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

Brain Lower Grade Glioma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1639NDM

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 48 focal events and 12 molecular subtypes across 463 patients, 178 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_1q43 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_2p24.3 cnv correlated to 'MRNASEQ_CNMF'.
amp_3q26.32 cnv correlated to 'MRNASEQ_CNMF'.
amp_4q12 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_7q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_7q32.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_8q24.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_12p13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_12q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_13q34 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_15q26.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_17q25.1 cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_xp11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p36.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p32.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_3p21.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q29 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_5p15.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_5q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_6p25.3 cnv correlated to 'CN_CNMF'.
del_6q24.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_8q24.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_9p23 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_10q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_12q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_13q34 cnv correlated to 'CN_CNMF'.
del_14q24.3 cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.42 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF'.
del_xq21.1 cnv correlated to 'MRNASEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 48 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 178 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test
del 1p32 3	179 (39%)	284	0.0286 (1.00)	0.000173 (0.0703)	1.19e-42 (6.45e-40)	2.83e-92 (1.57e-89)	0.00049 (0.187)	0.22 (1.00)	1.69e-47 (9.22e-45)	4.89e-56 (2.7e-53)	3.56e-21 (1.89e-18)	1.8e-05 (0.00784)	6.55e-25 (3.5e-22)	0.000134 (0.0549)
del 10q26 3	139 (30%)	324	0.0838 (1.00)	0.164 (1.00)	6.84e-36 (3.71e-33)	4.29e-35 (2.32e-32)	8.98e-07 (0.000411)	0.000228 (0.0913)	5.82e-26 (3.13e-23)	9.08e-18 (4.76e-15)	1.18e-12 (5.97e-10)	4.5e-06 (0.00202)	8.57e-17 (4.47e-14)	0.000307 (0.121)
amp 7p11 2	121 (26%)	342	0.764 (1.00)	0.495 (1.00)	3.15e-54 (1.74e-51)	3.25e-29 (1.75e-26)	4.73e-05 (0.0201)	0.00405 (1.00)	1.07e-20 (5.66e-18)	2.9e-08 (1.37e-05)	2e-11 (1.01e-08)	7.91e-05 (0.0328)	1.34e-13 (6.85e-11)	0.0835 (1.00)
del 1p36 23	194 (42%)	269	0.00608 (1.00)	0.00067 (0.252)	7.23e-37 (3.92e-34)	7.01e-82 (3.87e-79)	0.00083 (0.308)	0.568 (1.00)	6.95e-43 (3.79e-40)	1.04e-50 (5.72e-48)	3.35e-21 (1.78e-18)	5.84e-05 (0.0246)	3.36e-25 (1.8e-22)	0.000312 (0.123)
del 9p21 3	158 (34%)	305	0.333 (1.00)	0.0153 (1.00)	6.16e-18 (3.23e-15)	4.21e-16 (2.19e-13)	1.75e-05 (0.00763)	4.94e-05 (0.0209)	1.09e-09 (5.31e-07)	3.52e-05 (0.0151)	1.05e-05 (0.00462)	0.0515 (1.00)	1.96e-06 (0.000892)	0.173 (1.00)
amp 7q31 2	164 (35%)	299	1 (1.00)	0.761 (1.00)	6.28e-47 (3.43e-44)	4.27e-16 (2.21e-13)	0.00435 (1.00)	0.0205 (1.00)	1.84e-09 (8.94e-07)	5.14e-07 (0.000236)	3.46e-05 (0.0148)	0.00172 (0.612)	4.68e-05 (0.0199)	0.563 (1.00)
amp 7q32 3	173 (37%)	290	0.695 (1.00)	0.948 (1.00)	2.53e-48 (1.39e-45)	2.18e-16 (1.13e-13)	0.00651 (1.00)	0.0155 (1.00)	6.92e-09 (3.33e-06)	6.46e-07 (0.000296)	2.86e-05 (0.0124)	0.00125 (0.449)	0.000106 (0.0435)	0.407 (1.00)
amp 10p15 3	62 (13%)	401	0.526 (1.00)	0.207 (1.00)	2.32e-19 (1.22e-16)	3.05e-16 (1.58e-13)	0.0299 (1.00)	0.184 (1.00)	1.11e-11 (5.61e-09)	1.99e-08 (9.45e-06)	0.000347 (0.135)	0.17 (1.00)	0.000281 (0.112)	0.421 (1.00)
amp 19p13 3	115 (25%)	348	0.0752 (1.00)	0.122 (1.00)	6.95e-10 (3.41e-07)	1.37e-17 (7.18e-15)	0.879 (1.00)	0.615 (1.00)	3.11e-11 (1.56e-08)	1.74e-06 (0.00079)	0.000177 (0.0717)	0.952 (1.00)	1.36e-06 (0.000618)	0.585 (1.00)
amp 19p13 2	109 (24%)	354	0.0752 (1.00)	0.122 (1.00)	8.89e-13 (4.53e-10)	7.34e-21 (3.89e-18)	0.276 (1.00)	0.265 (1.00)	1.18e-12 (6e-10)	4.86e-06 (0.00217)	4.82e-06 (0.00215)	0.388 (1.00)	8.27e-08 (3.87e-05)	0.358 (1.00)
del 5q34	56 (12%)	407	0.446 (1.00)	0.0182 (1.00)	6.87e-12 (3.48e-09)	7.67e-08 (3.6e-05)	0.171 (1.00)	1 (1.00)	2.19e-07 (0.000102)	0.000396 (0.152)	2.03e-06 (0.000917)	0.313 (1.00)	9.73e-06 (0.00429)	0.00587 (1.00)
del 19q13 42	250 (54%)	213	0.0353 (1.00)	0.127 (1.00)	3.99e-30 (2.15e-27)	2.68e-52 (1.47e-49)	0.00215 (0.76)	0.608 (1.00)	8.21e-25 (4.38e-22)	1.28e-32 (6.92e-30)	1.3e-10 (6.46e-08)	0.000992 (0.365)	1e-11 (5.06e-09)	0.0976 (1.00)
amp 8q24 13	92 (20%)	371	0.37 (1.00)	0.164 (1.00)	5.52e-19 (2.9e-16)	5.22e-15 (2.69e-12)	0.043 (1.00)	0.917 (1.00)	1.29e-09 (6.3e-07)	0.000271 (0.109)	0.00286 (0.99)	0.77 (1.00)	0.000104 (0.0429)	0.0876 (1.00)
amp 12p13 32	66 (14%)	397	0.864 (1.00)	0.0486 (1.00)	5.59e-14 (2.87e-11)	8.12e-08 (3.81e-05)	0.117 (1.00)	0.211 (1.00)	0.000276 (0.11)	2.66e-05 (0.0115)	4.8e-05 (0.0204)	0.0145 (1.00)	0.00305 (1.00)	0.00483 (1.00)
amp 12q14 1	34 (7%)	429			1.19e-05 (0.0052)	6.53e-06 (0.0029)	0.0161 (1.00)	0.708 (1.00)	7.82e-09 (3.74e-06)	0.00362 (1.00)	4.37e-06 (0.00196)	0.00301 (1.00)	1.11e-07 (5.2e-05)	0.017 (1.00)
del 3p21 1	45 (10%)	418	1 (1.00)	0.00815 (1.00)	3.24e-06 (0.00146)	0.000943 (0.349)	0.000608 (0.23)	0.129 (1.00)	5.06e-11 (2.53e-08)	0.000147 (0.0599)	0.00429 (1.00)	0.0446 (1.00)	0.0511 (1.00)	0.000331 (0.129)
del 13q14 2	129 (28%)	334	0.18 (1.00)	0.000618 (0.234)	2.16e-13 (1.1e-10)	0.000484 (0.185)	0.034 (1.00)	0.807 (1.00)	0.000605 (0.23)	0.000282 (0.112)	0.0217 (1.00)	0.173 (1.00)	0.0456 (1.00)	0.101 (1.00)
