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 78 focal events and 10 molecular subtypes across 351 patients, 315 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p36.22 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q42.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q27.1 cnv correlated to 'CN_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q21 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_7q21.2 cnv correlated to 'CN_CNMF'.
amp_8p23.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_9p24.1 cnv correlated to 'CN_CNMF'.
amp_9q34.3 cnv correlated to 'CN_CNMF'.
amp_10p11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10q22.2 cnv correlated to 'CN_CNMF'.
amp_10q26.13 cnv correlated to 'CN_CNMF'.
amp_11p13 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_12p12.1 cnv correlated to 'CN_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF'.
amp_13q12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF'.
amp_19p13.2 cnv correlated to 'CN_CNMF'.
amp_19q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq27.3 cnv correlated to 'CN_CNMF'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_2q37.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p26.1 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_6q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_6q26 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_7q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_7q36.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q21.11 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q22.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.4 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_11q23.2 cnv correlated to 'CN_CNMF'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q12.11 cnv correlated to 'CN_CNMF'.
del_14q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q32.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q24.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_21q22.13 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF'.
del_xq21.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 78 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 315 significant findings detected.


		Clinical Features	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	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 1q21 3	129 (37%)	222	1.32e-25 (1.02e-22)	6.27e-10 (4.42e-07)	0.0339 (1.00)	0.0131 (1.00)	1.12e-12 (8.19e-10)	1.23e-07 (8.14e-05)	7.76e-12 (5.6e-09)	6.56e-07 (0.000425)	3.07e-07 (2e-04)	5.75e-08 (3.84e-05)
amp 5p15 33	98 (28%)	253	7.96e-21 (6.12e-18)	4.51e-09 (3.13e-06)	0.132 (1.00)	0.396 (1.00)	4.13e-10 (2.92e-07)	3.56e-06 (0.00222)	6.17e-06 (0.00377)	6.63e-07 (0.000428)	0.000162 (0.0834)	1.37e-08 (9.4e-06)
del 4p16 3	135 (38%)	216	5.25e-13 (3.85e-10)	0.000237 (0.12)	0.453 (1.00)	0.0279 (1.00)	1.05e-05 (0.0063)	3.66e-05 (0.0208)	2.42e-06 (0.00153)	4.26e-08 (2.87e-05)	0.000237 (0.12)	9.59e-08 (6.36e-05)
del 5q11 2	129 (37%)	222	9.41e-26 (7.33e-23)	4.73e-15 (3.56e-12)	0.241 (1.00)	0.428 (1.00)	5.1e-13 (3.75e-10)	3.3e-12 (2.39e-09)	9.63e-11 (6.87e-08)	1.21e-11 (8.71e-09)	2.67e-08 (1.81e-05)	5.64e-15 (4.24e-12)
del 5q23 2	116 (33%)	235	1.65e-25 (1.28e-22)	1.19e-14 (8.9e-12)	0.119 (1.00)	0.462 (1.00)	4.2e-13 (3.09e-10)	5.96e-11 (4.26e-08)	1.56e-11 (1.12e-08)	3.75e-10 (2.66e-07)	9.47e-08 (6.3e-05)	1.8e-12 (1.31e-09)
del 15q15 1	97 (28%)	254	3.9e-13 (2.88e-10)	2.99e-07 (0.000195)	0.00369 (1.00)	0.0583 (1.00)	5.63e-08 (3.77e-05)	1.32e-08 (9.09e-06)	4.07e-06 (0.00253)	9.6e-09 (6.61e-06)	6.81e-05 (0.0374)	9.82e-07 (0.000632)
del 16p13 3	71 (20%)	280	3.99e-14 (2.98e-11)	0.000467 (0.22)	0.698 (1.00)	0.955 (1.00)	8.06e-09 (5.6e-06)	2.34e-09 (1.64e-06)	4.25e-06 (0.00263)	1.72e-05 (0.0101)	1.02e-06 (0.000657)	2.43e-06 (0.00153)
del 17p12	134 (38%)	217	7.04e-25 (5.47e-22)	1.34e-14 (1e-11)	0.398 (1.00)	0.889 (1.00)	9.4e-09 (6.49e-06)	5.58e-08 (3.75e-05)	9.94e-06 (0.00596)	4.36e-08 (2.93e-05)	0.000114 (0.0598)	4.31e-11 (3.08e-08)
del 19p13 3	123 (35%)	228	3.92e-29 (3.06e-26)	5.67e-14 (4.22e-11)	0.0021 (0.887)	0.348 (1.00)	4.46e-17 (3.38e-14)	8.76e-19 (6.68e-16)	2.64e-09 (1.84e-06)	1.21e-21 (9.35e-19)	4.78e-05 (0.0268)	1.22e-19 (9.36e-17)
amp 1q42 3	117 (33%)	234	1.81e-16 (1.37e-13)	2.73e-05 (0.0156)	0.398 (1.00)	0.736 (1.00)	3.41e-08 (2.31e-05)	9.18e-05 (0.0495)	9.75e-09 (6.71e-06)	1.25e-07 (8.27e-05)	0.00109 (0.482)	1.6e-07 (0.000105)
amp 5p13 1	98 (28%)	253	7.96e-21 (6.12e-18)	3.08e-06 (0.00193)	0.716 (1.00)	0.923 (1.00)	8.75e-09 (6.05e-06)	3.9e-05 (0.022)	1.8e-05 (0.0105)	3.5e-06 (0.00219)	0.00422 (1.00)	2.16e-06 (0.00137)
amp 6q12	69 (20%)	282	9.95e-13 (7.27e-10)	5.33e-07 (0.000346)	0.0656 (1.00)	0.283 (1.00)	2.21e-05 (0.0127)	4.29e-05 (0.0242)	0.000226 (0.114)	7.84e-05 (0.0427)	0.00279 (1.00)	4.6e-05 (0.0258)
amp 13q22 1	141 (40%)	210	3.51e-15 (2.65e-12)	1.65e-05 (0.00975)	0.195 (1.00)	0.23 (1.00)	1.26e-05 (0.00748)	0.002 (0.848)	1.21e-05 (0.0072)	9.2e-06 (0.00552)	0.000477 (0.224)	2.47e-08 (1.68e-05)
amp 19q12	108 (31%)	243	3.93e-22 (3.03e-19)	1.88e-08 (1.28e-05)	0.00609 (1.00)	0.161 (1.00)	3.26e-14 (2.43e-11)	3.34e-08 (2.26e-05)	2.46e-07 (0.000161)	1.37e-13 (1.02e-10)	0.0384 (1.00)	1.87e-13 (1.38e-10)
amp 20q13 2	233 (66%)	118	1.58e-21 (1.22e-18)	5.46e-10 (3.85e-07)	0.00634 (1.00)	0.929 (1.00)	5.66e-08 (3.79e-05)	2.76e-05 (0.0158)	1.08e-07 (7.13e-05)	4.55e-12 (3.3e-09)	0.0109 (1.00)	1.23e-10 (8.73e-08)
del 1p36 11	100 (28%)	251	1.18e-14 (8.86e-12)	3.2e-10 (2.27e-07)	0.157 (1.00)	0.235 (1.00)	0.00033 (0.16)	0.000108 (0.057)	7.46e-06 (0.00451)	1.4e-06 (0.000891)	0.00267 (1.00)	7.85e-06 (0.00472)
del 4q34 3	155 (44%)	196	1.86e-21 (1.43e-18)	1.1e-06 (0.000702)	0.051 (1.00)	0.572 (1.00)	1.24e-05 (0.00737)	2.78e-05 (0.0159)	5.03e-06 (0.00309)	2.98e-07 (0.000195)	0.0044 (1.00)	2.67e-07 (0.000175)
del 7q36 3	75 (21%)	276	9.59e-21 (7.34e-18)	9.73e-05 (0.0521)	0.388 (1.00)	0.8 (1.00)	3.17e-06 (0.00199)	5.43e-06 (0.00333)	9.78e-05 (0.0522)	8.16e-07 (0.000526)	0.0021 (0.887)	6.52e-06 (0.00397)
del 9p21 3	145 (41%)	206	4.32e-23 (3.35e-20)	3.78e-07 (0.000246)	4.93e-05 (0.0276)	0.0227 (1.00)	2.56e-09 (1.78e-06)	1.73e-05 (0.0101)	0.012 (1.00)	0.000442 (0.21)	0.172 (1.00)	3.78e-06 (0.00235)
amp 6p21 1	95 (27%)	256	2.03e-19 (1.55e-16)	1.54e-12 (1.12e-09)	0.338 (1.00)	0.228 (1.00)	0.000387 (0.186)	0.000607 (0.28)	0.000106 (0.056)	5.2e-05 (0.029)	0.00225 (0.94)	1.47e-06 (0.000936)
amp 17q12	110 (31%)	241	1.23e-18 (9.37e-16)	9.01e-08 (6e-05)	0.78 (1.00)	0.541 (1.00)	0.000106 (0.056)	0.000293 (0.145)	2.85e-06 (0.00179)	0.0004 (0.191)	0.0477 (1.00)	0.00102 (0.456)
del 3p14 2	127 (36%)	224	1.98e-09 (1.39e-06)	1.28e-05 (0.00755)	0.402 (1.00)	0.904 (1.00)	9.21e-05 (0.0496)	3.72e-05 (0.0211)	0.000311 (0.152)	0.00277 (1.00)	0.063 (1.00)	3e-05 (0.0171)
del 8p23 2	93 (26%)	258	1.85e-14 (1.38e-11)	0.000243 (0.122)	0.0619 (1.00)	0.283 (1.00)	7.1e-06 (0.00431)	4.9e-06 (0.00301)	0.00421 (1.00)	1.07e-06 (0.000687)	0.0169 (1.00)	1.77e-06 (0.00112)
del 10q23 31	84 (24%)	267	1.46e-13 (1.08e-10)	9.26e-05 (0.0497)	0.0655 (1.00)	0.332 (1.00)	8.64e-07 (0.000556)	0.00215 (0.904)	5.47e-05 (0.0304)	0.000116 (0.061)	0.0934 (1.00)	0.000316 (0.155)
del 14q12	91 (26%)	260	3.46e-12 (2.51e-09)	5.54e-05 (0.0307)	0.584 (1.00)	0.755 (1.00)	0.000346 (0.167)	0.000165 (0.0847)	0.000176 (0.0898)	0.00141 (0.611)	0.0136 (1.00)	0.000104 (0.0552)
del 19q13 11	53 (15%)	298	6.94e-10 (4.89e-07)	8.11e-09 (5.62e-06)	0.204 (1.00)	0.499 (1.00)	0.000121 (0.0633)	0.000999 (0.447)	7.92e-05 (0.043)	2.45e-05 (0.0141)	0.00112 (0.493)	0.000128 (0.0665)
del 22q13 31	122 (35%)	229	4.52e-19 (3.45e-16)	4.96e-08 (3.33e-05)	0.0489 (1.00)	0.503 (1.00)	0.000837 (0.379)	0.000159 (0.0821)	7.85e-05 (0.0427)	7.48e-08 (4.99e-05)	0.0274 (1.00)	4.38e-06 (0.00271)
amp 10p11 22	95 (27%)	256	1.84e-13 (1.36e-10)	1.78e-06 (0.00113)	0.144 (1.00)	0.607 (1.00)	0.000641 (0.294)	0.00224 (0.935)	5.11e-05 (0.0286)	0.000436 (0.207)	0.00447 (1.00)	0.000256 (0.128)
amp 13q12 3	136 (39%)	215	4.58e-15 (3.45e-12)	6.28e-05 (0.0347)	0.323 (1.00)	0.545 (1.00)	0.0152 (1.00)	0.217 (1.00)	0.000165 (0.0844)	0.000534 (0.249)	0.0136 (1.00)	3.81e-05 (0.0216)
del 2q37 2	53 (15%)	298	0.000208 (0.106)	0.00046 (0.217)	0.268 (1.00)	0.124 (1.00)	0.00458 (1.00)	0.264 (1.00)	0.000516 (0.241)	7.7e-06 (0.00464)	0.103 (1.00)	1.48e-05 (0.00872)
