0.395 (1.00)	0.322 (1.00)	0.685 (1.00)
amp 19q12	54 (29%)	130	0.00476 (1.00)	0.156 (1.00)	0.00604 (1.00)	0.0438 (1.00)	0.0389 (1.00)	0.272 (1.00)	0.123 (1.00)	0.0515 (1.00)
amp xq28	69 (38%)	115	0.061 (1.00)	0.0313 (1.00)	0.0113 (1.00)	0.0358 (1.00)	0.0291 (1.00)	0.00193 (1.00)	0.365 (1.00)	0.00367 (1.00)
del 1p36 11	75 (41%)	109	0.0107 (1.00)	0.00908 (1.00)	0.00067 (0.388)	0.205 (1.00)	0.00305 (1.00)	0.0234 (1.00)	0.0423 (1.00)	0.0386 (1.00)
del 1q44	17 (9%)	167	0.855 (1.00)	0.743 (1.00)	0.804 (1.00)	0.496 (1.00)	0.718 (1.00)	0.642 (1.00)	0.802 (1.00)	0.255 (1.00)
del 2q33 3	36 (20%)	148	0.293 (1.00)	0.0659 (1.00)	0.159 (1.00)	0.0642 (1.00)	0.0134 (1.00)	0.0695 (1.00)	0.0728 (1.00)	0.0277 (1.00)
del 3q11 1	33 (18%)	151	0.592 (1.00)	0.623 (1.00)	0.385 (1.00)	0.64 (1.00)	0.863 (1.00)	0.792 (1.00)	0.886 (1.00)	0.629 (1.00)
del 4p15 2	106 (58%)	78	0.00548 (1.00)	0.098 (1.00)	0.00531 (1.00)	0.292 (1.00)	0.0478 (1.00)	0.747 (1.00)	0.265 (1.00)	0.954 (1.00)
del 5q12 1	112 (61%)	72	0.00046 (0.271)	0.00071 (0.41)	0.361 (1.00)	1 (1.00)	0.0224 (1.00)	0.0255 (1.00)	0.436 (1.00)	0.0575 (1.00)
del 6p25 3	74 (40%)	110	0.0161 (1.00)	0.0224 (1.00)	0.0741 (1.00)	0.522 (1.00)	0.123 (1.00)	0.0215 (1.00)	0.313 (1.00)	0.0915 (1.00)
del 6q16 3	55 (30%)	129	0.142 (1.00)	0.436 (1.00)	0.0281 (1.00)	0.182 (1.00)	0.127 (1.00)	0.508 (1.00)	0.541 (1.00)	0.284 (1.00)
del 6q26	50 (27%)	134	0.272 (1.00)	0.927 (1.00)	0.0392 (1.00)	0.176 (1.00)	0.196 (1.00)	0.732 (1.00)	0.773 (1.00)	0.333 (1.00)
del 7q31 1	56 (30%)	128	0.224 (1.00)	0.0868 (1.00)	0.0731 (1.00)	0.593 (1.00)	0.401 (1.00)	0.0961 (1.00)	0.11 (1.00)	0.0235 (1.00)
del 7q36 3	67 (36%)	117	0.906 (1.00)	0.709 (1.00)	0.255 (1.00)	0.753 (1.00)	0.361 (1.00)	0.15 (1.00)	0.377 (1.00)	0.163 (1.00)
del 9p23	108 (59%)	76	0.416 (1.00)	0.121 (1.00)	0.251 (1.00)	0.0607 (1.00)	0.427 (1.00)	0.723 (1.00)	0.915 (1.00)	0.695 (1.00)
del 10p15 3	54 (29%)	130	0.00077 (0.444)	0.0197 (1.00)	0.291 (1.00)	0.0209 (1.00)	0.00613 (1.00)	0.0116 (1.00)	0.0889 (1.00)	0.0612 (1.00)
del 10q21 1	46 (25%)	138	0.00218 (1.00)	0.0203 (1.00)	0.361 (1.00)	0.197 (1.00)	0.0173 (1.00)	0.0576 (1.00)	0.234 (1.00)	0.0495 (1.00)
del 10q23 31	65 (35%)	119	0.0215 (1.00)	0.0363 (1.00)	0.729 (1.00)	0.446 (1.00)	0.119 (1.00)	0.282 (1.00)	0.371 (1.00)	0.453 (1.00)
del 11p15 4	79 (43%)	105	0.129 (1.00)	0.0448 (1.00)	0.625 (1.00)	0.686 (1.00)	0.625 (1.00)	0.182 (1.00)	0.805 (1.00)	0.458 (1.00)