del 13q14 2	131 (28%)	332	0.18 (1.00)	0.000618 (0.234)	8.51e-14 (4.36e-11)	0.000272 (0.109)	0.0336 (1.00)	0.749 (1.00)	0.000377 (0.146)	0.000131 (0.0538)	0.0203 (1.00)	0.109 (1.00)	0.0325 (1.00)	0.0749 (1.00)
del 22q13 31	68 (15%)	395	0.25 (1.00)	0.0588 (1.00)	2.01e-14 (1.03e-11)	1.61e-09 (7.83e-07)	0.000215 (0.0867)	0.0104 (1.00)	3.59e-10 (1.78e-07)	3.38e-07 (0.000157)	0.031 (1.00)	0.06 (1.00)	0.00529 (1.00)	0.0177 (1.00)
del 22q13 31	68 (15%)	395	0.25 (1.00)	0.0588 (1.00)	2.01e-14 (1.03e-11)	1.61e-09 (7.83e-07)	0.000215 (0.0867)	0.0104 (1.00)	3.59e-10 (1.78e-07)	3.38e-07 (0.000157)	0.031 (1.00)	0.06 (1.00)	0.00529 (1.00)	0.0177 (1.00)
del 2q37 3	69 (15%)	394	0.37 (1.00)	0.164 (1.00)	9.92e-10 (4.86e-07)	3.39e-11 (1.7e-08)	0.00512 (1.00)	0.0126 (1.00)	1.22e-07 (5.68e-05)	2.03e-06 (0.000917)	0.0913 (1.00)	0.0367 (1.00)	0.0262 (1.00)	0.00221 (0.777)
del 11p15 5	95 (21%)	368	0.642 (1.00)	0.000741 (0.277)	1.16e-19 (6.12e-17)	8.29e-22 (4.42e-19)	0.101 (1.00)	0.897 (1.00)	3.62e-09 (1.75e-06)	3.58e-11 (1.79e-08)	0.225 (1.00)	0.449 (1.00)	0.155 (1.00)	0.0903 (1.00)
del 14q24 3	107 (23%)	356	0.303 (1.00)	0.171 (1.00)	0.00898 (1.00)	0.0173 (1.00)	0.0016 (0.57)	0.0125 (1.00)	0.000322 (0.126)	0.00241 (0.842)	4.07e-05 (0.0174)	0.00358 (1.00)	0.000175 (0.071)	0.000288 (0.114)
amp 1q32 1	38 (8%)	425			3.82e-10 (1.88e-07)	7.46e-09 (3.57e-06)	0.167 (1.00)	0.893 (1.00)	4.04e-08 (1.91e-05)	0.0115 (1.00)	0.00342 (1.00)	0.399 (1.00)	0.000949 (0.35)	0.344 (1.00)
amp 1q43	28 (6%)	435			6.27e-05 (0.0263)	0.000185 (0.0746)	0.0507 (1.00)	1 (1.00)	6.59e-10 (3.24e-07)	0.0748 (1.00)	0.00833 (1.00)	0.541 (1.00)	0.00113 (0.412)	0.046 (1.00)
amp 4q12	26 (6%)	437	1 (1.00)	0.0879 (1.00)	7.57e-05 (0.0316)	0.00112 (0.409)	0.00883 (1.00)	0.594 (1.00)	1.37e-15 (7.06e-13)	0.00115 (0.417)	0.000368 (0.143)	0.422 (1.00)	0.00992 (1.00)	0.0209 (1.00)
amp xp11 22	47 (10%)	416	0.651 (1.00)	0.892 (1.00)	2e-10 (9.91e-08)	4.71e-09 (2.28e-06)	0.0956 (1.00)	0.202 (1.00)	0.00277 (0.966)	0.000386 (0.149)	0.197 (1.00)	0.185 (1.00)	0.116 (1.00)	0.0669 (1.00)
del 4q34 3	127 (27%)	336	1 (1.00)	0.602 (1.00)	9.16e-05 (0.0379)	5.67e-08 (2.67e-05)	0.163 (1.00)	0.0515 (1.00)	5.67e-05 (0.0239)	0.0966 (1.00)	0.0279 (1.00)	0.193 (1.00)	0.0652 (1.00)	0.79 (1.00)
del 12q12	64 (14%)	399	1 (1.00)	0.00815 (1.00)	1.5e-10 (7.45e-08)	9.81e-09 (4.67e-06)	0.9 (1.00)	0.861 (1.00)	0.00813 (1.00)	7e-05 (0.0292)	0.00184 (0.651)	0.434 (1.00)	0.00076 (0.284)	0.254 (1.00)
amp 13q34	19 (4%)	444			1.38e-05 (0.00602)	0.000419 (0.161)	0.188 (1.00)	0.27 (1.00)	0.0391 (1.00)	0.0127 (1.00)	0.847 (1.00)	0.347 (1.00)	0.854 (1.00)	0.244 (1.00)
amp 15q26 3	18 (4%)	445	1 (1.00)	0.0879 (1.00)	5.87e-06 (0.00261)	0.000738 (0.277)	0.222 (1.00)	0.628 (1.00)	9.21e-07 (0.000421)	0.00743 (1.00)	0.0132 (1.00)	0.761 (1.00)	0.269 (1.00)	0.648 (1.00)
amp 17q25 1	35 (8%)	428			0.0199 (1.00)	0.359 (1.00)	0.331 (1.00)	0.782 (1.00)	2.64e-07 (0.000123)	0.225 (1.00)	0.0904 (1.00)	0.173 (1.00)	0.253 (1.00)	0.000458 (0.175)
del 3q29	41 (9%)	422	0.175 (1.00)	0.561 (1.00)	7.42e-09 (3.56e-06)	0.00315 (1.00)	0.405 (1.00)	0.668 (1.00)	5.02e-09 (2.42e-06)	0.00296 (1.00)	0.197 (1.00)	0.0493 (1.00)	0.335 (1.00)	0.0155 (1.00)
del 5p15 33	47 (10%)	416	1 (1.00)	0.0422 (1.00)	8.95e-09 (4.27e-06)	3.13e-05 (0.0135)	0.86 (1.00)	0.614 (1.00)	0.0162 (1.00)	0.00179 (0.637)	0.00153 (0.547)	0.686 (1.00)	0.00307 (1.00)	0.289 (1.00)
del 6q24 3	74 (16%)	389	0.17 (1.00)	0.24 (1.00)	0.000373 (0.145)	3.28e-05 (0.0141)	0.101 (1.00)	0.339 (1.00)	0.00879 (1.00)	0.00109 (0.4)	0.00486 (1.00)	0.0434 (1.00)	0.00282 (0.978)	0.0288 (1.00)
del 8q24 3	26 (6%)	437			2.83e-06 (0.00128)	7.69e-06 (0.0034)	0.928 (1.00)	0.64 (1.00)	0.0122 (1.00)	0.00115 (0.417)	0.00311 (1.00)	0.0349 (1.00)	0.0883 (1.00)	0.0577 (1.00)
del 9p23	134 (29%)	329	0.446 (1.00)	0.607 (1.00)	1.66e-08 (7.87e-06)	1.3e-05 (0.00567)	0.0394 (1.00)	0.028 (1.00)	0.00105 (0.385)	0.0888 (1.00)	0.0405 (1.00)	0.705 (1.00)	0.207 (1.00)	0.285 (1.00)
amp 2p24 3	20 (4%)	443	0.615 (1.00)	0.0468 (1.00)	0.000815 (0.303)	0.119 (1.00)	0.49 (1.00)	0.321 (1.00)	7.25e-06 (0.00321)	0.122 (1.00)	0.243 (1.00)	0.347 (1.00)	0.367 (1.00)	0.244 (1.00)
amp 3q26 32	18 (4%)	445			0.0295 (1.00)	0.0034 (1.00)	0.0147 (1.00)	0.605 (1.00)	6.16e-05 (0.0259)	0.0238 (1.00)	0.00307 (1.00)	0.0904 (1.00)	0.00115 (0.416)	0.0699 (1.00)
del 6p25 3	48 (10%)	415			0.000135 (0.0553)	0.148 (1.00)	0.238 (1.00)	0.652 (1.00)	0.0249 (1.00)	0.0644 (1.00)	0.331 (1.00)	0.183 (1.00)	0.251 (1.00)	0.634 (1.00)
del 13q34	98 (21%)	365	0.508 (1.00)	0.106 (1.00)	4.7e-07 (0.000217)	0.0628 (1.00)	0.087 (1.00)	0.526 (1.00)	0.018 (1.00)	0.00881 (1.00)	0.0185 (1.00)	0.126 (1.00)	0.0513 (1.00)	0.0508 (1.00)
del xp21 1	93 (20%)	370	0.839 (1.00)	0.131 (1.00)	7.65e-05 (0.0318)	0.0102 (1.00)	0.0144 (1.00)	0.0894 (1.00)	0.0413 (1.00)	0.0178 (1.00)	0.101 (1.00)	1 (1.00)	0.0867 (1.00)	0.021 (1.00)
del xq21 1	67 (14%)	396	0.839 (1.00)	0.022 (1.00)	0.252 (1.00)	0.024 (1.00)	0.0544 (1.00)	0.0317 (1.00)	2.1e-05 (0.0091)	0.00802 (1.00)	0.00326 (1.00)	0.922 (1.00)	0.00278 (0.969)	0.447 (1.00)
amp 11q23 3	76 (16%)	387	0.225 (1.00)	0.025 (1.00)	0.284 (1.00)	0.0437 (1.00)	0.106 (1.00)	0.143 (1.00)	0.6 (1.00)	0.73 (1.00)	0.701 (1.00)	0.938 (1.00)	0.306 (1.00)	0.798 (1.00)
del 1q43	29 (6%)	434			0.0935 (1.00)	0.0164 (1.00)	0.1 (1.00)	0.54 (1.00)	0.16 (1.00)	0.0342 (1.00)	0.145 (1.00)	0.6 (1.00)	0.334 (1.00)	0.54 (1.00)
del 7p22 3	20 (4%)	443			0.0193 (1.00)	0.0549 (1.00)	0.32 (1.00)	0.383 (1.00)	0.137 (1.00)	0.578 (1.00)	0.813 (1.00)	0.761 (1.00)	0.695 (1.00)	0.257 (1.00)
del 12p13 1	37 (8%)	426			0.0164 (1.00)	0.00227 (0.798)	0.197 (1.00)	0.875 (1.00)	0.00641 (1.00)	0.00114 (0.414)	0.015 (1.00)	0.399 (1.00)	0.0992 (1.00)	0.846 (1.00)
del 18q23	71 (15%)	392	0.321 (1.00)	0.316 (1.00)	0.439 (1.00)	0.0112 (1.00)	0.454 (1.00)	0.11 (1.00)	0.417 (1.00)	0.61 (1.00)	0.876 (1.00)	0.142 (1.00)	0.895 (1.00)	0.796 (1.00)