del 3q26 31	43 (12%)	308	3.84e-06 (0.00239)	1.77e-05 (0.0103)	0.128 (1.00)	0.456 (1.00)	0.000338 (0.163)	0.000495 (0.232)	0.000128 (0.0667)	0.00988 (1.00)	0.0127 (1.00)	0.0166 (1.00)
del 4q22 1	153 (44%)	198	2.03e-22 (1.57e-19)	6.2e-06 (0.00378)	0.11 (1.00)	0.329 (1.00)	0.00239 (0.98)	0.000324 (0.158)	0.00239 (0.98)	9e-05 (0.0487)	0.11 (1.00)	2.13e-05 (0.0123)
del 9p23	149 (42%)	202	2.87e-22 (2.22e-19)	6.81e-05 (0.0374)	0.0281 (1.00)	0.208 (1.00)	4.43e-06 (0.00273)	0.000217 (0.11)	0.0111 (1.00)	0.0023 (0.952)	0.559 (1.00)	6.44e-05 (0.0355)
del 12p13 1	54 (15%)	297	1.77e-13 (1.31e-10)	2.98e-08 (2.02e-05)	0.519 (1.00)	1 (1.00)	2.96e-06 (0.00186)	6.3e-07 (0.000409)	0.0605 (1.00)	0.0281 (1.00)	0.129 (1.00)	0.000293 (0.145)
amp 7p22 1	180 (51%)	171	5.49e-16 (4.15e-13)	6.36e-06 (0.00387)	0.627 (1.00)	0.89 (1.00)	0.000192 (0.0976)	0.00749 (1.00)	0.0518 (1.00)	0.0095 (1.00)	0.00946 (1.00)	2.42e-05 (0.0139)
amp 15q26 1	83 (24%)	268	6.18e-16 (4.68e-13)	1.95e-05 (0.0113)	0.447 (1.00)	0.697 (1.00)	1.88e-05 (0.0109)	4.33e-06 (0.00268)	0.0071 (1.00)	0.0123 (1.00)	0.0109 (1.00)	0.00366 (1.00)
del 6p25 3	85 (24%)	266	2.46e-09 (1.72e-06)	4.37e-05 (0.0246)	0.134 (1.00)	0.0903 (1.00)	9.48e-05 (0.0508)	1.81e-05 (0.0105)	0.00225 (0.94)	0.000616 (0.284)	0.0288 (1.00)	0.0112 (1.00)
del 11p15 4	74 (21%)	277	6.05e-13 (4.43e-10)	5.26e-05 (0.0293)	1.84e-06 (0.00116)	0.00166 (0.716)	0.000739 (0.339)	7.66e-05 (0.0418)	0.179 (1.00)	0.00575 (1.00)	0.498 (1.00)	0.00313 (1.00)
del 16q23 1	141 (40%)	210	1.46e-08 (9.97e-06)	0.0125 (1.00)	0.464 (1.00)	0.135 (1.00)	0.00161 (0.692)	0.000112 (0.0589)	0.00105 (0.467)	0.00468 (1.00)	0.000296 (0.146)	0.000121 (0.0631)
del 18q21 2	162 (46%)	189	2.59e-18 (1.97e-15)	0.000115 (0.0603)	0.662 (1.00)	0.472 (1.00)	0.000324 (0.158)	0.00235 (0.97)	0.000296 (0.146)	0.0131 (1.00)	0.0114 (1.00)	0.0219 (1.00)
del 21q11 2	130 (37%)	221	4.06e-11 (2.91e-08)	3.86e-05 (0.0218)	0.34 (1.00)	0.194 (1.00)	0.00169 (0.725)	1.26e-06 (0.000806)	0.000337 (0.163)	0.00724 (1.00)	0.0043 (1.00)	0.00599 (1.00)
del xp22 2	66 (19%)	285	2.44e-11 (1.75e-08)	7.96e-05 (0.0431)	0.349 (1.00)	0.859 (1.00)	0.000284 (0.141)	0.0294 (1.00)	0.0545 (1.00)	0.000102 (0.0541)	0.34 (1.00)	0.0249 (1.00)
amp 6q21	64 (18%)	287	1.01e-07 (6.67e-05)	0.0014 (0.608)	0.369 (1.00)	0.899 (1.00)	0.000578 (0.268)	2.66e-05 (0.0153)	0.00279 (1.00)	0.00257 (1.00)	0.00199 (0.848)	0.00031 (0.152)
amp 8q24 21	244 (70%)	107	2.01e-07 (0.000132)	0.000824 (0.374)	0.37 (1.00)	0.159 (1.00)	0.00749 (1.00)	0.00856 (1.00)	0.00142 (0.614)	0.000474 (0.223)	0.000123 (0.064)	0.0012 (0.525)
amp 11q13 3	85 (24%)	266	2.06e-09 (1.44e-06)	0.0122 (1.00)	0.186 (1.00)	0.769 (1.00)	0.107 (1.00)	0.00236 (0.973)	5.62e-06 (0.00344)	0.00204 (0.861)	7e-05 (0.0384)	0.0176 (1.00)
del 1p13 2	70 (20%)	281	9.61e-13 (7.03e-10)	1.03e-06 (0.000662)	0.0777 (1.00)	0.191 (1.00)	0.000628 (0.289)	0.000431 (0.205)	0.00167 (0.716)	0.00264 (1.00)	0.397 (1.00)	0.00922 (1.00)
del 3p26 1	109 (31%)	242	1.02e-11 (7.37e-09)	0.000772 (0.352)	0.338 (1.00)	0.693 (1.00)	0.00627 (1.00)	0.00123 (0.536)	0.000329 (0.16)	0.000569 (0.264)	0.0112 (1.00)	0.000163 (0.0839)
del 6q14 1	69 (20%)	282	2.5e-08 (1.7e-05)	0.000375 (0.18)	0.218 (1.00)	0.861 (1.00)	0.000425 (0.203)	0.0781 (1.00)	0.811 (1.00)	0.0263 (1.00)	0.767 (1.00)	0.0222 (1.00)
del 7q31 1	50 (14%)	301	8.11e-09 (5.62e-06)	6.99e-06 (0.00424)	0.711 (1.00)	0.647 (1.00)	0.00447 (1.00)	0.013 (1.00)	0.00821 (1.00)	0.0342 (1.00)	5.89e-05 (0.0326)	0.0679 (1.00)
del 14q32 33	102 (29%)	249	1.56e-10 (1.11e-07)	0.00014 (0.0723)	0.977 (1.00)	0.378 (1.00)	0.000557 (0.259)	7.45e-06 (0.00451)	0.0102 (1.00)	0.0413 (1.00)	0.00291 (1.00)	0.000878 (0.396)
amp 1p36 22	48 (14%)	303	1.01e-09 (7.12e-07)	0.0108 (1.00)	0.506 (1.00)	0.118 (1.00)	0.000237 (0.12)	0.0991 (1.00)	0.339 (1.00)	0.0505 (1.00)	0.258 (1.00)	0.0375 (1.00)
amp 7p11 2	163 (46%)	188	2.78e-12 (2.02e-09)	0.000243 (0.122)	0.899 (1.00)	0.931 (1.00)	0.0417 (1.00)	0.137 (1.00)	0.138 (1.00)	0.205 (1.00)	0.045 (1.00)	0.00908 (1.00)
amp 8p23 1	141 (40%)	210	9.11e-05 (0.0492)	0.00017 (0.0868)	0.595 (1.00)	0.585 (1.00)	0.061 (1.00)	0.00517 (1.00)	0.838 (1.00)	0.111 (1.00)	0.183 (1.00)	0.00958 (1.00)
amp 11p13	66 (19%)	285	0.00292 (1.00)	0.0243 (1.00)	0.642 (1.00)	0.263 (1.00)	0.000954 (0.428)	1.15e-05 (0.00686)	0.00483 (1.00)	0.000105 (0.0556)	0.131 (1.00)	0.00287 (1.00)
del 6q26	77 (22%)	274	5.42e-07 (0.000352)	0.00948 (1.00)	0.771 (1.00)	0.227 (1.00)	0.00104 (0.46)	0.000265 (0.132)	0.494 (1.00)	0.0181 (1.00)	0.221 (1.00)	0.145 (1.00)
del 9q21 11	90 (26%)	261	4.08e-13 (3.01e-10)	0.00366 (1.00)	0.141 (1.00)	0.125 (1.00)	0.00109 (0.481)	0.0187 (1.00)	0.000811 (0.369)	0.00359 (1.00)	0.0518 (1.00)	1.74e-05 (0.0102)
del 10q22 3	56 (16%)	295	3.41e-11 (2.44e-08)	0.0248 (1.00)	0.73 (1.00)	0.761 (1.00)	0.000151 (0.0783)	0.00238 (0.977)	0.00125 (0.544)	0.00676 (1.00)	0.0678 (1.00)	0.013 (1.00)
del 17q24 3	64 (18%)	287	1.36e-08 (9.31e-06)	2.29e-05 (0.0132)	0.183 (1.00)	0.448 (1.00)	0.00121 (0.528)	0.00398 (1.00)	0.00279 (1.00)	0.00517 (1.00)	0.0236 (1.00)	0.00548 (1.00)
del 21q22 13	142 (40%)	209	4.24e-13 (3.12e-10)	0.00561 (1.00)	0.103 (1.00)	0.44 (1.00)	0.00155 (0.668)	4.77e-06 (0.00294)	0.00226 (0.94)	0.00102 (0.456)	0.0143 (1.00)	0.0033 (1.00)
del xq21 33	45 (13%)	306	7.28e-05 (0.0398)	0.000413 (0.198)	0.797 (1.00)	0.765 (1.00)	0.00774 (1.00)	0.0122 (1.00)	0.0158 (1.00)	0.0974 (1.00)	0.0318 (1.00)	0.0508 (1.00)
amp 3q27 1	123 (35%)	228	1.06e-07 (7e-05)	0.000865 (0.391)	0.95 (1.00)	0.0926 (1.00)	0.315 (1.00)	0.852 (1.00)	0.256 (1.00)	0.0111 (1.00)	0.252 (1.00)	0.005 (1.00)
amp 7q21 2	159 (45%)	192	5.87e-12 (4.25e-09)	0.000771 (0.352)	0.2 (1.00)	0.98 (1.00)	0.511 (1.00)	0.297 (1.00)	0.198 (1.00)	0.104 (1.00)	0.082 (1.00)	0.0373 (1.00)
amp 9p24 1	55 (16%)	296	6.18e-05 (0.0342)	0.443 (1.00)	0.622 (1.00)	0.0211 (1.00)	0.14 (1.00)	0.0176 (1.00)	0.1 (1.00)	0.0691 (1.00)	0.103 (1.00)	0.397 (1.00)
amp 9q34 3	93 (26%)	258	0.000257 (0.128)	0.109 (1.00)	0.722 (1.00)	0.217 (1.00)	0.033 (1.00)	0.00369 (1.00)	0.183 (1.00)	0.371 (1.00)	0.00679 (1.00)	0.0822 (1.00)
amp 10q22 2	66 (19%)	285	1.38e-09 (9.71e-07)	0.00885 (1.00)	0.0276 (1.00)	0.474 (1.00)	0.0129 (1.00)	0.0117 (1.00)	0.0404 (1.00)	0.143 (1.00)	0.0895 (1.00)	0.0335 (1.00)
amp 10q26 13	71 (20%)	280	1.29e-05 (0.00762)	0.00636 (1.00)	0.0373 (1.00)	0.554 (1.00)	0.00393 (1.00)	0.00788 (1.00)	0.185 (1.00)	0.0626 (1.00)	1 (1.00)	0.0286 (1.00)
amp 12p12 1	105 (30%)	246	7.47e-06 (0.00451)	0.164 (1.00)	0.423 (1.00)	0.0623 (1.00)	0.184 (1.00)	0.642 (1.00)	0.0452 (1.00)	0.0911 (1.00)	0.0126 (1.00)	0.25 (1.00)
amp 12q15	91 (26%)	260	2e-05 (0.0116)	0.442 (1.00)	0.211 (1.00)	0.428 (1.00)	0.263 (1.00)	0.509 (1.00)	0.484 (1.00)	0.0957 (1.00)	0.136 (1.00)	0.544 (1.00)
amp 18q11 2	112 (32%)	239	3.79e-10 (2.68e-07)	0.00686 (1.00)	0.292 (1.00)	0.0782 (1.00)	0.0133 (1.00)	0.0266 (1.00)	0.0018 (0.768)	0.00103 (0.459)	0.0218 (1.00)	0.00901 (1.00)
amp 19p13 2	40 (11%)	311	0.000446 (0.211)	0.138 (1.00)	0.869 (1.00)	0.326 (1.00)	0.729 (1.00)	0.829 (1.00)	0.738 (1.00)	0.594 (1.00)	0.878 (1.00)	0.258 (1.00)
amp xq27 3	67 (19%)	284	0.000291 (0.144)	0.00176 (0.753)	0.586 (1.00)	0.167 (1.00)	0.176 (1.00)	0.345 (1.00)	0.0301 (1.00)	0.97 (1.00)	0.043 (1.00)	0.149 (1.00)
del 11q23 2	75 (21%)	276	1.23e-05 (0.00732)	0.0105 (1.00)	0.567 (1.00)	0.727 (1.00)	0.00222 (0.93)	0.531 (1.00)	0.182 (1.00)	0.0745 (1.00)	0.301 (1.00)	0.0873 (1.00)
del 13q12 11	50 (14%)	301	1.44e-08 (9.88e-06)	0.0998 (1.00)	0.413 (1.00)	0.138 (1.00)	0.0461 (1.00)	0.0245 (1.00)	0.346 (1.00)	0.159 (1.00)	0.533 (1.00)	0.0583 (1.00)
del xp21 1	63 (18%)	288	3.48e-08 (2.35e-05)	0.0186 (1.00)	0.0922 (1.00)	0.574 (1.00)	0.0243 (1.00)	0.0793 (1.00)	0.576 (1.00)	0.185 (1.00)	0.444 (1.00)	0.355 (1.00)
amp 9p13 3	66 (19%)	285	0.00345 (1.00)	0.224 (1.00)	0.263 (1.00)	0.621 (1.00)	0.0193 (1.00)	0.0206 (1.00)	0.0135 (1.00)	0.474 (1.00)	0.101 (1.00)	0.311 (1.00)
del 1q44	27 (8%)	324	0.0225 (1.00)	0.00543 (1.00)	0.176 (1.00)	0.0243 (1.00)	0.35 (1.00)	0.0143 (1.00)	0.00909 (1.00)	0.0155 (1.00)	0.0102 (1.00)	0.0929 (1.00)
del 2q32 1	49 (14%)	302	0.0105 (1.00)	0.066 (1.00)	0.462 (1.00)	0.116 (1.00)	0.11 (1.00)	0.683 (1.00)	0.0456 (1.00)	0.00392 (1.00)	0.471 (1.00)	0.0158 (1.00)
del 20p12 1	28 (8%)	323	0.00583 (1.00)	0.00092 (0.414)	0.644 (1.00)	1 (1.00)	0.00917 (1.00)	0.0679 (1.00)	0.00321 (1.00)	0.173 (1.00)	0.482 (1.00)	0.0401 (1.00)