del 12q23 1	51 (28%)	133	0.251 (1.00)	0.0188 (1.00)	0.32 (1.00)	0.188 (1.00)	0.101 (1.00)	0.133 (1.00)	0.181 (1.00)	0.046 (1.00)
del 13q14 2	74 (40%)	110	0.00162 (0.901)	0.00505 (1.00)	0.0109 (1.00)	0.011 (1.00)	0.0171 (1.00)	0.0246 (1.00)	0.0226 (1.00)	0.0253 (1.00)
del 13q21 31	69 (38%)	115	0.013 (1.00)	0.0529 (1.00)	0.202 (1.00)	0.0834 (1.00)	0.0881 (1.00)	0.134 (1.00)	0.0926 (1.00)	0.135 (1.00)
del 14q23 3	51 (28%)	133	0.00363 (1.00)	0.0153 (1.00)	0.00812 (1.00)	0.0141 (1.00)	0.0935 (1.00)	0.0131 (1.00)	0.028 (1.00)	0.00221 (1.00)
del 15q11 2	63 (34%)	121	0.404 (1.00)	0.159 (1.00)	0.0941 (1.00)	0.627 (1.00)	0.202 (1.00)	0.0189 (1.00)	0.64 (1.00)	0.00374 (1.00)
del 17q25 3	41 (22%)	143	0.372 (1.00)	0.818 (1.00)	0.689 (1.00)	0.902 (1.00)	0.13 (1.00)	0.538 (1.00)	0.037 (1.00)	0.71 (1.00)
del 18p11 23	60 (33%)	124	0.314 (1.00)	0.00575 (1.00)	0.443 (1.00)	0.522 (1.00)	0.0253 (1.00)	0.137 (1.00)	0.139 (1.00)	0.0481 (1.00)
del 18q21 2	119 (65%)	65	0.151 (1.00)	0.00083 (0.476)	0.0853 (1.00)	0.171 (1.00)	0.00463 (1.00)	0.00202 (1.00)	0.0155 (1.00)	0.00061 (0.354)
del 18q22 3	112 (61%)	72	0.962 (1.00)	0.0355 (1.00)	0.0698 (1.00)	0.607 (1.00)	0.214 (1.00)	0.00785 (1.00)	0.05 (1.00)	0.00071 (0.41)
del 19q11	48 (26%)	136	0.215 (1.00)	0.387 (1.00)	0.56 (1.00)	0.35 (1.00)	0.351 (1.00)	0.0145 (1.00)	0.00092 (0.523)	0.027 (1.00)
del 20p12 1	33 (18%)	151	0.034 (1.00)	0.161 (1.00)	0.436 (1.00)	0.0538 (1.00)	0.0166 (1.00)	0.0499 (1.00)	0.289 (1.00)	0.0409 (1.00)
del 21q11 2	107 (58%)	77	0.124 (1.00)	0.0276 (1.00)	0.305 (1.00)	0.604 (1.00)	0.0498 (1.00)	0.17 (1.00)	0.151 (1.00)	0.0959 (1.00)
del 21q21 1	107 (58%)	77	0.124 (1.00)	0.00846 (1.00)	0.0964 (1.00)	0.342 (1.00)	0.0875 (1.00)	0.174 (1.00)	0.0728 (1.00)	0.0737 (1.00)
del 21q22 12	108 (59%)	76	0.103 (1.00)	0.011 (1.00)	0.0879 (1.00)	0.431 (1.00)	0.0324 (1.00)	0.33 (1.00)	0.0719 (1.00)	0.204 (1.00)
del xp21 1	69 (38%)	115	0.00082 (0.471)	0.0371 (1.00)	0.003 (1.00)	0.0777 (1.00)	0.0548 (1.00)	0.16 (1.00)	0.114 (1.00)	0.15 (1.00)
del xp11 3	74 (40%)	110	0.00086 (0.491)	0.163 (1.00)	0.00127 (0.712)	0.00119 (0.671)	0.00306 (1.00)	0.0451 (1.00)	0.0335 (1.00)	0.0179 (1.00)
del xq11 2	42 (23%)	142	0.495 (1.00)	0.243 (1.00)	0.895 (1.00)	0.485 (1.00)	0.126 (1.00)	0.22 (1.00)	0.204 (1.00)	0.715 (1.00)
del xq21 33	40 (22%)	144	0.16 (1.00)	0.206 (1.00)	0.226 (1.00)	0.187 (1.00)	0.103 (1.00)	0.0288 (1.00)	0.152 (1.00)	0.185 (1.00)