'amp_1q32.1' versus 'CN_CNMF'

P value = 3.82e-10 (Fisher's exact test), Q value = 1.9e-07

Table S1. Gene #1: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 1(1Q32.1) MUTATED	6	27	5
AMP PEAK 1(1Q32.1) WILD-TYPE	133	83	209

Figure S1. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'METHLYATION_CNMF'

P value = 7.46e-09 (Fisher's exact test), Q value = 3.6e-06

Table S2. Gene #1: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
AMP PEAK 1(1Q32.1) MUTATED	9	21	3	5
AMP PEAK 1(1Q32.1) WILD-TYPE	190	44	50	136

Figure S2. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 4.04e-08 (Chi-square test), Q value = 1.9e-05

Table S3. Gene #1: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 1(1Q32.1) MUTATED	1	21	2	11	2	1
AMP PEAK 1(1Q32.1) WILD-TYPE	115	68	92	115	9	24

Figure S3. Get High-res Image Gene #1: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q43' versus 'CN_CNMF'

P value = 6.27e-05 (Fisher's exact test), Q value = 0.026

Table S4. Gene #2: 'amp_1q43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 2(1Q43) MUTATED	8	16	4
AMP PEAK 2(1Q43) WILD-TYPE	131	94	210

Figure S4. Get High-res Image Gene #2: 'amp_1q43' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q43' versus 'METHLYATION_CNMF'

P value = 0.000185 (Fisher's exact test), Q value = 0.075

Table S5. Gene #2: 'amp_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
AMP PEAK 2(1Q43) MUTATED	10	13	1	4
AMP PEAK 2(1Q43) WILD-TYPE	189	52	52	137

Figure S5. Get High-res Image Gene #2: 'amp_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q43' versus 'MRNASEQ_CNMF'

P value = 6.59e-10 (Chi-square test), Q value = 3.2e-07

Table S6. Gene #2: 'amp_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 2(1Q43) MUTATED	0	13	2	7	5	1
AMP PEAK 2(1Q43) WILD-TYPE	116	76	92	119	6	24