'amp_1p36.22' versus 'CN_CNMF'

P value = 1.01e-09 (Chi-square test), Q value = 7.1e-07

Table S1. Gene #1: 'amp_1p36.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 1(1P36.22) MUTATED	2	3	15	2	26
AMP PEAK 1(1P36.22) WILD-TYPE	157	30	47	10	59

Figure S1. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p36.22' versus 'MRNASEQ_CNMF'

P value = 0.000237 (Chi-square test), Q value = 0.12

Table S2. Gene #1: 'amp_1p36.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 1(1P36.22) MUTATED	2	2	6	6	16
AMP PEAK 1(1P36.22) WILD-TYPE	63	60	40	31	46

Figure S2. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1.32e-25 (Chi-square test), Q value = 1e-22

Table S3. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 2(1Q21.3) MUTATED	13	12	31	8	65
AMP PEAK 2(1Q21.3) WILD-TYPE	146	21	31	4	20

Figure S3. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 6.27e-10 (Fisher's exact test), Q value = 4.4e-07

Table S4. Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 2(1Q21.3) MUTATED	35	55	22
AMP PEAK 2(1Q21.3) WILD-TYPE	78	29	84

Figure S4. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 1.12e-12 (Chi-square test), Q value = 8.2e-10

Table S5. Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 2(1Q21.3) MUTATED	12	10	16	13	47
AMP PEAK 2(1Q21.3) WILD-TYPE	53	52	30	24	15

Figure S5. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.23e-07 (Fisher's exact test), Q value = 8.1e-05

Table S6. Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
AMP PEAK 2(1Q21.3) MUTATED	42	40	16
AMP PEAK 2(1Q21.3) WILD-TYPE	27	73	74

Figure S6. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 7.76e-12 (Fisher's exact test), Q value = 5.6e-09

Table S7. Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
AMP PEAK 2(1Q21.3) MUTATED	25	21	72
AMP PEAK 2(1Q21.3) WILD-TYPE	80	80	43

Figure S7. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.56e-07 (Fisher's exact test), Q value = 0.00042

Table S8. Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 2(1Q21.3) MUTATED	27	50	41
AMP PEAK 2(1Q21.3) WILD-TYPE	75	31	97

Figure S8. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.07e-07 (Fisher's exact test), Q value = 2e-04

Table S9. Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
AMP PEAK 2(1Q21.3) MUTATED	15	70	16
AMP PEAK 2(1Q21.3) WILD-TYPE	49	61	63

Figure S9. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.75e-08 (Fisher's exact test), Q value = 3.8e-05

Table S10. Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
AMP PEAK 2(1Q21.3) MUTATED	42	43	16
AMP PEAK 2(1Q21.3) WILD-TYPE	22	86	65

Figure S10. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q42.3' versus 'CN_CNMF'

P value = 1.81e-16 (Chi-square test), Q value = 1.4e-13

Table S11. Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 3(1Q42.3) MUTATED	18	14	22	7	56
AMP PEAK 3(1Q42.3) WILD-TYPE	141	19	40	5	29

Figure S11. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.3' versus 'METHLYATION_CNMF'

P value = 2.73e-05 (Fisher's exact test), Q value = 0.016

Table S12. Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 3(1Q42.3) MUTATED	31	45	25
AMP PEAK 3(1Q42.3) WILD-TYPE	82	39	81

Figure S12. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CNMF'

P value = 3.41e-08 (Chi-square test), Q value = 2.3e-05

Table S13. Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 3(1Q42.3) MUTATED	13	13	12	12	41
AMP PEAK 3(1Q42.3) WILD-TYPE	52	49	34	25	21

Figure S13. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.18e-05 (Fisher's exact test), Q value = 0.049

Table S14. Gene #3: 'amp_1q42.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
AMP PEAK 3(1Q42.3) MUTATED	37	35	19
AMP PEAK 3(1Q42.3) WILD-TYPE	32	78	71

Figure S14. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_CNMF'

P value = 9.75e-09 (Fisher's exact test), Q value = 6.7e-06

Table S15. Gene #3: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
AMP PEAK 3(1Q42.3) MUTATED	20	26	64
AMP PEAK 3(1Q42.3) WILD-TYPE	85	75	51

Figure S15. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q42.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-07 (Fisher's exact test), Q value = 8.3e-05

Table S16. Gene #3: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 3(1Q42.3) MUTATED	27	49	34
AMP PEAK 3(1Q42.3) WILD-TYPE	75	32	104

Figure S16. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.6e-07 (Fisher's exact test), Q value = 0.00011

Table S17. Gene #3: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
AMP PEAK 3(1Q42.3) MUTATED	41	36	18
AMP PEAK 3(1Q42.3) WILD-TYPE	23	93	63

Figure S17. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q27.1' versus 'CN_CNMF'

P value = 1.06e-07 (Chi-square test), Q value = 7e-05

Table S18. Gene #4: 'amp_3q27.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 4(3Q27.1) MUTATED	32	8	33	7	43
AMP PEAK 4(3Q27.1) WILD-TYPE	127	25	29	5	42

Figure S18. Get High-res Image Gene #4: 'amp_3q27.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 7.96e-21 (Chi-square test), Q value = 6.1e-18

Table S19. Gene #5: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 5(5P15.33) MUTATED	13	8	17	2	58
AMP PEAK 5(5P15.33) WILD-TYPE	146	25	45	10	27

Figure S19. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 4.51e-09 (Fisher's exact test), Q value = 3.1e-06

Table S20. Gene #5: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 5(5P15.33) MUTATED	20	46	19
AMP PEAK 5(5P15.33) WILD-TYPE	93	38	87

Figure S20. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 4.13e-10 (Chi-square test), Q value = 2.9e-07

Table S21. Gene #5: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 5(5P15.33) MUTATED	11	6	10	10	38
AMP PEAK 5(5P15.33) WILD-TYPE	54	56	36	27	24

Figure S21. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.56e-06 (Fisher's exact test), Q value = 0.0022

Table S22. Gene #5: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
AMP PEAK 5(5P15.33) MUTATED	34	29	12
AMP PEAK 5(5P15.33) WILD-TYPE	35	84	78

Figure S22. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 6.17e-06 (Fisher's exact test), Q value = 0.0038

Table S23. Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
AMP PEAK 5(5P15.33) MUTATED	23	16	51
AMP PEAK 5(5P15.33) WILD-TYPE	82	85	64

Figure S23. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.63e-07 (Fisher's exact test), Q value = 0.00043

Table S24. Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 5(5P15.33) MUTATED	21	42	27
AMP PEAK 5(5P15.33) WILD-TYPE	81	39	111

Figure S24. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.083

Table S25. Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
AMP PEAK 5(5P15.33) MUTATED	20	48	9
AMP PEAK 5(5P15.33) WILD-TYPE	44	83	70

Figure S25. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.37e-08 (Fisher's exact test), Q value = 9.4e-06

Table S26. Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
AMP PEAK 5(5P15.33) MUTATED	37	29	11
AMP PEAK 5(5P15.33) WILD-TYPE	27	100	70

Figure S26. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p13.1' versus 'CN_CNMF'

P value = 7.96e-21 (Chi-square test), Q value = 6.1e-18

Table S27. Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 6(5P13.1) MUTATED	13	8	17	2	58
AMP PEAK 6(5P13.1) WILD-TYPE	146	25	45	10	27

Figure S27. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p13.1' versus 'METHLYATION_CNMF'

P value = 3.08e-06 (Fisher's exact test), Q value = 0.0019

Table S28. Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 6(5P13.1) MUTATED	23	41	19
AMP PEAK 6(5P13.1) WILD-TYPE	90	43	87

Figure S28. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CNMF'

P value = 8.75e-09 (Chi-square test), Q value = 6e-06

Table S29. Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 6(5P13.1) MUTATED	11	8	10	9	37
AMP PEAK 6(5P13.1) WILD-TYPE	54	54	36	28	25

Figure S29. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.9e-05 (Fisher's exact test), Q value = 0.022

Table S30. Gene #6: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
AMP PEAK 6(5P13.1) MUTATED	33	28	14
AMP PEAK 6(5P13.1) WILD-TYPE	36	85	76

Figure S30. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_CNMF'

P value = 1.8e-05 (Fisher's exact test), Q value = 0.011

Table S31. Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
AMP PEAK 6(5P13.1) MUTATED	21	19	51
AMP PEAK 6(5P13.1) WILD-TYPE	84	82	64

Figure S31. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.5e-06 (Fisher's exact test), Q value = 0.0022

Table S32. Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 6(5P13.1) MUTATED	23	41	27
AMP PEAK 6(5P13.1) WILD-TYPE	79	40	111

Figure S32. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.16e-06 (Fisher's exact test), Q value = 0.0014

Table S33. Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
AMP PEAK 6(5P13.1) MUTATED	34	29	13
AMP PEAK 6(5P13.1) WILD-TYPE	30	100	68

Figure S33. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 2.03e-19 (Chi-square test), Q value = 1.5e-16

Table S34. Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 7(6P21.1) MUTATED	7	11	21	4	52
AMP PEAK 7(6P21.1) WILD-TYPE	152	22	41	8	33

Figure S34. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1.54e-12 (Fisher's exact test), Q value = 1.1e-09

Table S35. Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 7(6P21.1) MUTATED	22	47	10
AMP PEAK 7(6P21.1) WILD-TYPE	91	37	96

Figure S35. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.000387 (Chi-square test), Q value = 0.19

Table S36. Gene #7: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 7(6P21.1) MUTATED	10	11	10	11	29
AMP PEAK 7(6P21.1) WILD-TYPE	55	51	36	26	33

Figure S36. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 0.000106 (Fisher's exact test), Q value = 0.056

Table S37. Gene #7: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
AMP PEAK 7(6P21.1) MUTATED	24	15	46
AMP PEAK 7(6P21.1) WILD-TYPE	81	86	69

Figure S37. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.2e-05 (Fisher's exact test), Q value = 0.029

Table S38. Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 7(6P21.1) MUTATED	18	37	30
AMP PEAK 7(6P21.1) WILD-TYPE	84	44	108

Figure S38. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.47e-06 (Fisher's exact test), Q value = 0.00094

Table S39. Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
AMP PEAK 7(6P21.1) MUTATED	32	28	10
AMP PEAK 7(6P21.1) WILD-TYPE	32	101	71

Figure S39. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

P value = 9.95e-13 (Chi-square test), Q value = 7.3e-10

Table S40. Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 8(6Q12) MUTATED	8	6	12	3	40
AMP PEAK 8(6Q12) WILD-TYPE	151	27	50	9	45

Figure S40. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 5.33e-07 (Fisher's exact test), Q value = 0.00035

Table S41. Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 8(6Q12) MUTATED	14	32	9
AMP PEAK 8(6Q12) WILD-TYPE	99	52	97

Figure S41. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 2.21e-05 (Chi-square test), Q value = 0.013

Table S42. Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 8(6Q12) MUTATED	6	7	9	6	26
AMP PEAK 8(6Q12) WILD-TYPE	59	55	37	31	36

Figure S42. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.29e-05 (Fisher's exact test), Q value = 0.024

Table S43. Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
AMP PEAK 8(6Q12) MUTATED	27	17	10
AMP PEAK 8(6Q12) WILD-TYPE	42	96	80

Figure S43. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CNMF'

P value = 0.000226 (Fisher's exact test), Q value = 0.11

Table S44. Gene #8: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
AMP PEAK 8(6Q12) MUTATED	16	11	37
AMP PEAK 8(6Q12) WILD-TYPE	89	90	78

Figure S44. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.84e-05 (Fisher's exact test), Q value = 0.043

Table S45. Gene #8: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 8(6Q12) MUTATED	12	30	22
AMP PEAK 8(6Q12) WILD-TYPE	90	51	116

Figure S45. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.6e-05 (Fisher's exact test), Q value = 0.026

Table S46. Gene #8: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
AMP PEAK 8(6Q12) MUTATED	24	19	7
AMP PEAK 8(6Q12) WILD-TYPE	40	110	74

Figure S46. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

P value = 1.01e-07 (Chi-square test), Q value = 6.7e-05

Table S47. Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 9(6Q21) MUTATED	9	6	16	2	31
AMP PEAK 9(6Q21) WILD-TYPE	150	27	46	10	54

Figure S47. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.015

Table S48. Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
AMP PEAK 9(6Q21) MUTATED	26	15	9
AMP PEAK 9(6Q21) WILD-TYPE	43	98	81

Figure S48. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.15

Table S49. Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
AMP PEAK 9(6Q21) MUTATED	21	19	6
AMP PEAK 9(6Q21) WILD-TYPE	43	110	75

Figure S49. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p22.1' versus 'CN_CNMF'

P value = 5.49e-16 (Chi-square test), Q value = 4.2e-13

Table S50. Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 10(7P22.1) MUTATED	45	32	37	5	61
AMP PEAK 10(7P22.1) WILD-TYPE	114	1	25	7	24

Figure S50. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'METHLYATION_CNMF'

P value = 6.36e-06 (Fisher's exact test), Q value = 0.0039

Table S51. Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 10(7P22.1) MUTATED	60	59	37
AMP PEAK 10(7P22.1) WILD-TYPE	53	25	69

Figure S51. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.000192 (Chi-square test), Q value = 0.098

Table S52. Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 10(7P22.1) MUTATED	29	25	16	20	46
AMP PEAK 10(7P22.1) WILD-TYPE	36	37	30	17	16

Figure S52. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.42e-05 (Fisher's exact test), Q value = 0.014

Table S53. Gene #10: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
AMP PEAK 10(7P22.1) MUTATED	48	61	31
AMP PEAK 10(7P22.1) WILD-TYPE	16	68	50

Figure S53. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 2.78e-12 (Chi-square test), Q value = 2e-09

Table S54. Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 11(7P11.2) MUTATED	43	31	36	6	47
AMP PEAK 11(7P11.2) WILD-TYPE	116	2	26	6	38

Figure S54. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 0.000243 (Fisher's exact test), Q value = 0.12

Table S55. Gene #11: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 11(7P11.2) MUTATED	57	50	33
AMP PEAK 11(7P11.2) WILD-TYPE	56	34	73

Figure S55. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'CN_CNMF'

P value = 5.87e-12 (Chi-square test), Q value = 4.2e-09

Table S56. Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 12(7Q21.2) MUTATED	43	30	40	6	40
AMP PEAK 12(7Q21.2) WILD-TYPE	116	3	22	6	45

Figure S56. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'CN_CNMF'

P value = 9.11e-05 (Chi-square test), Q value = 0.049

Table S57. Gene #13: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 13(8P23.1) MUTATED	70	12	22	12	25
AMP PEAK 13(8P23.1) WILD-TYPE	89	21	40	0	60

Figure S57. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.087

Table S58. Gene #13: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 13(8P23.1) MUTATED	61	23	34
AMP PEAK 13(8P23.1) WILD-TYPE	52	61	72

Figure S58. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 2.01e-07 (Chi-square test), Q value = 0.00013

Table S59. Gene #14: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 14(8Q24.21) MUTATED	90	28	39	12	75
AMP PEAK 14(8Q24.21) WILD-TYPE	69	5	23	0	10

Figure S59. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000474 (Fisher's exact test), Q value = 0.22

Table S60. Gene #14: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 14(8Q24.21) MUTATED	57	67	94
AMP PEAK 14(8Q24.21) WILD-TYPE	45	14	44