'amp_1q42.3' versus 'CN_CNMF'

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

Table S1. Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
AMP PEAK 3(1Q42.3) MUTATED	39	10	47
AMP PEAK 3(1Q42.3) WILD-TYPE	26	34	28

Figure S1. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S2. Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
AMP PEAK 6(3Q26.2) MUTATED	40	14	74
AMP PEAK 6(3Q26.2) WILD-TYPE	25	30	1

Figure S2. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S3. Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	32	76
AMP PEAK 6(3Q26.2) MUTATED	41	19	68
AMP PEAK 6(3Q26.2) WILD-TYPE	35	13	8

Figure S3. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S4. Gene #6: 'amp_3q26.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	11	26	31	11
AMP PEAK 6(3Q26.2) MUTATED	21	7	26	26	9
AMP PEAK 6(3Q26.2) WILD-TYPE	25	4	0	5	2

Figure S4. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S5. Gene #6: 'amp_3q26.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	74	12
AMP PEAK 6(3Q26.2) MUTATED	18	67	4
AMP PEAK 6(3Q26.2) WILD-TYPE	21	7	8

Figure S5. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S6. Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
AMP PEAK 6(3Q26.2) MUTATED	44	75	8
AMP PEAK 6(3Q26.2) WILD-TYPE	40	12	4

Figure S6. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S7. Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
AMP PEAK 6(3Q26.2) MUTATED	33	13	56	25
AMP PEAK 6(3Q26.2) WILD-TYPE	29	13	6	8

Figure S7. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S8. Gene #6: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	66	35	11
AMP PEAK 6(3Q26.2) MUTATED	35	62	23	6
AMP PEAK 6(3Q26.2) WILD-TYPE	31	4	12	5

Figure S8. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S9. Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	22	94
AMP PEAK 6(3Q26.2) MUTATED	35	11	80
AMP PEAK 6(3Q26.2) WILD-TYPE	27	11	14

Figure S9. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S10. Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
AMP PEAK 8(5P15.33) MUTATED	31	11	56
AMP PEAK 8(5P15.33) WILD-TYPE	34	33	19

Figure S10. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

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

Table S11. Gene #8: 'amp_5p15.33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
AMP PEAK 8(5P15.33) MUTATED	34	60	4
AMP PEAK 8(5P15.33) WILD-TYPE	50	27	8

Figure S11. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_8p23.1' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.025

Table S12. Gene #13: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
AMP PEAK 13(8P23.1) MUTATED	26	18	8
AMP PEAK 13(8P23.1) WILD-TYPE	39	26	67

Figure S12. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.17

Table S13. Gene #13: 'amp_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	66	35	11
AMP PEAK 13(8P23.1) MUTATED	28	7	11	2
AMP PEAK 13(8P23.1) WILD-TYPE	38	59	24	9

Figure S13. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S14. Gene #20: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
AMP PEAK 20(11Q13.3) MUTATED	28	15	61
AMP PEAK 20(11Q13.3) WILD-TYPE	37	29	14

Figure S14. Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.17

Table S15. Gene #23: 'amp_13q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
AMP PEAK 23(13Q22.1) MUTATED	42	21	1
AMP PEAK 23(13Q22.1) WILD-TYPE	42	66	11

Figure S15. Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S16. Gene #23: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	22	94
AMP PEAK 23(13Q22.1) MUTATED	33	10	21
AMP PEAK 23(13Q22.1) WILD-TYPE	29	12	73