Figure S6. Get High-res Image Gene #2: 'amp_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CNMF'

P value = 7.25e-06 (Chi-square test), Q value = 0.0032

Table S7. Gene #3: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 3(2P24.3) MUTATED	3	6	2	5	4	0
AMP PEAK 3(2P24.3) WILD-TYPE	113	83	92	121	7	25

Figure S7. Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CNMF'

P value = 6.16e-05 (Chi-square test), Q value = 0.026

Table S8. Gene #4: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 4(3Q26.32) MUTATED	2	8	1	4	3	0
AMP PEAK 4(3Q26.32) WILD-TYPE	114	81	93	122	8	25

Figure S8. Get High-res Image Gene #4: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q12' versus 'CN_CNMF'

P value = 7.57e-05 (Fisher's exact test), Q value = 0.032

Table S9. Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 5(4Q12) MUTATED	17	6	3
AMP PEAK 5(4Q12) WILD-TYPE	122	104	211

Figure S9. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 1.37e-15 (Chi-square test), Q value = 7.1e-13

Table S10. Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 5(4Q12) MUTATED	4	8	0	5	7	2
AMP PEAK 5(4Q12) WILD-TYPE	112	81	94	121	4	23

Figure S10. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MIRSEQ_CNMF'

P value = 0.000368 (Chi-square test), Q value = 0.14

Table S11. Gene #5: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
AMP PEAK 5(4Q12) MUTATED	1	6	7	2	7	0	1
AMP PEAK 5(4Q12) WILD-TYPE	61	70	23	39	129	63	26

Figure S11. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'CN_CNMF'

P value = 3.15e-54 (Fisher's exact test), Q value = 1.7e-51

Table S12. Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 6(7P11.2) MUTATED	21	92	8
AMP PEAK 6(7P11.2) WILD-TYPE	118	18	206

Figure S12. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 3.25e-29 (Fisher's exact test), Q value = 1.7e-26

Table S13. Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
AMP PEAK 6(7P11.2) MUTATED	36	56	14	13
AMP PEAK 6(7P11.2) WILD-TYPE	163	9	39	128

Figure S13. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 4.73e-05 (Fisher's exact test), Q value = 0.02

Table S14. Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
AMP PEAK 6(7P11.2) MUTATED	13	31	12	12
AMP PEAK 6(7P11.2) WILD-TYPE	39	31	56	62

Figure S14. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 1.07e-20 (Chi-square test), Q value = 5.7e-18

Table S15. Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 6(7P11.2) MUTATED	19	59	8	25	5	3
AMP PEAK 6(7P11.2) WILD-TYPE	97	30	86	101	6	22

Figure S15. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.9e-08 (Fisher's exact test), Q value = 1.4e-05

Table S16. Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
AMP PEAK 6(7P11.2) MUTATED	84	7	28
AMP PEAK 6(7P11.2) WILD-TYPE	140	73	129

Figure S16. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 2e-11 (Chi-square test), Q value = 1e-08

Table S17. Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
AMP PEAK 6(7P11.2) MUTATED	14	46	8	4	23	16	3
AMP PEAK 6(7P11.2) WILD-TYPE	48	30	22	37	113	47	24

Figure S17. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.91e-05 (Fisher's exact test), Q value = 0.033

Table S18. Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	16	225
AMP PEAK 6(7P11.2) MUTATED	35	1	78
AMP PEAK 6(7P11.2) WILD-TYPE	159	15	147

Figure S18. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.34e-13 (Chi-square test), Q value = 6.9e-11

Table S19. Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
AMP PEAK 6(7P11.2) MUTATED	17	49	5	23	7	7	6
AMP PEAK 6(7P11.2) WILD-TYPE	70	28	50	101	32	15	25

Figure S19. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'CN_CNMF'

P value = 6.28e-47 (Fisher's exact test), Q value = 3.4e-44

Table S20. Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 7(7Q31.2) MUTATED	45	98	21
AMP PEAK 7(7Q31.2) WILD-TYPE	94	12	193

Figure S20. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 4.27e-16 (Fisher's exact test), Q value = 2.2e-13

Table S21. Gene #7: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
AMP PEAK 7(7Q31.2) MUTATED	70	52	13	27
AMP PEAK 7(7Q31.2) WILD-TYPE	129	13	40	114

Figure S21. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1.84e-09 (Chi-square test), Q value = 8.9e-07

Table S22. Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 7(7Q31.2) MUTATED	43	55	14	38	6	6
AMP PEAK 7(7Q31.2) WILD-TYPE	73	34	80	88	5	19

Figure S22. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.14e-07 (Fisher's exact test), Q value = 0.00024

Table S23. Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
AMP PEAK 7(7Q31.2) MUTATED	103	12	47
AMP PEAK 7(7Q31.2) WILD-TYPE	121	68	110

Figure S23. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 3.46e-05 (Chi-square test), Q value = 0.015

Table S24. Gene #7: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
AMP PEAK 7(7Q31.2) MUTATED	23	45	10	7	41	25	5
AMP PEAK 7(7Q31.2) WILD-TYPE	39	31	20	34	95	38	22

Figure S24. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.68e-05 (Chi-square test), Q value = 0.02

Table S25. Gene #7: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
AMP PEAK 7(7Q31.2) MUTATED	33	46	11	37	14	8	7
AMP PEAK 7(7Q31.2) WILD-TYPE	54	31	44	87	25	14	24

Figure S25. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q32.3' versus 'CN_CNMF'

P value = 2.53e-48 (Fisher's exact test), Q value = 1.4e-45

Table S26. Gene #8: 'amp_7q32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 8(7Q32.3) MUTATED	48	101	24
AMP PEAK 8(7Q32.3) WILD-TYPE	91	9	190

Figure S26. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q32.3' versus 'METHLYATION_CNMF'

P value = 2.18e-16 (Fisher's exact test), Q value = 1.1e-13

Table S27. Gene #8: 'amp_7q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
AMP PEAK 8(7Q32.3) MUTATED	76	53	14	28
AMP PEAK 8(7Q32.3) WILD-TYPE	123	12	39	113

Figure S27. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CNMF'

P value = 6.92e-09 (Chi-square test), Q value = 3.3e-06

Table S28. Gene #8: 'amp_7q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 8(7Q32.3) MUTATED	48	55	15	41	6	6
AMP PEAK 8(7Q32.3) WILD-TYPE	68	34	79	85	5	19

Figure S28. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.46e-07 (Fisher's exact test), Q value = 3e-04

Table S29. Gene #8: 'amp_7q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
AMP PEAK 8(7Q32.3) MUTATED	107	13	51
AMP PEAK 8(7Q32.3) WILD-TYPE	117	67	106

Figure S29. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_CNMF'

P value = 2.86e-05 (Chi-square test), Q value = 0.012

Table S30. Gene #8: 'amp_7q32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
AMP PEAK 8(7Q32.3) MUTATED	29	45	10	7	44	25	5
AMP PEAK 8(7Q32.3) WILD-TYPE	33	31	20	34	92	38	22