Figure S60. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000123 (Fisher's exact test), Q value = 0.064

Table S61. Gene #14: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
AMP PEAK 14(8Q24.21) MUTATED	41	102	39
AMP PEAK 14(8Q24.21) WILD-TYPE	23	29	40

Figure S61. Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9p24.1' versus 'CN_CNMF'

P value = 6.18e-05 (Chi-square test), Q value = 0.034

Table S62. Gene #15: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 15(9P24.1) MUTATED	24	2	1	3	25
AMP PEAK 15(9P24.1) WILD-TYPE	135	31	61	9	60

Figure S62. Get High-res Image Gene #15: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

P value = 0.000257 (Chi-square test), Q value = 0.13

Table S63. Gene #17: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 17(9Q34.3) MUTATED	25	11	18	3	36
AMP PEAK 17(9Q34.3) WILD-TYPE	134	22	44	9	49

Figure S63. Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'CN_CNMF'

P value = 1.84e-13 (Chi-square test), Q value = 1.4e-10

Table S64. Gene #18: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 18(10P11.22) MUTATED	12	10	32	2	39
AMP PEAK 18(10P11.22) WILD-TYPE	147	23	30	10	46

Figure S64. Get High-res Image Gene #18: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'METHLYATION_CNMF'

P value = 1.78e-06 (Fisher's exact test), Q value = 0.0011

Table S65. Gene #18: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 18(10P11.22) MUTATED	25	41	17
AMP PEAK 18(10P11.22) WILD-TYPE	88	43	89

Figure S65. Get High-res Image Gene #18: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10p11.22' versus 'MIRSEQ_CNMF'

P value = 5.11e-05 (Fisher's exact test), Q value = 0.029

Table S66. Gene #18: 'amp_10p11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
AMP PEAK 18(10P11.22) MUTATED	16	22	47
AMP PEAK 18(10P11.22) WILD-TYPE	89	79	68

Figure S66. Get High-res Image Gene #18: 'amp_10p11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_10p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000436 (Fisher's exact test), Q value = 0.21

Table S67. Gene #18: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 18(10P11.22) MUTATED	24	35	26
AMP PEAK 18(10P11.22) WILD-TYPE	78	46	112

Figure S67. Get High-res Image Gene #18: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_10p11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000256 (Fisher's exact test), Q value = 0.13

Table S68. Gene #18: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
AMP PEAK 18(10P11.22) MUTATED	30	28	15
AMP PEAK 18(10P11.22) WILD-TYPE	34	101	66

Figure S68. Get High-res Image Gene #18: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.2' versus 'CN_CNMF'

P value = 1.38e-09 (Chi-square test), Q value = 9.7e-07

Table S69. Gene #19: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 19(10Q22.2) MUTATED	11	3	28	3	21
AMP PEAK 19(10Q22.2) WILD-TYPE	148	30	34	9	64

Figure S69. Get High-res Image Gene #19: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q26.13' versus 'CN_CNMF'

P value = 1.29e-05 (Chi-square test), Q value = 0.0076

Table S70. Gene #20: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 20(10Q26.13) MUTATED	15	7	23	1	25
AMP PEAK 20(10Q26.13) WILD-TYPE	144	26	39	11	60

Figure S70. Get High-res Image Gene #20: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0069

Table S71. Gene #21: 'amp_11p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
AMP PEAK 21(11P13) MUTATED	23	7	17
AMP PEAK 21(11P13) WILD-TYPE	46	106	73

Figure S71. Get High-res Image Gene #21: 'amp_11p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000105 (Fisher's exact test), Q value = 0.056

Table S72. Gene #21: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 21(11P13) MUTATED	15	27	14
AMP PEAK 21(11P13) WILD-TYPE	87	54	124

Figure S72. Get High-res Image Gene #21: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 2.06e-09 (Chi-square test), Q value = 1.4e-06

Table S73. Gene #22: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 22(11Q13.3) MUTATED	16	5	31	4	29
AMP PEAK 22(11Q13.3) WILD-TYPE	143	28	31	8	56

Figure S73. Get High-res Image Gene #22: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 5.62e-06 (Fisher's exact test), Q value = 0.0034

Table S74. Gene #22: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
AMP PEAK 22(11Q13.3) MUTATED	17	12	44
AMP PEAK 22(11Q13.3) WILD-TYPE	88	89	71

Figure S74. Get High-res Image Gene #22: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.038

Table S75. Gene #22: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
AMP PEAK 22(11Q13.3) MUTATED	6	44	11
AMP PEAK 22(11Q13.3) WILD-TYPE	58	87	68

Figure S75. Get High-res Image Gene #22: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'CN_CNMF'

P value = 7.47e-06 (Chi-square test), Q value = 0.0045

Table S76. Gene #23: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 23(12P12.1) MUTATED	29	11	34	4	27
AMP PEAK 23(12P12.1) WILD-TYPE	130	22	28	8	58

Figure S76. Get High-res Image Gene #23: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 2e-05 (Chi-square test), Q value = 0.012

Table S77. Gene #24: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 24(12Q15) MUTATED	28	7	31	1	24
AMP PEAK 24(12Q15) WILD-TYPE	131	26	31	11	61

Figure S77. Get High-res Image Gene #24: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'CN_CNMF'

P value = 4.58e-15 (Chi-square test), Q value = 3.5e-12

Table S78. Gene #25: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 25(13Q12.3) MUTATED	33	29	19	4	51
AMP PEAK 25(13Q12.3) WILD-TYPE	126	4	43	8	34

Figure S78. Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'METHLYATION_CNMF'

P value = 6.28e-05 (Fisher's exact test), Q value = 0.035

Table S79. Gene #25: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 25(13Q12.3) MUTATED	38	49	30
AMP PEAK 25(13Q12.3) WILD-TYPE	75	35	76

Figure S79. Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q12.3' versus 'MIRSEQ_CNMF'

P value = 0.000165 (Fisher's exact test), Q value = 0.084

Table S80. Gene #25: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
AMP PEAK 25(13Q12.3) MUTATED	31	31	62
AMP PEAK 25(13Q12.3) WILD-TYPE	74	70	53

Figure S80. Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000534 (Fisher's exact test), Q value = 0.25

Table S81. Gene #25: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 25(13Q12.3) MUTATED	31	46	47
AMP PEAK 25(13Q12.3) WILD-TYPE	71	35	91

Figure S81. Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.81e-05 (Fisher's exact test), Q value = 0.022

Table S82. Gene #25: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
AMP PEAK 25(13Q12.3) MUTATED	39	46	20
AMP PEAK 25(13Q12.3) WILD-TYPE	25	83	61

Figure S82. Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 3.51e-15 (Chi-square test), Q value = 2.7e-12

Table S83. Gene #26: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 26(13Q22.1) MUTATED	37	27	16	4	57
AMP PEAK 26(13Q22.1) WILD-TYPE	122	6	46	8	28

Figure S83. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1.65e-05 (Fisher's exact test), Q value = 0.0097

Table S84. Gene #26: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 26(13Q22.1) MUTATED	36	51	32
AMP PEAK 26(13Q22.1) WILD-TYPE	77	33	74

Figure S84. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 1.26e-05 (Chi-square test), Q value = 0.0075

Table S85. Gene #26: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 26(13Q22.1) MUTATED	23	16	9	17	39
AMP PEAK 26(13Q22.1) WILD-TYPE	42	46	37	20	23

Figure S85. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0072

Table S86. Gene #26: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
AMP PEAK 26(13Q22.1) MUTATED	32	30	66
AMP PEAK 26(13Q22.1) WILD-TYPE	73	71	49

Figure S86. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.2e-06 (Fisher's exact test), Q value = 0.0055

Table S87. Gene #26: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 26(13Q22.1) MUTATED	28	50	50
AMP PEAK 26(13Q22.1) WILD-TYPE	74	31	88

Figure S87. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000477 (Fisher's exact test), Q value = 0.22

Table S88. Gene #26: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
AMP PEAK 26(13Q22.1) MUTATED	24	65	18
AMP PEAK 26(13Q22.1) WILD-TYPE	40	66	61

Figure S88. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.47e-08 (Fisher's exact test), Q value = 1.7e-05

Table S89. Gene #26: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
AMP PEAK 26(13Q22.1) MUTATED	45	42	20
AMP PEAK 26(13Q22.1) WILD-TYPE	19	87	61

Figure S89. Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.1' versus 'CN_CNMF'

P value = 6.18e-16 (Chi-square test), Q value = 4.7e-13

Table S90. Gene #27: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 27(15Q26.1) MUTATED	11	4	23	0	45
AMP PEAK 27(15Q26.1) WILD-TYPE	148	29	39	12	40

Figure S90. Get High-res Image Gene #27: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.1' versus 'METHLYATION_CNMF'

P value = 1.95e-05 (Fisher's exact test), Q value = 0.011

Table S91. Gene #27: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 27(15Q26.1) MUTATED	19	36	17
AMP PEAK 27(15Q26.1) WILD-TYPE	94	48	89

Figure S91. Get High-res Image Gene #27: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CNMF'

P value = 1.88e-05 (Chi-square test), Q value = 0.011

Table S92. Gene #27: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 27(15Q26.1) MUTATED	12	4	11	9	28
AMP PEAK 27(15Q26.1) WILD-TYPE	53	58	35	28	34

Figure S92. Get High-res Image Gene #27: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.33e-06 (Fisher's exact test), Q value = 0.0027

Table S93. Gene #27: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
AMP PEAK 27(15Q26.1) MUTATED	31	23	10
AMP PEAK 27(15Q26.1) WILD-TYPE	38	90	80

Figure S93. Get High-res Image Gene #27: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1.23e-18 (Chi-square test), Q value = 9.4e-16

Table S94. Gene #28: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 28(17Q12) MUTATED	17	14	20	1	58
AMP PEAK 28(17Q12) WILD-TYPE	142	19	42	11	27

Figure S94. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 9.01e-08 (Fisher's exact test), Q value = 6e-05

Table S95. Gene #28: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 28(17Q12) MUTATED	30	47	19
AMP PEAK 28(17Q12) WILD-TYPE	83	37	87

Figure S95. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.000106 (Chi-square test), Q value = 0.056

Table S96. Gene #28: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 28(17Q12) MUTATED	14	10	15	8	32
AMP PEAK 28(17Q12) WILD-TYPE	51	52	31	29	30

Figure S96. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000293 (Fisher's exact test), Q value = 0.14

Table S97. Gene #28: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
AMP PEAK 28(17Q12) MUTATED	33	29	17
AMP PEAK 28(17Q12) WILD-TYPE	36	84	73

Figure S97. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 2.85e-06 (Fisher's exact test), Q value = 0.0018

Table S98. Gene #28: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
AMP PEAK 28(17Q12) MUTATED	22	20	55
AMP PEAK 28(17Q12) WILD-TYPE	83	81	60

Figure S98. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.19

Table S99. Gene #28: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 28(17Q12) MUTATED	25	39	33
AMP PEAK 28(17Q12) WILD-TYPE	77	42	105

Figure S99. Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 3.79e-10 (Chi-square test), Q value = 2.7e-07

Table S100. Gene #29: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 29(18Q11.2) MUTATED	22	12	34	3	41
AMP PEAK 29(18Q11.2) WILD-TYPE	137	21	28	9	44

Figure S100. Get High-res Image Gene #29: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 0.000446 (Chi-square test), Q value = 0.21

Table S101. Gene #30: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 30(19P13.2) MUTATED	8	9	12	0	11
AMP PEAK 30(19P13.2) WILD-TYPE	151	24	50	12	74

Figure S101. Get High-res Image Gene #30: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 3.93e-22 (Chi-square test), Q value = 3e-19

Table S102. Gene #31: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 31(19Q12) MUTATED	18	9	17	1	63
AMP PEAK 31(19Q12) WILD-TYPE	141	24	45	11	22

Figure S102. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1.88e-08 (Fisher's exact test), Q value = 1.3e-05

Table S103. Gene #31: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 31(19Q12) MUTATED	20	48	28
AMP PEAK 31(19Q12) WILD-TYPE	93	36	78

Figure S103. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 3.26e-14 (Chi-square test), Q value = 2.4e-11

Table S104. Gene #31: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 31(19Q12) MUTATED	10	9	10	6	44
AMP PEAK 31(19Q12) WILD-TYPE	55	53	36	31	18

Figure S104. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.34e-08 (Fisher's exact test), Q value = 2.3e-05

Table S105. Gene #31: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
AMP PEAK 31(19Q12) MUTATED	39	27	13
AMP PEAK 31(19Q12) WILD-TYPE	30	86	77

Figure S105. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 2.46e-07 (Fisher's exact test), Q value = 0.00016

Table S106. Gene #31: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
AMP PEAK 31(19Q12) MUTATED	19	20	56
AMP PEAK 31(19Q12) WILD-TYPE	86	81	59

Figure S106. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.37e-13 (Fisher's exact test), Q value = 1e-10

Table S107. Gene #31: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 31(19Q12) MUTATED	21	52	22
AMP PEAK 31(19Q12) WILD-TYPE	81	29	116

Figure S107. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.87e-13 (Fisher's exact test), Q value = 1.4e-10

Table S108. Gene #31: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
AMP PEAK 31(19Q12) MUTATED	45	22	17
AMP PEAK 31(19Q12) WILD-TYPE	19	107	64

Figure S108. Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1.58e-21 (Chi-square test), Q value = 1.2e-18

Table S109. Gene #32: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 32(20Q13.2) MUTATED	61	31	55	9	77
AMP PEAK 32(20Q13.2) WILD-TYPE	98	2	7	3	8

Figure S109. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 5.46e-10 (Fisher's exact test), Q value = 3.9e-07

Table S110. Gene #32: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
AMP PEAK 32(20Q13.2) MUTATED	63	78	60
AMP PEAK 32(20Q13.2) WILD-TYPE	50	6	46

Figure S110. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 5.66e-08 (Chi-square test), Q value = 3.8e-05

Table S111. Gene #32: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 32(20Q13.2) MUTATED	31	31	31	24	59
AMP PEAK 32(20Q13.2) WILD-TYPE	34	31	15	13	3

Figure S111. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.76e-05 (Fisher's exact test), Q value = 0.016