Figure S16. Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q21.1' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.14

Table S17. Gene #24: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
AMP PEAK 24(14Q21.1) MUTATED	19	6	36
AMP PEAK 24(14Q21.1) WILD-TYPE	46	38	39

Figure S17. Get High-res Image Gene #24: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.18

Table S18. Gene #28: 'amp_18q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
AMP PEAK 28(18Q11.2) MUTATED	38	21	0
AMP PEAK 28(18Q11.2) WILD-TYPE	46	66	12

Figure S18. Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.037

Table S19. Gene #33: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 2(1P13.2) MUTATED	29	4	31
DEL PEAK 2(1P13.2) WILD-TYPE	36	40	44

Figure S19. Get High-res Image Gene #33: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S20. Gene #35: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 4(2Q22.1) MUTATED	11	8	40
DEL PEAK 4(2Q22.1) WILD-TYPE	54	36	35

Figure S20. Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S21. Gene #35: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	32	76
DEL PEAK 4(2Q22.1) MUTATED	10	8	41
DEL PEAK 4(2Q22.1) WILD-TYPE	66	24	35

Figure S21. Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.061

Table S22. Gene #35: 'del_2q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	11	26	31	11
DEL PEAK 4(2Q22.1) MUTATED	8	3	18	14	2
DEL PEAK 4(2Q22.1) WILD-TYPE	38	8	8	17	9

Figure S22. Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S23. Gene #35: 'del_2q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
DEL PEAK 4(2Q22.1) MUTATED	12	45	2
DEL PEAK 4(2Q22.1) WILD-TYPE	72	42	10

Figure S23. Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S24. Gene #35: 'del_2q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 4(2Q22.1) MUTATED	10	3	26	20
DEL PEAK 4(2Q22.1) WILD-TYPE	52	23	36	13

Figure S24. Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.079

Table S25. Gene #35: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	66	35	11
DEL PEAK 4(2Q22.1) MUTATED	11	35	10	3
DEL PEAK 4(2Q22.1) WILD-TYPE	55	31	25	8

Figure S25. Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S26. Gene #35: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	22	94
DEL PEAK 4(2Q22.1) MUTATED	10	3	46
DEL PEAK 4(2Q22.1) WILD-TYPE	52	19	48

Figure S26. Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S27. Gene #37: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 6(3P26.2) MUTATED	32	16	63
DEL PEAK 6(3P26.2) WILD-TYPE	33	28	12

Figure S27. Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S28. Gene #37: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	32	76
DEL PEAK 6(3P26.2) MUTATED	33	18	60
DEL PEAK 6(3P26.2) WILD-TYPE	43	14	16

Figure S28. Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MIRSEQ_CNMF'

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

Table S29. Gene #37: 'del_3p26.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
DEL PEAK 6(3P26.2) MUTATED	38	66	7
DEL PEAK 6(3P26.2) WILD-TYPE	46	21	5

Figure S29. Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.1

Table S30. Gene #37: 'del_3p26.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 6(3P26.2) MUTATED	29	10	48	24
DEL PEAK 6(3P26.2) WILD-TYPE	33	16	14	9

Figure S30. Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S31. Gene #37: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	22	94
DEL PEAK 6(3P26.2) MUTATED	29	10	71
DEL PEAK 6(3P26.2) WILD-TYPE	33	12	23

Figure S31. Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S32. Gene #38: 'del_3p14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 7(3P14.3) MUTATED	37	18	71
DEL PEAK 7(3P14.3) WILD-TYPE	28	26	4

Figure S32. Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S33. Gene #38: 'del_3p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	32	76
DEL PEAK 7(3P14.3) MUTATED	37	23	66
DEL PEAK 7(3P14.3) WILD-TYPE	39	9	10

Figure S33. Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.3' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.17

Table S34. Gene #38: 'del_3p14.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	11	26	31	11
DEL PEAK 7(3P14.3) MUTATED	24	5	24	27	8
DEL PEAK 7(3P14.3) WILD-TYPE	22	6	2	4	3

Figure S34. Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S35. Gene #38: 'del_3p14.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	74	12
DEL PEAK 7(3P14.3) MUTATED	20	64	4
DEL PEAK 7(3P14.3) WILD-TYPE	19	10	8