Figure S30. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000106 (Chi-square test), Q value = 0.044

Table S31. Gene #8: 'amp_7q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
AMP PEAK 8(7Q32.3) MUTATED	38	46	12	40	14	8	7
AMP PEAK 8(7Q32.3) WILD-TYPE	49	31	43	84	25	14	24

Figure S31. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.13' versus 'CN_CNMF'

P value = 5.52e-19 (Fisher's exact test), Q value = 2.9e-16

Table S32. Gene #9: 'amp_8q24.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 9(8Q24.13) MUTATED	64	15	13
AMP PEAK 9(8Q24.13) WILD-TYPE	75	95	201

Figure S32. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.13' versus 'METHLYATION_CNMF'

P value = 5.22e-15 (Fisher's exact test), Q value = 2.7e-12

Table S33. Gene #9: 'amp_8q24.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
AMP PEAK 9(8Q24.13) MUTATED	75	3	5	9
AMP PEAK 9(8Q24.13) WILD-TYPE	124	62	48	132

Figure S33. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.13' versus 'MRNASEQ_CNMF'

P value = 1.29e-09 (Chi-square test), Q value = 6.3e-07

Table S34. Gene #9: 'amp_8q24.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 9(8Q24.13) MUTATED	44	6	6	23	5	7
AMP PEAK 9(8Q24.13) WILD-TYPE	72	83	88	103	6	18

Figure S34. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000271 (Fisher's exact test), Q value = 0.11

Table S35. Gene #9: 'amp_8q24.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
AMP PEAK 9(8Q24.13) MUTATED	58	5	28
AMP PEAK 9(8Q24.13) WILD-TYPE	166	75	129

Figure S35. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000104 (Chi-square test), Q value = 0.043

Table S36. Gene #9: 'amp_8q24.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
AMP PEAK 9(8Q24.13) MUTATED	32	7	4	22	9	5	6
AMP PEAK 9(8Q24.13) WILD-TYPE	55	70	51	102	30	17	25

Figure S36. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10p15.3' versus 'CN_CNMF'

P value = 2.32e-19 (Fisher's exact test), Q value = 1.2e-16

Table S37. Gene #10: 'amp_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 10(10P15.3) MUTATED	51	5	6
AMP PEAK 10(10P15.3) WILD-TYPE	88	105	208

Figure S37. Get High-res Image Gene #10: 'amp_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.3' versus 'METHLYATION_CNMF'

P value = 3.05e-16 (Fisher's exact test), Q value = 1.6e-13

Table S38. Gene #10: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
AMP PEAK 10(10P15.3) MUTATED	56	2	4	0
AMP PEAK 10(10P15.3) WILD-TYPE	143	63	49	141

Figure S38. Get High-res Image Gene #10: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.3' versus 'MRNASEQ_CNMF'

P value = 1.11e-11 (Chi-square test), Q value = 5.6e-09

Table S39. Gene #10: 'amp_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 10(10P15.3) MUTATED	34	6	0	13	6	3
AMP PEAK 10(10P15.3) WILD-TYPE	82	83	94	113	5	22

Figure S39. Get High-res Image Gene #10: 'amp_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.99e-08 (Fisher's exact test), Q value = 9.4e-06

Table S40. Gene #10: 'amp_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
AMP PEAK 10(10P15.3) MUTATED	49	0	13
AMP PEAK 10(10P15.3) WILD-TYPE	175	80	144

Figure S40. Get High-res Image Gene #10: 'amp_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.000347 (Chi-square test), Q value = 0.14

Table S41. Gene #10: 'amp_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
AMP PEAK 10(10P15.3) MUTATED	14	8	11	2	12	10	2
AMP PEAK 10(10P15.3) WILD-TYPE	48	68	19	39	124	53	25

Figure S41. Get High-res Image Gene #10: 'amp_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000281 (Chi-square test), Q value = 0.11

Table S42. Gene #10: 'amp_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
AMP PEAK 10(10P15.3) MUTATED	22	5	3	12	7	7	3
AMP PEAK 10(10P15.3) WILD-TYPE	65	72	52	112	32	15	28

Figure S42. Get High-res Image Gene #10: 'amp_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.32' versus 'CN_CNMF'

P value = 5.59e-14 (Fisher's exact test), Q value = 2.9e-11

Table S43. Gene #12: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 12(12P13.32) MUTATED	46	13	7
AMP PEAK 12(12P13.32) WILD-TYPE	93	97	207

Figure S43. Get High-res Image Gene #12: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.32' versus 'METHLYATION_CNMF'

P value = 8.12e-08 (Fisher's exact test), Q value = 3.8e-05

Table S44. Gene #12: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
AMP PEAK 12(12P13.32) MUTATED	49	9	3	5
AMP PEAK 12(12P13.32) WILD-TYPE	150	56	50	136

Figure S44. Get High-res Image Gene #12: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CNMF'

P value = 0.000276 (Chi-square test), Q value = 0.11

Table S45. Gene #12: 'amp_12p13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 12(12P13.32) MUTATED	27	15	5	10	4	5
AMP PEAK 12(12P13.32) WILD-TYPE	89	74	89	116	7	20

Figure S45. Get High-res Image Gene #12: 'amp_12p13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.012

Table S46. Gene #12: 'amp_12p13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
AMP PEAK 12(12P13.32) MUTATED	49	4	13
AMP PEAK 12(12P13.32) WILD-TYPE	175	76	144

Figure S46. Get High-res Image Gene #12: 'amp_12p13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'MIRSEQ_CNMF'

P value = 4.8e-05 (Chi-square test), Q value = 0.02

Table S47. Gene #12: 'amp_12p13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
AMP PEAK 12(12P13.32) MUTATED	16	10	12	6	10	11	1
AMP PEAK 12(12P13.32) WILD-TYPE	46	66	18	35	126	52	26

Figure S47. Get High-res Image Gene #12: 'amp_12p13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.0052

Table S48. Gene #13: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 13(12Q14.1) MUTATED	10	19	5
AMP PEAK 13(12Q14.1) WILD-TYPE	129	91	209

Figure S48. Get High-res Image Gene #13: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

P value = 6.53e-06 (Fisher's exact test), Q value = 0.0029

Table S49. Gene #13: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
AMP PEAK 13(12Q14.1) MUTATED	13	16	1	4
AMP PEAK 13(12Q14.1) WILD-TYPE	186	49	52	137

Figure S49. Get High-res Image Gene #13: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 7.82e-09 (Chi-square test), Q value = 3.7e-06

Table S50. Gene #13: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 13(12Q14.1) MUTATED	3	20	4	3	3	1
AMP PEAK 13(12Q14.1) WILD-TYPE	113	69	90	123	8	24

Figure S50. Get High-res Image Gene #13: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MIRSEQ_CNMF'

P value = 4.37e-06 (Chi-square test), Q value = 0.002

Table S51. Gene #13: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
AMP PEAK 13(12Q14.1) MUTATED	2	16	6	1	4	3	1
AMP PEAK 13(12Q14.1) WILD-TYPE	60	60	24	40	132	60	26