Table S112. Gene #32: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
AMP PEAK 32(20Q13.2) MUTATED	59	70	47
AMP PEAK 32(20Q13.2) WILD-TYPE	10	43	43

Figure S112. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 1.08e-07 (Fisher's exact test), Q value = 7.1e-05

Table S113. Gene #32: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
AMP PEAK 32(20Q13.2) MUTATED	61	53	98
AMP PEAK 32(20Q13.2) WILD-TYPE	44	48	17

Figure S113. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.55e-12 (Fisher's exact test), Q value = 3.3e-09

Table S114. Gene #32: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
AMP PEAK 32(20Q13.2) MUTATED	51	77	84
AMP PEAK 32(20Q13.2) WILD-TYPE	51	4	54

Figure S114. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.23e-10 (Fisher's exact test), Q value = 8.7e-08

Table S115. Gene #32: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
AMP PEAK 32(20Q13.2) MUTATED	62	77	42
AMP PEAK 32(20Q13.2) WILD-TYPE	2	52	39

Figure S115. Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq27.3' versus 'CN_CNMF'

P value = 0.000291 (Chi-square test), Q value = 0.14

Table S116. Gene #33: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
AMP PEAK 33(XQ27.3) MUTATED	15	12	13	4	23
AMP PEAK 33(XQ27.3) WILD-TYPE	144	21	49	8	62

Figure S116. Get High-res Image Gene #33: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 1.18e-14 (Chi-square test), Q value = 8.9e-12

Table S117. Gene #34: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 1(1P36.11) MUTATED	12	10	30	3	45
DEL PEAK 1(1P36.11) WILD-TYPE	147	23	32	9	40

Figure S117. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 3.2e-10 (Fisher's exact test), Q value = 2.3e-07

Table S118. Gene #34: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 1(1P36.11) MUTATED	22	46	14
DEL PEAK 1(1P36.11) WILD-TYPE	91	38	92

Figure S118. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Chi-square test), Q value = 0.16

Table S119. Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 1(1P36.11) MUTATED	12	8	17	11	28
DEL PEAK 1(1P36.11) WILD-TYPE	53	54	29	26	34

Figure S119. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.057

Table S120. Gene #34: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 1(1P36.11) MUTATED	32	30	14
DEL PEAK 1(1P36.11) WILD-TYPE	37	83	76

Figure S120. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 7.46e-06 (Fisher's exact test), Q value = 0.0045

Table S121. Gene #34: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 1(1P36.11) MUTATED	27	15	51
DEL PEAK 1(1P36.11) WILD-TYPE	78	86	64

Figure S121. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.4e-06 (Fisher's exact test), Q value = 0.00089

Table S122. Gene #34: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 1(1P36.11) MUTATED	16	41	36
DEL PEAK 1(1P36.11) WILD-TYPE	86	40	102

Figure S122. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.85e-06 (Fisher's exact test), Q value = 0.0047

Table S123. Gene #34: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 1(1P36.11) MUTATED	33	30	13
DEL PEAK 1(1P36.11) WILD-TYPE	31	99	68

Figure S123. Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 9.61e-13 (Chi-square test), Q value = 7e-10

Table S124. Gene #35: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 2(1P13.2) MUTATED	5	7	19	2	37
DEL PEAK 2(1P13.2) WILD-TYPE	154	26	43	10	48

Figure S124. Get High-res Image Gene #35: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 1.03e-06 (Fisher's exact test), Q value = 0.00066

Table S125. Gene #35: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 2(1P13.2) MUTATED	19	33	9
DEL PEAK 2(1P13.2) WILD-TYPE	94	51	97

Figure S125. Get High-res Image Gene #35: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000431 (Fisher's exact test), Q value = 0.21

Table S126. Gene #35: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 2(1P13.2) MUTATED	23	18	8
DEL PEAK 2(1P13.2) WILD-TYPE	46	95	82

Figure S126. Get High-res Image Gene #35: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.2' versus 'CN_CNMF'

P value = 0.000208 (Chi-square test), Q value = 0.11

Table S127. Gene #38: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 5(2Q37.2) MUTATED	10	4	13	3	23
DEL PEAK 5(2Q37.2) WILD-TYPE	149	29	49	9	62

Figure S127. Get High-res Image Gene #38: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.2' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.22

Table S128. Gene #38: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 5(2Q37.2) MUTATED	11	25	12
DEL PEAK 5(2Q37.2) WILD-TYPE	102	59	94

Figure S128. Get High-res Image Gene #38: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.2' versus 'MIRSEQ_CNMF'

P value = 0.000516 (Fisher's exact test), Q value = 0.24

Table S129. Gene #38: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 5(2Q37.2) MUTATED	8	12	30
DEL PEAK 5(2Q37.2) WILD-TYPE	97	89	85

Figure S129. Get High-res Image Gene #38: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.7e-06 (Fisher's exact test), Q value = 0.0046

Table S130. Gene #38: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 5(2Q37.2) MUTATED	8	27	15
DEL PEAK 5(2Q37.2) WILD-TYPE	94	54	123

Figure S130. Get High-res Image Gene #38: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.48e-05 (Fisher's exact test), Q value = 0.0087

Table S131. Gene #38: 'del_2q37.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 5(2Q37.2) MUTATED	23	18	5
DEL PEAK 5(2Q37.2) WILD-TYPE	41	111	76

Figure S131. Get High-res Image Gene #38: 'del_2q37.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.1' versus 'CN_CNMF'

P value = 1.02e-11 (Chi-square test), Q value = 7.4e-09

Table S132. Gene #39: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 6(3P26.1) MUTATED	18	19	30	3	39
DEL PEAK 6(3P26.1) WILD-TYPE	141	14	32	9	46

Figure S132. Get High-res Image Gene #39: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.1' versus 'MIRSEQ_CNMF'

P value = 0.000329 (Fisher's exact test), Q value = 0.16

Table S133. Gene #39: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 6(3P26.1) MUTATED	23	22	50
DEL PEAK 6(3P26.1) WILD-TYPE	82	79	65

Figure S133. Get High-res Image Gene #39: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000163 (Fisher's exact test), Q value = 0.084

Table S134. Gene #39: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 6(3P26.1) MUTATED	32	34	15
DEL PEAK 6(3P26.1) WILD-TYPE	32	95	66

Figure S134. Get High-res Image Gene #39: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1.98e-09 (Chi-square test), Q value = 1.4e-06

Table S135. Gene #40: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 7(3P14.2) MUTATED	28	16	36	4	43
DEL PEAK 7(3P14.2) WILD-TYPE	131	17	26	8	42

Figure S135. Get High-res Image Gene #40: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1.28e-05 (Fisher's exact test), Q value = 0.0075

Table S136. Gene #40: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 7(3P14.2) MUTATED	41	48	25
DEL PEAK 7(3P14.2) WILD-TYPE	72	36	81

Figure S136. Get High-res Image Gene #40: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 9.21e-05 (Chi-square test), Q value = 0.05

Table S137. Gene #40: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 7(3P14.2) MUTATED	16	10	15	13	34
DEL PEAK 7(3P14.2) WILD-TYPE	49	52	31	24	28

Figure S137. Get High-res Image Gene #40: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.72e-05 (Fisher's exact test), Q value = 0.021

Table S138. Gene #40: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 7(3P14.2) MUTATED	37	33	18
DEL PEAK 7(3P14.2) WILD-TYPE	32	80	72

Figure S138. Get High-res Image Gene #40: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.15

Table S139. Gene #40: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 7(3P14.2) MUTATED	28	26	56
DEL PEAK 7(3P14.2) WILD-TYPE	77	75	59

Figure S139. Get High-res Image Gene #40: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S140. Gene #40: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 7(3P14.2) MUTATED	36	45	16
DEL PEAK 7(3P14.2) WILD-TYPE	28	84	65

Figure S140. Get High-res Image Gene #40: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.31' versus 'CN_CNMF'

P value = 3.84e-06 (Chi-square test), Q value = 0.0024

Table S141. Gene #41: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 8(3Q26.31) MUTATED	4	10	12	1	16
DEL PEAK 8(3Q26.31) WILD-TYPE	155	23	50	11	69

Figure S141. Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.31' versus 'METHLYATION_CNMF'

P value = 1.77e-05 (Fisher's exact test), Q value = 0.01

Table S142. Gene #41: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 8(3Q26.31) MUTATED	14	21	3
DEL PEAK 8(3Q26.31) WILD-TYPE	99	63	103

Figure S142. Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q26.31' versus 'MRNASEQ_CNMF'

P value = 0.000338 (Chi-square test), Q value = 0.16

Table S143. Gene #41: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 8(3Q26.31) MUTATED	2	3	3	7	15
DEL PEAK 8(3Q26.31) WILD-TYPE	63	59	43	30	47

Figure S143. Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000495 (Fisher's exact test), Q value = 0.23

Table S144. Gene #41: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 8(3Q26.31) MUTATED	16	11	3
DEL PEAK 8(3Q26.31) WILD-TYPE	53	102	87

Figure S144. Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.067

Table S145. Gene #41: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 8(3Q26.31) MUTATED	5	8	26
DEL PEAK 8(3Q26.31) WILD-TYPE	100	93	89

Figure S145. Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'CN_CNMF'

P value = 5.25e-13 (Chi-square test), Q value = 3.9e-10

Table S146. Gene #42: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 9(4P16.3) MUTATED	27	14	38	4	52
DEL PEAK 9(4P16.3) WILD-TYPE	132	19	24	8	33

Figure S146. Get High-res Image Gene #42: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.12

Table S147. Gene #42: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 9(4P16.3) MUTATED	31	47	38
DEL PEAK 9(4P16.3) WILD-TYPE	82	37	68

Figure S147. Get High-res Image Gene #42: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1.05e-05 (Chi-square test), Q value = 0.0063

Table S148. Gene #42: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 9(4P16.3) MUTATED	11	23	15	11	38
DEL PEAK 9(4P16.3) WILD-TYPE	54	39	31	26	24

Figure S148. Get High-res Image Gene #42: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.66e-05 (Fisher's exact test), Q value = 0.021

Table S149. Gene #42: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 9(4P16.3) MUTATED	40	28	30
DEL PEAK 9(4P16.3) WILD-TYPE	29	85	60

Figure S149. Get High-res Image Gene #42: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 2.42e-06 (Fisher's exact test), Q value = 0.0015

Table S150. Gene #42: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 9(4P16.3) MUTATED	22	38	62
DEL PEAK 9(4P16.3) WILD-TYPE	83	63	53

Figure S150. Get High-res Image Gene #42: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.26e-08 (Fisher's exact test), Q value = 2.9e-05

Table S151. Gene #42: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 9(4P16.3) MUTATED	36	52	34
DEL PEAK 9(4P16.3) WILD-TYPE	66	29	104

Figure S151. Get High-res Image Gene #42: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.12

Table S152. Gene #42: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
DEL PEAK 9(4P16.3) MUTATED	11	60	33
DEL PEAK 9(4P16.3) WILD-TYPE	53	71	46

Figure S152. Get High-res Image Gene #42: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.59e-08 (Fisher's exact test), Q value = 6.4e-05

Table S153. Gene #42: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 9(4P16.3) MUTATED	43	32	29
DEL PEAK 9(4P16.3) WILD-TYPE	21	97	52

Figure S153. Get High-res Image Gene #42: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 2.03e-22 (Chi-square test), Q value = 1.6e-19

Table S154. Gene #43: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 10(4Q22.1) MUTATED	24	17	48	4	60
DEL PEAK 10(4Q22.1) WILD-TYPE	135	16	14	8	25

Figure S154. Get High-res Image Gene #43: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 6.2e-06 (Fisher's exact test), Q value = 0.0038

Table S155. Gene #43: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 10(4Q22.1) MUTATED	44	55	33
DEL PEAK 10(4Q22.1) WILD-TYPE	69	29	73

Figure S155. Get High-res Image Gene #43: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000324 (Fisher's exact test), Q value = 0.16

Table S156. Gene #43: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 10(4Q22.1) MUTATED	43	42	29
DEL PEAK 10(4Q22.1) WILD-TYPE	26	71	61

Figure S156. Get High-res Image Gene #43: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.049

Table S157. Gene #43: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 10(4Q22.1) MUTATED	36	52	52
DEL PEAK 10(4Q22.1) WILD-TYPE	66	29	86

Figure S157. Get High-res Image Gene #43: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.13e-05 (Fisher's exact test), Q value = 0.012

Table S158. Gene #43: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 10(4Q22.1) MUTATED	44	49	27
DEL PEAK 10(4Q22.1) WILD-TYPE	20	80	54

Figure S158. Get High-res Image Gene #43: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1.86e-21 (Chi-square test), Q value = 1.4e-18

Table S159. Gene #44: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 11(4Q34.3) MUTATED	28	14	47	3	63
DEL PEAK 11(4Q34.3) WILD-TYPE	131	19	15	9	22

Figure S159. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1.1e-06 (Fisher's exact test), Q value = 7e-04

Table S160. Gene #44: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 11(4Q34.3) MUTATED	40	58	38
DEL PEAK 11(4Q34.3) WILD-TYPE	73	26	68

Figure S160. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1.24e-05 (Chi-square test), Q value = 0.0074

Table S161. Gene #44: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 11(4Q34.3) MUTATED	14	21	21	16	41
DEL PEAK 11(4Q34.3) WILD-TYPE	51	41	25	21	21

Figure S161. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.016

Table S162. Gene #44: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 11(4Q34.3) MUTATED	45	38	30
DEL PEAK 11(4Q34.3) WILD-TYPE	24	75	60

Figure S162. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 5.03e-06 (Fisher's exact test), Q value = 0.0031

Table S163. Gene #44: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 11(4Q34.3) MUTATED	31	37	70
DEL PEAK 11(4Q34.3) WILD-TYPE	74	64	45

Figure S163. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.98e-07 (Fisher's exact test), Q value = 0.00019

Table S164. Gene #44: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 11(4Q34.3) MUTATED	35	56	47
DEL PEAK 11(4Q34.3) WILD-TYPE	67	25	91

Figure S164. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.67e-07 (Fisher's exact test), Q value = 0.00018

Table S165. Gene #44: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 11(4Q34.3) MUTATED	47	43	30
DEL PEAK 11(4Q34.3) WILD-TYPE	17	86	51