Figure S35. Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S36. Gene #38: 'del_3p14.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
DEL PEAK 7(3P14.3) MUTATED	43	76	7
DEL PEAK 7(3P14.3) WILD-TYPE	41	11	5

Figure S36. Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S37. Gene #38: 'del_3p14.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 7(3P14.3) MUTATED	32	12	54	28
DEL PEAK 7(3P14.3) WILD-TYPE	30	14	8	5

Figure S37. Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S38. Gene #38: 'del_3p14.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	66	35	11
DEL PEAK 7(3P14.3) MUTATED	32	59	25	8
DEL PEAK 7(3P14.3) WILD-TYPE	34	7	10	3

Figure S38. Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p14.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S39. Gene #38: 'del_3p14.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	22	94
DEL PEAK 7(3P14.3) MUTATED	32	11	81
DEL PEAK 7(3P14.3) WILD-TYPE	30	11	13

Figure S39. Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S40. Gene #39: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 8(3P14.2) MUTATED	38	17	70
DEL PEAK 8(3P14.2) WILD-TYPE	27	27	5

Figure S40. Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

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

Table S41. Gene #39: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	32	76
DEL PEAK 8(3P14.2) MUTATED	38	22	65
DEL PEAK 8(3P14.2) WILD-TYPE	38	10	11

Figure S41. Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.037

Table S42. Gene #39: 'del_3p14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	74	12
DEL PEAK 8(3P14.2) MUTATED	20	63	5
DEL PEAK 8(3P14.2) WILD-TYPE	19	11	7

Figure S42. Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S43. Gene #39: 'del_3p14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
DEL PEAK 8(3P14.2) MUTATED	43	75	7
DEL PEAK 8(3P14.2) WILD-TYPE	41	12	5

Figure S43. Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S44. Gene #39: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 8(3P14.2) MUTATED	33	11	53	28
DEL PEAK 8(3P14.2) WILD-TYPE	29	15	9	5

Figure S44. Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.025

Table S45. Gene #39: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	66	35	11
DEL PEAK 8(3P14.2) MUTATED	34	58	24	7
DEL PEAK 8(3P14.2) WILD-TYPE	32	8	11	4

Figure S45. Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S46. Gene #39: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	22	94
DEL PEAK 8(3P14.2) MUTATED	33	10	80
DEL PEAK 8(3P14.2) WILD-TYPE	29	12	14

Figure S46. Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.31' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S47. Gene #41: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	32	76
DEL PEAK 10(3Q26.31) MUTATED	15	0	1
DEL PEAK 10(3Q26.31) WILD-TYPE	61	32	75

Figure S47. Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q26.31' versus 'MIRSEQ_CNMF'

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

Table S48. Gene #41: 'del_3q26.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
DEL PEAK 10(3Q26.31) MUTATED	15	1	0
DEL PEAK 10(3Q26.31) WILD-TYPE	69	86	12

Figure S48. Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S49. Gene #41: 'del_3q26.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 10(3Q26.31) MUTATED	11	4	0	1
DEL PEAK 10(3Q26.31) WILD-TYPE	51	22	62	32

Figure S49. Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.043

Table S50. Gene #41: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	22	94
DEL PEAK 10(3Q26.31) MUTATED	11	4	1
DEL PEAK 10(3Q26.31) WILD-TYPE	51	18	93

Figure S50. Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

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

Table S51. Gene #43: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 12(4Q22.1) MUTATED	49	16	40
DEL PEAK 12(4Q22.1) WILD-TYPE	16	28	35

Figure S51. Get High-res Image Gene #43: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

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

Table S52. Gene #44: 'del_4q34.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	11	26	31	11
DEL PEAK 13(4Q34.3) MUTATED	32	2	16	16	1
DEL PEAK 13(4Q34.3) WILD-TYPE	14	9	10	15	10

Figure S52. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.055

Table S53. Gene #51: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 20(8P23.2) MUTATED	30	11	49
DEL PEAK 20(8P23.2) WILD-TYPE	35	33	26

Figure S53. Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p12' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.17

Table S54. Gene #52: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 21(8P12) MUTATED	29	7	39
DEL PEAK 21(8P12) WILD-TYPE	36	37	36