Figure S51. Get High-res Image Gene #13: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.11e-07 (Chi-square test), Q value = 5.2e-05

Table S52. Gene #13: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
AMP PEAK 13(12Q14.1) MUTATED	2	17	1	2	4	5	2
AMP PEAK 13(12Q14.1) WILD-TYPE	85	60	54	122	35	17	29

Figure S52. Get High-res Image Gene #13: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'CN_CNMF'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.006

Table S53. Gene #14: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 14(13Q34) MUTATED	11	8	0
AMP PEAK 14(13Q34) WILD-TYPE	128	102	214

Figure S53. Get High-res Image Gene #14: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 0.000419 (Fisher's exact test), Q value = 0.16

Table S54. Gene #14: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
AMP PEAK 14(13Q34) MUTATED	16	3	0	0
AMP PEAK 14(13Q34) WILD-TYPE	183	62	53	141

Figure S54. Get High-res Image Gene #14: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 5.87e-06 (Fisher's exact test), Q value = 0.0026

Table S55. Gene #15: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 15(15Q26.3) MUTATED	13	5	0
AMP PEAK 15(15Q26.3) WILD-TYPE	126	105	214

Figure S55. Get High-res Image Gene #15: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 9.21e-07 (Chi-square test), Q value = 0.00042

Table S56. Gene #15: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 15(15Q26.3) MUTATED	6	4	0	3	4	1
AMP PEAK 15(15Q26.3) WILD-TYPE	110	85	94	123	7	24

Figure S56. Get High-res Image Gene #15: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 2.64e-07 (Chi-square test), Q value = 0.00012

Table S57. Gene #16: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 16(17Q25.1) MUTATED	7	9	6	7	6	0
AMP PEAK 16(17Q25.1) WILD-TYPE	109	80	88	119	5	25

Figure S57. Get High-res Image Gene #16: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000458 (Fisher's exact test), Q value = 0.18

Table S58. Gene #16: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	196	234
AMP PEAK 16(17Q25.1) MUTATED	3	8	22
AMP PEAK 16(17Q25.1) WILD-TYPE	2	188	212

Figure S58. Get High-res Image Gene #16: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.3' versus 'CN_CNMF'

P value = 6.95e-10 (Fisher's exact test), Q value = 3.4e-07

Table S59. Gene #17: 'amp_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 17(19P13.3) MUTATED	9	36	70
AMP PEAK 17(19P13.3) WILD-TYPE	130	74	144

Figure S59. Get High-res Image Gene #17: 'amp_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.3' versus 'METHLYATION_CNMF'

P value = 1.37e-17 (Fisher's exact test), Q value = 7.2e-15

Table S60. Gene #17: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
AMP PEAK 17(19P13.3) MUTATED	17	24	4	66
AMP PEAK 17(19P13.3) WILD-TYPE	182	41	49	75

Figure S60. Get High-res Image Gene #17: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CNMF'

P value = 3.11e-11 (Chi-square test), Q value = 1.6e-08

Table S61. Gene #17: 'amp_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 17(19P13.3) MUTATED	9	26	47	31	1	1
AMP PEAK 17(19P13.3) WILD-TYPE	107	63	47	95	10	24

Figure S61. Get High-res Image Gene #17: 'amp_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.74e-06 (Fisher's exact test), Q value = 0.00079

Table S62. Gene #17: 'amp_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
AMP PEAK 17(19P13.3) MUTATED	37	37	41
AMP PEAK 17(19P13.3) WILD-TYPE	187	43	116

Figure S62. Get High-res Image Gene #17: 'amp_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.000177 (Chi-square test), Q value = 0.072

Table S63. Gene #17: 'amp_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
AMP PEAK 17(19P13.3) MUTATED	5	22	5	21	34	15	6
AMP PEAK 17(19P13.3) WILD-TYPE	57	54	25	20	102	48	21

Figure S63. Get High-res Image Gene #17: 'amp_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.36e-06 (Chi-square test), Q value = 0.00062

Table S64. Gene #17: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
AMP PEAK 17(19P13.3) MUTATED	7	24	28	31	10	3	5
AMP PEAK 17(19P13.3) WILD-TYPE	80	53	27	93	29	19	26

Figure S64. Get High-res Image Gene #17: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 8.89e-13 (Fisher's exact test), Q value = 4.5e-10

Table S65. Gene #18: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 18(19P13.2) MUTATED	5	39	65
AMP PEAK 18(19P13.2) WILD-TYPE	134	71	149

Figure S65. Get High-res Image Gene #18: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 7.34e-21 (Fisher's exact test), Q value = 3.9e-18

Table S66. Gene #18: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
AMP PEAK 18(19P13.2) MUTATED	11	27	4	63
AMP PEAK 18(19P13.2) WILD-TYPE	188	38	49	78

Figure S66. Get High-res Image Gene #18: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1.18e-12 (Chi-square test), Q value = 6e-10

Table S67. Gene #18: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
AMP PEAK 18(19P13.2) MUTATED	5	30	45	26	1	2
AMP PEAK 18(19P13.2) WILD-TYPE	111	59	49	100	10	23

Figure S67. Get High-res Image Gene #18: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.86e-06 (Fisher's exact test), Q value = 0.0022

Table S68. Gene #18: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
AMP PEAK 18(19P13.2) MUTATED	37	36	36
AMP PEAK 18(19P13.2) WILD-TYPE	187	44	121

Figure S68. Get High-res Image Gene #18: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_CNMF'

P value = 4.82e-06 (Chi-square test), Q value = 0.0022

Table S69. Gene #18: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
AMP PEAK 18(19P13.2) MUTATED	4	26	4	21	30	13	5
AMP PEAK 18(19P13.2) WILD-TYPE	58	50	26	20	106	50	22

Figure S69. Get High-res Image Gene #18: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.27e-08 (Chi-square test), Q value = 3.9e-05

Table S70. Gene #18: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
AMP PEAK 18(19P13.2) MUTATED	6	28	27	27	8	3	4
AMP PEAK 18(19P13.2) WILD-TYPE	81	49	28	97	31	19	27

Figure S70. Get High-res Image Gene #18: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xp11.22' versus 'CN_CNMF'

P value = 2e-10 (Fisher's exact test), Q value = 9.9e-08

Table S71. Gene #19: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
AMP PEAK 19(XP11.22) MUTATED	35	5	7
AMP PEAK 19(XP11.22) WILD-TYPE	104	105	207

Figure S71. Get High-res Image Gene #19: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.22' versus 'METHLYATION_CNMF'

P value = 4.71e-09 (Fisher's exact test), Q value = 2.3e-06

Table S72. Gene #19: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
AMP PEAK 19(XP11.22) MUTATED	40	3	3	1
AMP PEAK 19(XP11.22) WILD-TYPE	159	62	50	140

Figure S72. Get High-res Image Gene #19: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000386 (Fisher's exact test), Q value = 0.15