Figure S165. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 9.41e-26 (Chi-square test), Q value = 7.3e-23

Table S166. Gene #45: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 12(5Q11.2) MUTATED	12	14	35	4	64
DEL PEAK 12(5Q11.2) WILD-TYPE	147	19	27	8	21

Figure S166. Get High-res Image Gene #45: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 4.73e-15 (Fisher's exact test), Q value = 3.6e-12

Table S167. Gene #45: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 12(5Q11.2) MUTATED	33	62	20
DEL PEAK 12(5Q11.2) WILD-TYPE	80	22	86

Figure S167. Get High-res Image Gene #45: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q11.2' versus 'MRNASEQ_CNMF'

P value = 5.1e-13 (Chi-square test), Q value = 3.8e-10

Table S168. Gene #45: 'del_5q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 12(5Q11.2) MUTATED	17	4	11	14	44
DEL PEAK 12(5Q11.2) WILD-TYPE	48	58	35	23	18

Figure S168. Get High-res Image Gene #45: 'del_5q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.3e-12 (Fisher's exact test), Q value = 2.4e-09

Table S169. Gene #45: 'del_5q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 12(5Q11.2) MUTATED	44	37	9
DEL PEAK 12(5Q11.2) WILD-TYPE	25	76	81

Figure S169. Get High-res Image Gene #45: 'del_5q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

P value = 9.63e-11 (Fisher's exact test), Q value = 6.9e-08

Table S170. Gene #45: 'del_5q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 12(5Q11.2) MUTATED	34	15	67
DEL PEAK 12(5Q11.2) WILD-TYPE	71	86	48

Figure S170. Get High-res Image Gene #45: 'del_5q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.21e-11 (Fisher's exact test), Q value = 8.7e-09

Table S171. Gene #45: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 12(5Q11.2) MUTATED	17	54	45
DEL PEAK 12(5Q11.2) WILD-TYPE	85	27	93

Figure S171. Get High-res Image Gene #45: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.67e-08 (Fisher's exact test), Q value = 1.8e-05

Table S172. Gene #45: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
DEL PEAK 12(5Q11.2) MUTATED	20	71	12
DEL PEAK 12(5Q11.2) WILD-TYPE	44	60	67

Figure S172. Get High-res Image Gene #45: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.64e-15 (Fisher's exact test), Q value = 4.2e-12

Table S173. Gene #45: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 12(5Q11.2) MUTATED	50	41	12
DEL PEAK 12(5Q11.2) WILD-TYPE	14	88	69

Figure S173. Get High-res Image Gene #45: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q23.2' versus 'CN_CNMF'

P value = 1.65e-25 (Chi-square test), Q value = 1.3e-22

Table S174. Gene #46: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 13(5Q23.2) MUTATED	9	13	27	4	63
DEL PEAK 13(5Q23.2) WILD-TYPE	150	20	35	8	22

Figure S174. Get High-res Image Gene #46: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q23.2' versus 'METHLYATION_CNMF'

P value = 1.19e-14 (Fisher's exact test), Q value = 8.9e-12

Table S175. Gene #46: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 13(5Q23.2) MUTATED	28	58	17
DEL PEAK 13(5Q23.2) WILD-TYPE	85	26	89

Figure S175. Get High-res Image Gene #46: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q23.2' versus 'MRNASEQ_CNMF'

P value = 4.2e-13 (Chi-square test), Q value = 3.1e-10

Table S176. Gene #46: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 13(5Q23.2) MUTATED	15	3	10	11	42
DEL PEAK 13(5Q23.2) WILD-TYPE	50	59	36	26	20

Figure S176. Get High-res Image Gene #46: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.96e-11 (Fisher's exact test), Q value = 4.3e-08

Table S177. Gene #46: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 13(5Q23.2) MUTATED	39	35	7
DEL PEAK 13(5Q23.2) WILD-TYPE	30	78	83

Figure S177. Get High-res Image Gene #46: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_CNMF'

P value = 1.56e-11 (Fisher's exact test), Q value = 1.1e-08

Table S178. Gene #46: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 13(5Q23.2) MUTATED	26	12	63
DEL PEAK 13(5Q23.2) WILD-TYPE	79	89	52

Figure S178. Get High-res Image Gene #46: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.75e-10 (Fisher's exact test), Q value = 2.7e-07

Table S179. Gene #46: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 13(5Q23.2) MUTATED	13	47	41
DEL PEAK 13(5Q23.2) WILD-TYPE	89	34	97

Figure S179. Get High-res Image Gene #46: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.47e-08 (Fisher's exact test), Q value = 6.3e-05

Table S180. Gene #46: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
DEL PEAK 13(5Q23.2) MUTATED	14	64	11
DEL PEAK 13(5Q23.2) WILD-TYPE	50	67	68

Figure S180. Get High-res Image Gene #46: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.8e-12 (Fisher's exact test), Q value = 1.3e-09

Table S181. Gene #46: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 13(5Q23.2) MUTATED	44	35	10
DEL PEAK 13(5Q23.2) WILD-TYPE	20	94	71

Figure S181. Get High-res Image Gene #46: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 2.46e-09 (Chi-square test), Q value = 1.7e-06

Table S182. Gene #47: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 14(6P25.3) MUTATED	15	6	25	2	37
DEL PEAK 14(6P25.3) WILD-TYPE	144	27	37	10	48

Figure S182. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 4.37e-05 (Fisher's exact test), Q value = 0.025

Table S183. Gene #47: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 14(6P25.3) MUTATED	27	36	15
DEL PEAK 14(6P25.3) WILD-TYPE	86	48	91

Figure S183. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 9.48e-05 (Chi-square test), Q value = 0.051

Table S184. Gene #47: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 14(6P25.3) MUTATED	7	6	14	6	24
DEL PEAK 14(6P25.3) WILD-TYPE	58	56	32	31	38

Figure S184. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.81e-05 (Fisher's exact test), Q value = 0.011

Table S185. Gene #47: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 14(6P25.3) MUTATED	28	20	9
DEL PEAK 14(6P25.3) WILD-TYPE	41	93	81

Figure S185. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q14.1' versus 'CN_CNMF'

P value = 2.5e-08 (Chi-square test), Q value = 1.7e-05

Table S186. Gene #48: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 15(6Q14.1) MUTATED	10	7	24	1	27
DEL PEAK 15(6Q14.1) WILD-TYPE	149	26	38	11	58

Figure S186. Get High-res Image Gene #48: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.1' versus 'METHLYATION_CNMF'

P value = 0.000375 (Fisher's exact test), Q value = 0.18

Table S187. Gene #48: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 15(6Q14.1) MUTATED	17	29	13
DEL PEAK 15(6Q14.1) WILD-TYPE	96	55	93

Figure S187. Get High-res Image Gene #48: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q14.1' versus 'MRNASEQ_CNMF'

P value = 0.000425 (Chi-square test), Q value = 0.2

Table S188. Gene #48: 'del_6q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 15(6Q14.1) MUTATED	7	4	17	6	14
DEL PEAK 15(6Q14.1) WILD-TYPE	58	58	29	31	48

Figure S188. Get High-res Image Gene #48: 'del_6q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 5.42e-07 (Chi-square test), Q value = 0.00035

Table S189. Gene #49: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 16(6Q26) MUTATED	17	10	27	0	23
DEL PEAK 16(6Q26) WILD-TYPE	142	23	35	12	62

Figure S189. Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000265 (Fisher's exact test), Q value = 0.13

Table S190. Gene #49: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 16(6Q26) MUTATED	27	19	12
DEL PEAK 16(6Q26) WILD-TYPE	42	94	78

Figure S190. Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q31.1' versus 'CN_CNMF'

P value = 8.11e-09 (Chi-square test), Q value = 5.6e-06

Table S191. Gene #50: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 17(7Q31.1) MUTATED	7	0	19	1	23
DEL PEAK 17(7Q31.1) WILD-TYPE	152	33	43	11	62

Figure S191. Get High-res Image Gene #50: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 6.99e-06 (Fisher's exact test), Q value = 0.0042

Table S192. Gene #50: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 17(7Q31.1) MUTATED	17	22	3
DEL PEAK 17(7Q31.1) WILD-TYPE	96	62	103

Figure S192. Get High-res Image Gene #50: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.89e-05 (Fisher's exact test), Q value = 0.033

Table S193. Gene #50: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
DEL PEAK 17(7Q31.1) MUTATED	3	32	5
DEL PEAK 17(7Q31.1) WILD-TYPE	61	99	74

Figure S193. Get High-res Image Gene #50: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_7q36.3' versus 'CN_CNMF'

P value = 9.59e-21 (Chi-square test), Q value = 7.3e-18

Table S194. Gene #51: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 18(7Q36.3) MUTATED	4	1	32	1	37
DEL PEAK 18(7Q36.3) WILD-TYPE	155	32	30	11	48

Figure S194. Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

P value = 9.73e-05 (Fisher's exact test), Q value = 0.052

Table S195. Gene #51: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 18(7Q36.3) MUTATED	21	32	13
DEL PEAK 18(7Q36.3) WILD-TYPE	92	52	93

Figure S195. Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 3.17e-06 (Chi-square test), Q value = 0.002

Table S196. Gene #51: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 18(7Q36.3) MUTATED	7	8	8	3	27
DEL PEAK 18(7Q36.3) WILD-TYPE	58	54	38	34	35

Figure S196. Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.43e-06 (Fisher's exact test), Q value = 0.0033

Table S197. Gene #51: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 18(7Q36.3) MUTATED	28	16	9
DEL PEAK 18(7Q36.3) WILD-TYPE	41	97	81

Figure S197. Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_CNMF'

P value = 9.78e-05 (Fisher's exact test), Q value = 0.052

Table S198. Gene #51: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 18(7Q36.3) MUTATED	18	10	38
DEL PEAK 18(7Q36.3) WILD-TYPE	87	91	77

Figure S198. Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.16e-07 (Fisher's exact test), Q value = 0.00053

Table S199. Gene #51: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 18(7Q36.3) MUTATED	9	33	24
DEL PEAK 18(7Q36.3) WILD-TYPE	93	48	114

Figure S199. Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.52e-06 (Fisher's exact test), Q value = 0.004

Table S200. Gene #51: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 18(7Q36.3) MUTATED	27	24	7
DEL PEAK 18(7Q36.3) WILD-TYPE	37	105	74

Figure S200. Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1.85e-14 (Chi-square test), Q value = 1.4e-11

Table S201. Gene #52: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 19(8P23.2) MUTATED	11	14	26	0	42
DEL PEAK 19(8P23.2) WILD-TYPE	148	19	36	12	43

Figure S201. Get High-res Image Gene #52: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.000243 (Fisher's exact test), Q value = 0.12

Table S202. Gene #52: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 19(8P23.2) MUTATED	23	37	21
DEL PEAK 19(8P23.2) WILD-TYPE	90	47	85

Figure S202. Get High-res Image Gene #52: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 7.1e-06 (Chi-square test), Q value = 0.0043

Table S203. Gene #52: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 19(8P23.2) MUTATED	10	9	8	9	31
DEL PEAK 19(8P23.2) WILD-TYPE	55	53	38	28	31

Figure S203. Get High-res Image Gene #52: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.9e-06 (Fisher's exact test), Q value = 0.003

Table S204. Gene #52: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 19(8P23.2) MUTATED	33	19	15
DEL PEAK 19(8P23.2) WILD-TYPE	36	94	75

Figure S204. Get High-res Image Gene #52: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.00069

Table S205. Gene #52: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 19(8P23.2) MUTATED	16	39	27
DEL PEAK 19(8P23.2) WILD-TYPE	86	42	111

Figure S205. Get High-res Image Gene #52: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.77e-06 (Fisher's exact test), Q value = 0.0011

Table S206. Gene #52: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 19(8P23.2) MUTATED	33	22	16
DEL PEAK 19(8P23.2) WILD-TYPE	31	107	65

Figure S206. Get High-res Image Gene #52: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 2.87e-22 (Chi-square test), Q value = 2.2e-19

Table S207. Gene #53: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 20(9P23) MUTATED	23	18	52	5	51
DEL PEAK 20(9P23) WILD-TYPE	136	15	10	7	34

Figure S207. Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 6.81e-05 (Fisher's exact test), Q value = 0.037

Table S208. Gene #53: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 20(9P23) MUTATED	39	53	38
DEL PEAK 20(9P23) WILD-TYPE	74	31	68

Figure S208. Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 4.43e-06 (Chi-square test), Q value = 0.0027

Table S209. Gene #53: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 20(9P23) MUTATED	14	18	23	13	40
DEL PEAK 20(9P23) WILD-TYPE	51	44	23	24	22

Figure S209. Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000217 (Fisher's exact test), Q value = 0.11

Table S210. Gene #53: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 20(9P23) MUTATED	42	37	29
DEL PEAK 20(9P23) WILD-TYPE	27	76	61

Figure S210. Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.44e-05 (Fisher's exact test), Q value = 0.035

Table S211. Gene #53: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 20(9P23) MUTATED	41	47	24
DEL PEAK 20(9P23) WILD-TYPE	23	82	57

Figure S211. Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 4.32e-23 (Chi-square test), Q value = 3.3e-20

Table S212. Gene #54: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 21(9P21.3) MUTATED	21	16	52	5	51
DEL PEAK 21(9P21.3) WILD-TYPE	138	17	10	7	34

Figure S212. Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 3.78e-07 (Fisher's exact test), Q value = 0.00025

Table S213. Gene #54: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 21(9P21.3) MUTATED	34	56	37
DEL PEAK 21(9P21.3) WILD-TYPE	79	28	69

Figure S213. Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 4.93e-05 (Fisher's exact test), Q value = 0.028

Table S214. Gene #54: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 21(9P21.3) MUTATED	17	41	47
DEL PEAK 21(9P21.3) WILD-TYPE	65	49	44

Figure S214. Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 2.56e-09 (Chi-square test), Q value = 1.8e-06

Table S215. Gene #54: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 21(9P21.3) MUTATED	9	18	23	15	43
DEL PEAK 21(9P21.3) WILD-TYPE	56	44	23	22	19

Figure S215. Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.73e-05 (Fisher's exact test), Q value = 0.01