Figure S54. Get High-res Image Gene #52: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S55. Gene #54: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 23(9P21.3) MUTATED	46	25	70
DEL PEAK 23(9P21.3) WILD-TYPE	19	19	5

Figure S55. Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S56. Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 25(10P11.21) MUTATED	9	5	38
DEL PEAK 25(10P11.21) WILD-TYPE	56	39	37

Figure S56. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S57. Gene #56: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	32	76
DEL PEAK 25(10P11.21) MUTATED	9	10	33
DEL PEAK 25(10P11.21) WILD-TYPE	67	22	43

Figure S57. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S58. Gene #56: 'del_10p11.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	74	12
DEL PEAK 25(10P11.21) MUTATED	2	32	2
DEL PEAK 25(10P11.21) WILD-TYPE	37	42	10

Figure S58. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S59. Gene #56: 'del_10p11.21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
DEL PEAK 25(10P11.21) MUTATED	10	40	1
DEL PEAK 25(10P11.21) WILD-TYPE	74	47	11

Figure S59. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S60. Gene #56: 'del_10p11.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 25(10P11.21) MUTATED	7	3	27	14
DEL PEAK 25(10P11.21) WILD-TYPE	55	23	35	19

Figure S60. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S61. Gene #56: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	22	94
DEL PEAK 25(10P11.21) MUTATED	7	3	41
DEL PEAK 25(10P11.21) WILD-TYPE	55	19	53

Figure S61. Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S62. Gene #60: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 29(11Q25) MUTATED	24	9	48
DEL PEAK 29(11Q25) WILD-TYPE	41	35	27

Figure S62. Get High-res Image Gene #60: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'CN_CNMF'

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

Table S63. Gene #62: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 31(13Q12.11) MUTATED	24	9	43
DEL PEAK 31(13Q12.11) WILD-TYPE	41	35	32

Figure S63. Get High-res Image Gene #62: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'CN_CNMF'

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

Table S64. Gene #67: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 36(16P13.3) MUTATED	39	10	16
DEL PEAK 36(16P13.3) WILD-TYPE	26	34	59

Figure S64. Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.025

Table S65. Gene #67: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	32	76
DEL PEAK 36(16P13.3) MUTATED	41	8	16
DEL PEAK 36(16P13.3) WILD-TYPE	35	24	60

Figure S65. Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.17

Table S66. Gene #67: 'del_16p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	11	26	31	11
DEL PEAK 36(16P13.3) MUTATED	24	2	6	2	4
DEL PEAK 36(16P13.3) WILD-TYPE	22	9	20	29	7

Figure S66. Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S67. Gene #67: 'del_16p13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
DEL PEAK 36(16P13.3) MUTATED	44	18	2
DEL PEAK 36(16P13.3) WILD-TYPE	40	69	10

Figure S67. Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S68. Gene #67: 'del_16p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 36(16P13.3) MUTATED	37	9	14	4
DEL PEAK 36(16P13.3) WILD-TYPE	25	17	48	29

Figure S68. Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.025

Table S69. Gene #67: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	66	35	11
DEL PEAK 36(16P13.3) MUTATED	38	13	9	3
DEL PEAK 36(16P13.3) WILD-TYPE	28	53	26	8

Figure S69. Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S70. Gene #67: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	22	94
DEL PEAK 36(16P13.3) MUTATED	36	9	18
DEL PEAK 36(16P13.3) WILD-TYPE	26	13	76

Figure S70. Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S71. Gene #68: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 37(16Q23.1) MUTATED	50	18	16
DEL PEAK 37(16Q23.1) WILD-TYPE	15	26	59

Figure S71. Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S72. Gene #68: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	32	76
DEL PEAK 37(16Q23.1) MUTATED	56	11	17
DEL PEAK 37(16Q23.1) WILD-TYPE	20	21	59

Figure S72. Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S73. Gene #68: 'del_16q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	11	26	31	11
DEL PEAK 37(16Q23.1) MUTATED	34	3	5	7	4
DEL PEAK 37(16Q23.1) WILD-TYPE	12	8	21	24	7