Table S73. Gene #19: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
AMP PEAK 19(XP11.22) MUTATED	34	1	12
AMP PEAK 19(XP11.22) WILD-TYPE	190	79	145

Figure S73. Get High-res Image Gene #19: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'CN_CNMF'

P value = 7.23e-37 (Fisher's exact test), Q value = 3.9e-34

Table S74. Gene #20: 'del_1p36.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 1(1P36.23) MUTATED	10	32	152
DEL PEAK 1(1P36.23) WILD-TYPE	129	78	62

Figure S74. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.23' versus 'METHLYATION_CNMF'

P value = 7.01e-82 (Fisher's exact test), Q value = 3.9e-79

Table S75. Gene #20: 'del_1p36.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 1(1P36.23) MUTATED	12	19	18	141
DEL PEAK 1(1P36.23) WILD-TYPE	187	46	35	0

Figure S75. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.23' versus 'MRNASEQ_CNMF'

P value = 6.95e-43 (Chi-square test), Q value = 3.8e-40

Table S76. Gene #20: 'del_1p36.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 1(1P36.23) MUTATED	6	22	93	61	1	11
DEL PEAK 1(1P36.23) WILD-TYPE	110	67	1	65	10	14

Figure S76. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.04e-50 (Fisher's exact test), Q value = 5.7e-48

Table S77. Gene #20: 'del_1p36.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 1(1P36.23) MUTATED	30	80	84
DEL PEAK 1(1P36.23) WILD-TYPE	194	0	73

Figure S77. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_CNMF'

P value = 3.35e-21 (Chi-square test), Q value = 1.8e-18

Table S78. Gene #20: 'del_1p36.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
DEL PEAK 1(1P36.23) MUTATED	4	22	2	38	73	25	17
DEL PEAK 1(1P36.23) WILD-TYPE	58	54	28	3	63	38	10

Figure S78. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.84e-05 (Fisher's exact test), Q value = 0.025

Table S79. Gene #20: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	16	225
DEL PEAK 1(1P36.23) MUTATED	103	6	72
DEL PEAK 1(1P36.23) WILD-TYPE	91	10	153

Figure S79. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.36e-25 (Chi-square test), Q value = 1.8e-22

Table S80. Gene #20: 'del_1p36.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
DEL PEAK 1(1P36.23) MUTATED	4	28	50	67	14	1	17
DEL PEAK 1(1P36.23) WILD-TYPE	83	49	5	57	25	21	14

Figure S80. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000312 (Fisher's exact test), Q value = 0.12

Table S81. Gene #20: 'del_1p36.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	196	234
DEL PEAK 1(1P36.23) MUTATED	1	101	79
DEL PEAK 1(1P36.23) WILD-TYPE	4	95	155

Figure S81. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p32.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.000173 (Fisher's exact test), Q value = 0.07

Table S82. Gene #21: 'del_1p32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	6	10	4
DEL PEAK 2(1P32.3) MUTATED	7	2	1	0
DEL PEAK 2(1P32.3) WILD-TYPE	0	4	9	4

Figure S82. Get High-res Image Gene #21: 'del_1p32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p32.3' versus 'CN_CNMF'

P value = 1.19e-42 (Fisher's exact test), Q value = 6.5e-40

Table S83. Gene #21: 'del_1p32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 2(1P32.3) MUTATED	6	23	150
DEL PEAK 2(1P32.3) WILD-TYPE	133	87	64

Figure S83. Get High-res Image Gene #21: 'del_1p32.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p32.3' versus 'METHLYATION_CNMF'

P value = 2.83e-92 (Fisher's exact test), Q value = 1.6e-89

Table S84. Gene #21: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 2(1P32.3) MUTATED	5	12	18	141
DEL PEAK 2(1P32.3) WILD-TYPE	194	53	35	0

Figure S84. Get High-res Image Gene #21: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p32.3' versus 'RPPA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.19

Table S85. Gene #21: 'del_1p32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 2(1P32.3) MUTATED	8	16	28	35
DEL PEAK 2(1P32.3) WILD-TYPE	44	46	40	39

Figure S85. Get High-res Image Gene #21: 'del_1p32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p32.3' versus 'MRNASEQ_CNMF'

P value = 1.69e-47 (Chi-square test), Q value = 9.2e-45

Table S86. Gene #21: 'del_1p32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 2(1P32.3) MUTATED	4	16	93	56	0	10
DEL PEAK 2(1P32.3) WILD-TYPE	112	73	1	70	11	15

Figure S86. Get High-res Image Gene #21: 'del_1p32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.89e-56 (Fisher's exact test), Q value = 2.7e-53

Table S87. Gene #21: 'del_1p32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 2(1P32.3) MUTATED	21	80	78
DEL PEAK 2(1P32.3) WILD-TYPE	203	0	79

Figure S87. Get High-res Image Gene #21: 'del_1p32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_CNMF'

P value = 3.56e-21 (Chi-square test), Q value = 1.9e-18

Table S88. Gene #21: 'del_1p32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
DEL PEAK 2(1P32.3) MUTATED	4	17	2	37	68	23	17
DEL PEAK 2(1P32.3) WILD-TYPE	58	59	28	4	68	40	10

Figure S88. Get High-res Image Gene #21: 'del_1p32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.8e-05 (Fisher's exact test), Q value = 0.0078

Table S89. Gene #21: 'del_1p32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	16	225
DEL PEAK 2(1P32.3) MUTATED	98	6	64
DEL PEAK 2(1P32.3) WILD-TYPE	96	10	161

Figure S89. Get High-res Image Gene #21: 'del_1p32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.55e-25 (Chi-square test), Q value = 3.5e-22

Table S90. Gene #21: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
DEL PEAK 2(1P32.3) MUTATED	4	21	49	63	14	1	16
DEL PEAK 2(1P32.3) WILD-TYPE	83	56	6	61	25	21	15

Figure S90. Get High-res Image Gene #21: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000134 (Fisher's exact test), Q value = 0.055

Table S91. Gene #21: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	196	234
DEL PEAK 2(1P32.3) MUTATED	0	95	73
DEL PEAK 2(1P32.3) WILD-TYPE	5	101	161

Figure S91. Get High-res Image Gene #21: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 9.92e-10 (Fisher's exact test), Q value = 4.9e-07

Table S92. Gene #23: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 4(2Q37.3) MUTATED	42	16	11
DEL PEAK 4(2Q37.3) WILD-TYPE	97	94	203

Figure S92. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 3.39e-11 (Fisher's exact test), Q value = 1.7e-08

Table S93. Gene #23: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 4(2Q37.3) MUTATED	57	4	3	5
DEL PEAK 4(2Q37.3) WILD-TYPE	142	61	50	136

Figure S93. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 1.22e-07 (Chi-square test), Q value = 5.7e-05

Table S94. Gene #23: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 4(2Q37.3) MUTATED	29	12	4	13	7	4
DEL PEAK 4(2Q37.3) WILD-TYPE	87	77	90	113	4	21

Figure S94. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.03e-06 (Fisher's exact test), Q value = 0.00092