Table S216. Gene #54: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 21(9P21.3) MUTATED	44	35	29
DEL PEAK 21(9P21.3) WILD-TYPE	25	78	61

Figure S216. Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000442 (Fisher's exact test), Q value = 0.21

Table S217. Gene #54: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 21(9P21.3) MUTATED	36	47	44
DEL PEAK 21(9P21.3) WILD-TYPE	66	34	94

Figure S217. Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.78e-06 (Fisher's exact test), Q value = 0.0024

Table S218. Gene #54: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 21(9P21.3) MUTATED	43	42	25
DEL PEAK 21(9P21.3) WILD-TYPE	21	87	56

Figure S218. Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 4.08e-13 (Chi-square test), Q value = 3e-10

Table S219. Gene #55: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 22(9Q21.11) MUTATED	11	10	33	2	34
DEL PEAK 22(9Q21.11) WILD-TYPE	148	23	29	10	51

Figure S219. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.74e-05 (Fisher's exact test), Q value = 0.01

Table S220. Gene #55: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 22(9Q21.11) MUTATED	31	24	14
DEL PEAK 22(9Q21.11) WILD-TYPE	33	105	67

Figure S220. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q22.3' versus 'CN_CNMF'

P value = 3.41e-11 (Chi-square test), Q value = 2.4e-08

Table S221. Gene #56: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 23(10Q22.3) MUTATED	5	13	7	2	29
DEL PEAK 23(10Q22.3) WILD-TYPE	154	20	55	10	56

Figure S221. Get High-res Image Gene #56: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q22.3' versus 'MRNASEQ_CNMF'

P value = 0.000151 (Chi-square test), Q value = 0.078

Table S222. Gene #56: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 23(10Q22.3) MUTATED	7	2	4	8	19
DEL PEAK 23(10Q22.3) WILD-TYPE	58	60	42	29	43

Figure S222. Get High-res Image Gene #56: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1.46e-13 (Chi-square test), Q value = 1.1e-10

Table S223. Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 24(10Q23.31) MUTATED	10	12	15	3	44
DEL PEAK 24(10Q23.31) WILD-TYPE	149	21	47	9	41

Figure S223. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 9.26e-05 (Fisher's exact test), Q value = 0.05

Table S224. Gene #57: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 24(10Q23.31) MUTATED	20	34	16
DEL PEAK 24(10Q23.31) WILD-TYPE	93	50	90

Figure S224. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 8.64e-07 (Chi-square test), Q value = 0.00056

Table S225. Gene #57: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 24(10Q23.31) MUTATED	8	4	9	12	28
DEL PEAK 24(10Q23.31) WILD-TYPE	57	58	37	25	34

Figure S225. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 5.47e-05 (Fisher's exact test), Q value = 0.03

Table S226. Gene #57: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 24(10Q23.31) MUTATED	24	10	40
DEL PEAK 24(10Q23.31) WILD-TYPE	81	91	75

Figure S226. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000116 (Fisher's exact test), Q value = 0.061

Table S227. Gene #57: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 24(10Q23.31) MUTATED	13	32	29
DEL PEAK 24(10Q23.31) WILD-TYPE	89	49	109

Figure S227. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000316 (Fisher's exact test), Q value = 0.15

Table S228. Gene #57: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 24(10Q23.31) MUTATED	25	26	9
DEL PEAK 24(10Q23.31) WILD-TYPE	39	103	72

Figure S228. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.4' versus 'CN_CNMF'

P value = 6.05e-13 (Chi-square test), Q value = 4.4e-10

Table S229. Gene #58: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 25(11P15.4) MUTATED	9	3	21	2	39
DEL PEAK 25(11P15.4) WILD-TYPE	150	30	41	10	46

Figure S229. Get High-res Image Gene #58: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'METHLYATION_CNMF'

P value = 5.26e-05 (Fisher's exact test), Q value = 0.029

Table S230. Gene #58: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 25(11P15.4) MUTATED	16	31	13
DEL PEAK 25(11P15.4) WILD-TYPE	97	53	93

Figure S230. Get High-res Image Gene #58: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.4' versus 'RPPA_CNMF'

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

Table S231. Gene #58: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 25(11P15.4) MUTATED	6	15	35
DEL PEAK 25(11P15.4) WILD-TYPE	76	75	56

Figure S231. Get High-res Image Gene #58: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11p15.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.66e-05 (Fisher's exact test), Q value = 0.042

Table S232. Gene #58: 'del_11p15.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 25(11P15.4) MUTATED	24	18	7
DEL PEAK 25(11P15.4) WILD-TYPE	45	95	83

Figure S232. Get High-res Image Gene #58: 'del_11p15.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.2' versus 'CN_CNMF'

P value = 1.23e-05 (Chi-square test), Q value = 0.0073

Table S233. Gene #59: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 26(11Q23.2) MUTATED	16	6	22	2	29
DEL PEAK 26(11Q23.2) WILD-TYPE	143	27	40	10	56

Figure S233. Get High-res Image Gene #59: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 1.77e-13 (Chi-square test), Q value = 1.3e-10

Table S234. Gene #60: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 27(12P13.1) MUTATED	2	2	14	3	33
DEL PEAK 27(12P13.1) WILD-TYPE	157	31	48	9	52

Figure S234. Get High-res Image Gene #60: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 2.98e-08 (Fisher's exact test), Q value = 2e-05

Table S235. Gene #60: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 27(12P13.1) MUTATED	10	30	6
DEL PEAK 27(12P13.1) WILD-TYPE	103	54	100

Figure S235. Get High-res Image Gene #60: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 2.96e-06 (Chi-square test), Q value = 0.0019

Table S236. Gene #60: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 27(12P13.1) MUTATED	4	5	5	4	23
DEL PEAK 27(12P13.1) WILD-TYPE	61	57	41	33	39

Figure S236. Get High-res Image Gene #60: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.3e-07 (Fisher's exact test), Q value = 0.00041

Table S237. Gene #60: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 27(12P13.1) MUTATED	25	10	6
DEL PEAK 27(12P13.1) WILD-TYPE	44	103	84

Figure S237. Get High-res Image Gene #60: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000293 (Fisher's exact test), Q value = 0.14

Table S238. Gene #60: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 27(12P13.1) MUTATED	20	15	6
DEL PEAK 27(12P13.1) WILD-TYPE	44	114	75

Figure S238. Get High-res Image Gene #60: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 1.44e-08 (Chi-square test), Q value = 9.9e-06

Table S239. Gene #61: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 28(13Q12.11) MUTATED	7	1	22	2	18
DEL PEAK 28(13Q12.11) WILD-TYPE	152	32	40	10	67

Figure S239. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q12' versus 'CN_CNMF'

P value = 3.46e-12 (Chi-square test), Q value = 2.5e-09

Table S240. Gene #62: 'del_14q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 29(14Q12) MUTATED	13	7	33	4	34
DEL PEAK 29(14Q12) WILD-TYPE	146	26	29	8	51

Figure S240. Get High-res Image Gene #62: 'del_14q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q12' versus 'METHLYATION_CNMF'

P value = 5.54e-05 (Fisher's exact test), Q value = 0.031

Table S241. Gene #62: 'del_14q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 29(14Q12) MUTATED	20	38	23
DEL PEAK 29(14Q12) WILD-TYPE	93	46	83

Figure S241. Get High-res Image Gene #62: 'del_14q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q12' versus 'MRNASEQ_CNMF'

P value = 0.000346 (Chi-square test), Q value = 0.17

Table S242. Gene #62: 'del_14q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 29(14Q12) MUTATED	10	12	14	5	28
DEL PEAK 29(14Q12) WILD-TYPE	55	50	32	32	34

Figure S242. Get High-res Image Gene #62: 'del_14q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000165 (Fisher's exact test), Q value = 0.085

Table S243. Gene #62: 'del_14q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 29(14Q12) MUTATED	31	22	16
DEL PEAK 29(14Q12) WILD-TYPE	38	91	74

Figure S243. Get High-res Image Gene #62: 'del_14q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q12' versus 'MIRSEQ_CNMF'

P value = 0.000176 (Fisher's exact test), Q value = 0.09

Table S244. Gene #62: 'del_14q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 29(14Q12) MUTATED	18	20	46
DEL PEAK 29(14Q12) WILD-TYPE	87	81	69

Figure S244. Get High-res Image Gene #62: 'del_14q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000104 (Fisher's exact test), Q value = 0.055

Table S245. Gene #62: 'del_14q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 29(14Q12) MUTATED	31	28	15
DEL PEAK 29(14Q12) WILD-TYPE	33	101	66

Figure S245. Get High-res Image Gene #62: 'del_14q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.33' versus 'CN_CNMF'

P value = 1.56e-10 (Chi-square test), Q value = 1.1e-07

Table S246. Gene #63: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 30(14Q32.33) MUTATED	20	9	35	2	36
DEL PEAK 30(14Q32.33) WILD-TYPE	139	24	27	10	49

Figure S246. Get High-res Image Gene #63: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.33' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.072

Table S247. Gene #63: 'del_14q32.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 30(14Q32.33) MUTATED	26	40	23
DEL PEAK 30(14Q32.33) WILD-TYPE	87	44	83

Figure S247. Get High-res Image Gene #63: 'del_14q32.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.45e-06 (Fisher's exact test), Q value = 0.0045

Table S248. Gene #63: 'del_14q32.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 30(14Q32.33) MUTATED	37	25	19
DEL PEAK 30(14Q32.33) WILD-TYPE	32	88	71

Figure S248. Get High-res Image Gene #63: 'del_14q32.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 3.9e-13 (Chi-square test), Q value = 2.9e-10

Table S249. Gene #64: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 31(15Q15.1) MUTATED	12	13	25	3	44
DEL PEAK 31(15Q15.1) WILD-TYPE	147	20	37	9	41

Figure S249. Get High-res Image Gene #64: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 2.99e-07 (Fisher's exact test), Q value = 0.00019

Table S250. Gene #64: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 31(15Q15.1) MUTATED	22	43	19
DEL PEAK 31(15Q15.1) WILD-TYPE	91	41	87

Figure S250. Get High-res Image Gene #64: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 5.63e-08 (Chi-square test), Q value = 3.8e-05

Table S251. Gene #64: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 31(15Q15.1) MUTATED	11	3	16	7	31
DEL PEAK 31(15Q15.1) WILD-TYPE	54	59	30	30	31

Figure S251. Get High-res Image Gene #64: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.32e-08 (Fisher's exact test), Q value = 9.1e-06

Table S252. Gene #64: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 31(15Q15.1) MUTATED	34	27	7
DEL PEAK 31(15Q15.1) WILD-TYPE	35	86	83

Figure S252. Get High-res Image Gene #64: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CNMF'

P value = 4.07e-06 (Fisher's exact test), Q value = 0.0025

Table S253. Gene #64: 'del_15q15.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 31(15Q15.1) MUTATED	22	14	49
DEL PEAK 31(15Q15.1) WILD-TYPE	83	87	66

Figure S253. Get High-res Image Gene #64: 'del_15q15.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.6e-09 (Fisher's exact test), Q value = 6.6e-06

Table S254. Gene #64: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 31(15Q15.1) MUTATED	11	41	33
DEL PEAK 31(15Q15.1) WILD-TYPE	91	40	105

Figure S254. Get High-res Image Gene #64: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.81e-05 (Fisher's exact test), Q value = 0.037

Table S255. Gene #64: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
DEL PEAK 31(15Q15.1) MUTATED	16	48	8
DEL PEAK 31(15Q15.1) WILD-TYPE	48	83	71

Figure S255. Get High-res Image Gene #64: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.82e-07 (Fisher's exact test), Q value = 0.00063

Table S256. Gene #64: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 31(15Q15.1) MUTATED	31	33	8
DEL PEAK 31(15Q15.1) WILD-TYPE	33	96	73

Figure S256. Get High-res Image Gene #64: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 3.99e-14 (Chi-square test), Q value = 3e-11

Table S257. Gene #65: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 32(16P13.3) MUTATED	8	3	22	0	38
DEL PEAK 32(16P13.3) WILD-TYPE	151	30	40	12	47

Figure S257. Get High-res Image Gene #65: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.000467 (Fisher's exact test), Q value = 0.22

Table S258. Gene #65: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 32(16P13.3) MUTATED	17	30	15
DEL PEAK 32(16P13.3) WILD-TYPE	96	54	91

Figure S258. Get High-res Image Gene #65: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 8.06e-09 (Chi-square test), Q value = 5.6e-06

Table S259. Gene #65: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 32(16P13.3) MUTATED	8	6	4	3	29
DEL PEAK 32(16P13.3) WILD-TYPE	57	56	42	34	33

Figure S259. Get High-res Image Gene #65: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.34e-09 (Fisher's exact test), Q value = 1.6e-06

Table S260. Gene #65: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 32(16P13.3) MUTATED	31	13	6
DEL PEAK 32(16P13.3) WILD-TYPE	38	100	84

Figure S260. Get High-res Image Gene #65: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 4.25e-06 (Fisher's exact test), Q value = 0.0026

Table S261. Gene #65: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 32(16P13.3) MUTATED	12	11	40
DEL PEAK 32(16P13.3) WILD-TYPE	93	90	75

Figure S261. Get High-res Image Gene #65: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.72e-05 (Fisher's exact test), Q value = 0.01

Table S262. Gene #65: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 32(16P13.3) MUTATED	12	31	20
DEL PEAK 32(16P13.3) WILD-TYPE	90	50	118

Figure S262. Get High-res Image Gene #65: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.02e-06 (Fisher's exact test), Q value = 0.00066

Table S263. Gene #65: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
DEL PEAK 32(16P13.3) MUTATED	2	42	11
DEL PEAK 32(16P13.3) WILD-TYPE	62	89	68

Figure S263. Get High-res Image Gene #65: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.0015

Table S264. Gene #65: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 32(16P13.3) MUTATED	28	17	10
DEL PEAK 32(16P13.3) WILD-TYPE	36	112	71

Figure S264. Get High-res Image Gene #65: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1.46e-08 (Chi-square test), Q value = 1e-05

Table S265. Gene #66: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 33(16Q23.1) MUTATED	37	14	36	3	51
DEL PEAK 33(16Q23.1) WILD-TYPE	122	19	26	9	34

Figure S265. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000112 (Fisher's exact test), Q value = 0.059