Figure S73. Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S74. Gene #68: 'del_16q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	74	12
DEL PEAK 37(16Q23.1) MUTATED	27	18	8
DEL PEAK 37(16Q23.1) WILD-TYPE	12	56	4

Figure S74. Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S75. Gene #68: 'del_16q23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
DEL PEAK 37(16Q23.1) MUTATED	60	22	1
DEL PEAK 37(16Q23.1) WILD-TYPE	24	65	11

Figure S75. Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S76. Gene #68: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 37(16Q23.1) MUTATED	46	16	14	7
DEL PEAK 37(16Q23.1) WILD-TYPE	16	10	48	26

Figure S76. Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S77. Gene #68: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	66	35	11
DEL PEAK 37(16Q23.1) MUTATED	49	17	11	4
DEL PEAK 37(16Q23.1) WILD-TYPE	17	49	24	7

Figure S77. Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S78. Gene #68: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	22	94
DEL PEAK 37(16Q23.1) MUTATED	46	14	21
DEL PEAK 37(16Q23.1) WILD-TYPE	16	8	73

Figure S78. Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.055

Table S79. Gene #69: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 38(17P12) MUTATED	44	19	23
DEL PEAK 38(17P12) WILD-TYPE	21	25	52

Figure S79. Get High-res Image Gene #69: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S80. Gene #69: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	32	76
DEL PEAK 38(17P12) MUTATED	54	10	22
DEL PEAK 38(17P12) WILD-TYPE	22	22	54

Figure S80. Get High-res Image Gene #69: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S81. Gene #69: 'del_17p12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
DEL PEAK 38(17P12) MUTATED	56	29	1
DEL PEAK 38(17P12) WILD-TYPE	28	58	11

Figure S81. Get High-res Image Gene #69: 'del_17p12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S82. Gene #69: 'del_17p12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 38(17P12) MUTATED	41	17	19	9
DEL PEAK 38(17P12) WILD-TYPE	21	9	43	24

Figure S82. Get High-res Image Gene #69: 'del_17p12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S83. Gene #69: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	22	94
DEL PEAK 38(17P12) MUTATED	41	16	28
DEL PEAK 38(17P12) WILD-TYPE	21	6	66

Figure S83. Get High-res Image Gene #69: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S84. Gene #72: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	22	94
DEL PEAK 41(18Q12.2) MUTATED	39	21	49
DEL PEAK 41(18Q12.2) WILD-TYPE	23	1	45

Figure S84. Get High-res Image Gene #72: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

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

Table S85. Gene #75: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 44(19P13.3) MUTATED	43	12	38
DEL PEAK 44(19P13.3) WILD-TYPE	22	32	37

Figure S85. Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S86. Gene #81: 'del_22q11.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	44	75
DEL PEAK 50(22Q11.1) MUTATED	46	13	20
DEL PEAK 50(22Q11.1) WILD-TYPE	19	31	55

Figure S86. Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q11.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S87. Gene #81: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	32	76
DEL PEAK 50(22Q11.1) MUTATED	51	10	18
DEL PEAK 50(22Q11.1) WILD-TYPE	25	22	58

Figure S87. Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q11.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S88. Gene #81: 'del_22q11.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	87	12
DEL PEAK 50(22Q11.1) MUTATED	53	25	1
DEL PEAK 50(22Q11.1) WILD-TYPE	31	62	11

Figure S88. Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_22q11.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S89. Gene #81: 'del_22q11.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 50(22Q11.1) MUTATED	43	11	16	9
DEL PEAK 50(22Q11.1) WILD-TYPE	19	15	46	24

Figure S89. Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_22q11.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S90. Gene #81: 'del_22q11.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	66	35	11
DEL PEAK 50(22Q11.1) MUTATED	48	19	7	3
DEL PEAK 50(22Q11.1) WILD-TYPE	18	47	28	8

Figure S90. Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_22q11.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S91. Gene #81: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	22	94
DEL PEAK 50(22Q11.1) MUTATED	44	9	24
DEL PEAK 50(22Q11.1) WILD-TYPE	18	13	70

Figure S91. Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = ESCA-TP.transferedmergedcluster.txt
Number of patients = 184
Number of significantly focal cnvs = 85
Number of molecular subtypes = 8
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

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

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

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