Table S266. Gene #66: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 33(16Q23.1) MUTATED	41	40	24
DEL PEAK 33(16Q23.1) WILD-TYPE	28	73	66

Figure S266. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000296 (Fisher's exact test), Q value = 0.15

Table S267. Gene #66: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
DEL PEAK 33(16Q23.1) MUTATED	21	68	20
DEL PEAK 33(16Q23.1) WILD-TYPE	43	63	59

Figure S267. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000121 (Fisher's exact test), Q value = 0.063

Table S268. Gene #66: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 33(16Q23.1) MUTATED	37	53	19
DEL PEAK 33(16Q23.1) WILD-TYPE	27	76	62

Figure S268. Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 7.04e-25 (Chi-square test), Q value = 5.5e-22

Table S269. Gene #67: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 34(17P12) MUTATED	13	22	38	3	58
DEL PEAK 34(17P12) WILD-TYPE	146	11	24	9	27

Figure S269. Get High-res Image Gene #67: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1.34e-14 (Fisher's exact test), Q value = 1e-11

Table S270. Gene #67: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 34(17P12) MUTATED	36	62	20
DEL PEAK 34(17P12) WILD-TYPE	77	22	86

Figure S270. Get High-res Image Gene #67: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 9.4e-09 (Chi-square test), Q value = 6.5e-06

Table S271. Gene #67: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 34(17P12) MUTATED	15	10	19	12	42
DEL PEAK 34(17P12) WILD-TYPE	50	52	27	25	20

Figure S271. Get High-res Image Gene #67: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.58e-08 (Fisher's exact test), Q value = 3.7e-05

Table S272. Gene #67: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 34(17P12) MUTATED	44	36	18
DEL PEAK 34(17P12) WILD-TYPE	25	77	72

Figure S272. Get High-res Image Gene #67: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 9.94e-06 (Fisher's exact test), Q value = 0.006

Table S273. Gene #67: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 34(17P12) MUTATED	36	23	62
DEL PEAK 34(17P12) WILD-TYPE	69	78	53

Figure S273. Get High-res Image Gene #67: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.36e-08 (Fisher's exact test), Q value = 2.9e-05

Table S274. Gene #67: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 34(17P12) MUTATED	24	52	45
DEL PEAK 34(17P12) WILD-TYPE	78	29	93

Figure S274. Get High-res Image Gene #67: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000114 (Fisher's exact test), Q value = 0.06

Table S275. Gene #67: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
DEL PEAK 34(17P12) MUTATED	21	67	18
DEL PEAK 34(17P12) WILD-TYPE	43	64	61

Figure S275. Get High-res Image Gene #67: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.31e-11 (Fisher's exact test), Q value = 3.1e-08

Table S276. Gene #67: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 34(17P12) MUTATED	48	40	18
DEL PEAK 34(17P12) WILD-TYPE	16	89	63

Figure S276. Get High-res Image Gene #67: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.3' versus 'CN_CNMF'

P value = 1.36e-08 (Chi-square test), Q value = 9.3e-06

Table S277. Gene #68: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 35(17Q24.3) MUTATED	6	11	16	3	28
DEL PEAK 35(17Q24.3) WILD-TYPE	153	22	46	9	57

Figure S277. Get High-res Image Gene #68: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q24.3' versus 'METHLYATION_CNMF'

P value = 2.29e-05 (Fisher's exact test), Q value = 0.013

Table S278. Gene #68: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 35(17Q24.3) MUTATED	18	27	7
DEL PEAK 35(17Q24.3) WILD-TYPE	95	57	99

Figure S278. Get High-res Image Gene #68: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'CN_CNMF'

P value = 2.59e-18 (Chi-square test), Q value = 2e-15

Table S279. Gene #69: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 36(18Q21.2) MUTATED	33	23	44	2	60
DEL PEAK 36(18Q21.2) WILD-TYPE	126	10	18	10	25

Figure S279. Get High-res Image Gene #69: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.06

Table S280. Gene #69: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 36(18Q21.2) MUTATED	47	55	38
DEL PEAK 36(18Q21.2) WILD-TYPE	66	29	68

Figure S280. Get High-res Image Gene #69: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 0.000324 (Chi-square test), Q value = 0.16

Table S281. Gene #69: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 36(18Q21.2) MUTATED	26	19	23	11	41
DEL PEAK 36(18Q21.2) WILD-TYPE	39	43	23	26	21

Figure S281. Get High-res Image Gene #69: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 0.000296 (Fisher's exact test), Q value = 0.15

Table S282. Gene #69: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 36(18Q21.2) MUTATED	41	35	69
DEL PEAK 36(18Q21.2) WILD-TYPE	64	66	46

Figure S282. Get High-res Image Gene #69: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 3.92e-29 (Chi-square test), Q value = 3.1e-26

Table S283. Gene #70: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 37(19P13.3) MUTATED	9	11	34	3	66
DEL PEAK 37(19P13.3) WILD-TYPE	150	22	28	9	19

Figure S283. Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 5.67e-14 (Fisher's exact test), Q value = 4.2e-11

Table S284. Gene #70: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 37(19P13.3) MUTATED	27	59	21
DEL PEAK 37(19P13.3) WILD-TYPE	86	25	85

Figure S284. Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 4.46e-17 (Chi-square test), Q value = 3.4e-14

Table S285. Gene #70: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 37(19P13.3) MUTATED	14	4	13	8	48
DEL PEAK 37(19P13.3) WILD-TYPE	51	58	33	29	14

Figure S285. Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.76e-19 (Fisher's exact test), Q value = 6.7e-16

Table S286. Gene #70: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 37(19P13.3) MUTATED	51	29	7
DEL PEAK 37(19P13.3) WILD-TYPE	18	84	83

Figure S286. Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 2.64e-09 (Fisher's exact test), Q value = 1.8e-06

Table S287. Gene #70: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 37(19P13.3) MUTATED	26	18	64
DEL PEAK 37(19P13.3) WILD-TYPE	79	83	51

Figure S287. Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.21e-21 (Fisher's exact test), Q value = 9.3e-19

Table S288. Gene #70: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 37(19P13.3) MUTATED	13	63	32
DEL PEAK 37(19P13.3) WILD-TYPE	89	18	106

Figure S288. Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.78e-05 (Fisher's exact test), Q value = 0.027

Table S289. Gene #70: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	131	79
DEL PEAK 37(19P13.3) MUTATED	18	61	14
DEL PEAK 37(19P13.3) WILD-TYPE	46	70	65

Figure S289. Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.22e-19 (Fisher's exact test), Q value = 9.4e-17

Table S290. Gene #70: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 37(19P13.3) MUTATED	51	35	7
DEL PEAK 37(19P13.3) WILD-TYPE	13	94	74

Figure S290. Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.11' versus 'CN_CNMF'

P value = 6.94e-10 (Chi-square test), Q value = 4.9e-07

Table S291. Gene #71: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 38(19Q13.11) MUTATED	2	5	16	3	27
DEL PEAK 38(19Q13.11) WILD-TYPE	157	28	46	9	58

Figure S291. Get High-res Image Gene #71: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.11' versus 'METHLYATION_CNMF'

P value = 8.11e-09 (Fisher's exact test), Q value = 5.6e-06

Table S292. Gene #71: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 38(19Q13.11) MUTATED	14	29	3
DEL PEAK 38(19Q13.11) WILD-TYPE	99	55	103

Figure S292. Get High-res Image Gene #71: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.11' versus 'MRNASEQ_CNMF'

P value = 0.000121 (Chi-square test), Q value = 0.063

Table S293. Gene #71: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 38(19Q13.11) MUTATED	6	2	5	4	19
DEL PEAK 38(19Q13.11) WILD-TYPE	59	60	41	33	43

Figure S293. Get High-res Image Gene #71: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.11' versus 'MIRSEQ_CNMF'

P value = 7.92e-05 (Fisher's exact test), Q value = 0.043

Table S294. Gene #71: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 38(19Q13.11) MUTATED	11	6	30
DEL PEAK 38(19Q13.11) WILD-TYPE	94	95	85

Figure S294. Get High-res Image Gene #71: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.45e-05 (Fisher's exact test), Q value = 0.014

Table S295. Gene #71: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 38(19Q13.11) MUTATED	7	25	15
DEL PEAK 38(19Q13.11) WILD-TYPE	95	56	123

Figure S295. Get High-res Image Gene #71: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000128 (Fisher's exact test), Q value = 0.067

Table S296. Gene #71: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 38(19Q13.11) MUTATED	20	15	5
DEL PEAK 38(19Q13.11) WILD-TYPE	44	114	76

Figure S296. Get High-res Image Gene #71: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 4.06e-11 (Chi-square test), Q value = 2.9e-08

Table S297. Gene #73: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 40(21Q11.2) MUTATED	26	17	37	6	44
DEL PEAK 40(21Q11.2) WILD-TYPE	133	16	25	6	41

Figure S297. Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 3.86e-05 (Fisher's exact test), Q value = 0.022

Table S298. Gene #73: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 40(21Q11.2) MUTATED	36	49	30
DEL PEAK 40(21Q11.2) WILD-TYPE	77	35	76

Figure S298. Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.26e-06 (Fisher's exact test), Q value = 0.00081

Table S299. Gene #73: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 40(21Q11.2) MUTATED	42	28	24
DEL PEAK 40(21Q11.2) WILD-TYPE	27	85	66

Figure S299. Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.000337 (Fisher's exact test), Q value = 0.16

Table S300. Gene #73: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 40(21Q11.2) MUTATED	26	31	57
DEL PEAK 40(21Q11.2) WILD-TYPE	79	70	58

Figure S300. Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.13' versus 'CN_CNMF'

P value = 4.24e-13 (Chi-square test), Q value = 3.1e-10

Table S301. Gene #74: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 41(21Q22.13) MUTATED	29	17	43	6	47
DEL PEAK 41(21Q22.13) WILD-TYPE	130	16	19	6	38

Figure S301. Get High-res Image Gene #74: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.77e-06 (Fisher's exact test), Q value = 0.0029

Table S302. Gene #74: 'del_21q22.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 41(21Q22.13) MUTATED	43	31	27
DEL PEAK 41(21Q22.13) WILD-TYPE	26	82	63

Figure S302. Get High-res Image Gene #74: 'del_21q22.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 4.52e-19 (Chi-square test), Q value = 3.5e-16

Table S303. Gene #75: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 42(22Q13.31) MUTATED	16	11	42	4	49
DEL PEAK 42(22Q13.31) WILD-TYPE	143	22	20	8	36

Figure S303. Get High-res Image Gene #75: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 4.96e-08 (Fisher's exact test), Q value = 3.3e-05

Table S304. Gene #75: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 42(22Q13.31) MUTATED	34	50	21
DEL PEAK 42(22Q13.31) WILD-TYPE	79	34	85

Figure S304. Get High-res Image Gene #75: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000159 (Fisher's exact test), Q value = 0.082

Table S305. Gene #75: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	113	90
DEL PEAK 42(22Q13.31) MUTATED	37	32	21
DEL PEAK 42(22Q13.31) WILD-TYPE	32	81	69

Figure S305. Get High-res Image Gene #75: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 7.85e-05 (Fisher's exact test), Q value = 0.043

Table S306. Gene #75: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	101	115
DEL PEAK 42(22Q13.31) MUTATED	24	27	56
DEL PEAK 42(22Q13.31) WILD-TYPE	81	74	59

Figure S306. Get High-res Image Gene #75: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.48e-08 (Fisher's exact test), Q value = 5e-05

Table S307. Gene #75: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 42(22Q13.31) MUTATED	21	48	38
DEL PEAK 42(22Q13.31) WILD-TYPE	81	33	100

Figure S307. Get High-res Image Gene #75: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.38e-06 (Fisher's exact test), Q value = 0.0027

Table S308. Gene #75: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	129	81
DEL PEAK 42(22Q13.31) MUTATED	38	34	19
DEL PEAK 42(22Q13.31) WILD-TYPE	26	95	62

Figure S308. Get High-res Image Gene #75: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 2.44e-11 (Chi-square test), Q value = 1.8e-08

Table S309. Gene #76: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 43(XP22.2) MUTATED	6	4	22	2	32
DEL PEAK 43(XP22.2) WILD-TYPE	153	29	40	10	53

Figure S309. Get High-res Image Gene #76: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 7.96e-05 (Fisher's exact test), Q value = 0.043

Table S310. Gene #76: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 43(XP22.2) MUTATED	19	30	11
DEL PEAK 43(XP22.2) WILD-TYPE	94	54	95

Figure S310. Get High-res Image Gene #76: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.000284 (Chi-square test), Q value = 0.14

Table S311. Gene #76: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 43(XP22.2) MUTATED	3	8	8	10	21
DEL PEAK 43(XP22.2) WILD-TYPE	62	54	38	27	41

Figure S311. Get High-res Image Gene #76: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000102 (Fisher's exact test), Q value = 0.054

Table S312. Gene #76: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	81	138
DEL PEAK 43(XP22.2) MUTATED	12	29	20
DEL PEAK 43(XP22.2) WILD-TYPE	90	52	118

Figure S312. Get High-res Image Gene #76: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 3.48e-08 (Chi-square test), Q value = 2.3e-05

Table S313. Gene #77: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 44(XP21.1) MUTATED	8	6	21	1	27
DEL PEAK 44(XP21.1) WILD-TYPE	151	27	41	11	58

Figure S313. Get High-res Image Gene #77: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'CN_CNMF'

P value = 7.28e-05 (Chi-square test), Q value = 0.04

Table S314. Gene #78: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	159	33	62	12	85
DEL PEAK 45(XQ21.33) MUTATED	7	5	14	0	19
DEL PEAK 45(XQ21.33) WILD-TYPE	152	28	48	12	66

Figure S314. Get High-res Image Gene #78: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 0.000413 (Fisher's exact test), Q value = 0.2

Table S315. Gene #78: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	84	106
DEL PEAK 45(XQ21.33) MUTATED	12	20	5
DEL PEAK 45(XQ21.33) WILD-TYPE	101	64	101

Figure S315. Get High-res Image Gene #78: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = STAD-TP.transferedmergedcluster.txt
Number of patients = 351
Number of significantly focal cnvs = 78
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[2] 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)

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

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