Table S95. Gene #23: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 4(2Q37.3) MUTATED	53	5	11
DEL PEAK 4(2Q37.3) WILD-TYPE	171	75	146

Figure S95. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.1' versus 'CN_CNMF'

P value = 3.24e-06 (Fisher's exact test), Q value = 0.0015

Table S96. Gene #24: 'del_3p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 5(3P21.1) MUTATED	27	11	7
DEL PEAK 5(3P21.1) WILD-TYPE	112	99	207

Figure S96. Get High-res Image Gene #24: 'del_3p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.1' versus 'RPPA_CNMF'

P value = 0.000608 (Fisher's exact test), Q value = 0.23

Table S97. Gene #24: 'del_3p21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 5(3P21.1) MUTATED	4	16	3	4
DEL PEAK 5(3P21.1) WILD-TYPE	48	46	65	70

Figure S97. Get High-res Image Gene #24: 'del_3p21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.1' versus 'MRNASEQ_CNMF'

P value = 5.06e-11 (Chi-square test), Q value = 2.5e-08

Table S98. Gene #24: 'del_3p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 5(3P21.1) MUTATED	13	11	3	9	8	1
DEL PEAK 5(3P21.1) WILD-TYPE	103	78	91	117	3	24

Figure S98. Get High-res Image Gene #24: 'del_3p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000147 (Fisher's exact test), Q value = 0.06

Table S99. Gene #24: 'del_3p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 5(3P21.1) MUTATED	35	2	8
DEL PEAK 5(3P21.1) WILD-TYPE	189	78	149

Figure S99. Get High-res Image Gene #24: 'del_3p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000331 (Fisher's exact test), Q value = 0.13

Table S100. Gene #24: 'del_3p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	196	234
DEL PEAK 5(3P21.1) MUTATED	3	11	31
DEL PEAK 5(3P21.1) WILD-TYPE	2	185	203

Figure S100. Get High-res Image Gene #24: 'del_3p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 7.42e-09 (Fisher's exact test), Q value = 3.6e-06

Table S101. Gene #25: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 6(3Q29) MUTATED	29	8	4
DEL PEAK 6(3Q29) WILD-TYPE	110	102	210

Figure S101. Get High-res Image Gene #25: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 5.02e-09 (Chi-square test), Q value = 2.4e-06

Table S102. Gene #25: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 6(3Q29) MUTATED	13	8	2	9	7	2
DEL PEAK 6(3Q29) WILD-TYPE	103	81	92	117	4	23

Figure S102. Get High-res Image Gene #25: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'CN_CNMF'

P value = 9.16e-05 (Fisher's exact test), Q value = 0.038

Table S103. Gene #26: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 7(4Q34.3) MUTATED	55	17	55
DEL PEAK 7(4Q34.3) WILD-TYPE	84	93	159

Figure S103. Get High-res Image Gene #26: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 5.67e-08 (Fisher's exact test), Q value = 2.7e-05

Table S104. Gene #26: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 7(4Q34.3) MUTATED	69	5	4	49
DEL PEAK 7(4Q34.3) WILD-TYPE	130	60	49	92

Figure S104. Get High-res Image Gene #26: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 5.67e-05 (Chi-square test), Q value = 0.024

Table S105. Gene #26: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 7(4Q34.3) MUTATED	34	11	34	35	8	4
DEL PEAK 7(4Q34.3) WILD-TYPE	82	78	60	91	3	21

Figure S105. Get High-res Image Gene #26: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5p15.33' versus 'CN_CNMF'

P value = 8.95e-09 (Fisher's exact test), Q value = 4.3e-06

Table S106. Gene #27: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 8(5P15.33) MUTATED	32	9	6
DEL PEAK 8(5P15.33) WILD-TYPE	107	101	208

Figure S106. Get High-res Image Gene #27: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_5p15.33' versus 'METHLYATION_CNMF'

P value = 3.13e-05 (Fisher's exact test), Q value = 0.014

Table S107. Gene #27: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 8(5P15.33) MUTATED	34	7	3	3
DEL PEAK 8(5P15.33) WILD-TYPE	165	58	50	138

Figure S107. Get High-res Image Gene #27: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q34' versus 'CN_CNMF'

P value = 6.87e-12 (Fisher's exact test), Q value = 3.5e-09

Table S108. Gene #28: 'del_5q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 9(5Q34) MUTATED	41	4	11
DEL PEAK 9(5Q34) WILD-TYPE	98	106	203

Figure S108. Get High-res Image Gene #28: 'del_5q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q34' versus 'METHLYATION_CNMF'

P value = 7.67e-08 (Fisher's exact test), Q value = 3.6e-05

Table S109. Gene #28: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 9(5Q34) MUTATED	44	5	4	3
DEL PEAK 9(5Q34) WILD-TYPE	155	60	49	138

Figure S109. Get High-res Image Gene #28: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q34' versus 'MRNASEQ_CNMF'

P value = 2.19e-07 (Chi-square test), Q value = 1e-04

Table S110. Gene #28: 'del_5q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 9(5Q34) MUTATED	17	14	3	10	7	4
DEL PEAK 9(5Q34) WILD-TYPE	99	75	91	116	4	21

Figure S110. Get High-res Image Gene #28: 'del_5q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000396 (Fisher's exact test), Q value = 0.15

Table S111. Gene #28: 'del_5q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 9(5Q34) MUTATED	39	2	14
DEL PEAK 9(5Q34) WILD-TYPE	185	78	143

Figure S111. Get High-res Image Gene #28: 'del_5q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q34' versus 'MIRSEQ_CNMF'

P value = 2.03e-06 (Chi-square test), Q value = 0.00092

Table S112. Gene #28: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
DEL PEAK 9(5Q34) MUTATED	8	7	14	2	15	5	3
DEL PEAK 9(5Q34) WILD-TYPE	54	69	16	39	121	58	24

Figure S112. Get High-res Image Gene #28: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.73e-06 (Chi-square test), Q value = 0.0043

Table S113. Gene #28: 'del_5q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
DEL PEAK 9(5Q34) MUTATED	9	9	4	10	6	11	5
DEL PEAK 9(5Q34) WILD-TYPE	78	68	51	114	33	11	26

Figure S113. Get High-res Image Gene #28: 'del_5q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6p25.3' versus 'CN_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.055

Table S114. Gene #29: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 10(6P25.3) MUTATED	23	16	9
DEL PEAK 10(6P25.3) WILD-TYPE	116	94	205

Figure S114. Get High-res Image Gene #29: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q24.3' versus 'CN_CNMF'

P value = 0.000373 (Fisher's exact test), Q value = 0.14

Table S115. Gene #30: 'del_6q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 11(6Q24.3) MUTATED	30	25	19
DEL PEAK 11(6Q24.3) WILD-TYPE	109	85	195

Figure S115. Get High-res Image Gene #30: 'del_6q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q24.3' versus 'METHLYATION_CNMF'

P value = 3.28e-05 (Fisher's exact test), Q value = 0.014

Table S116. Gene #30: 'del_6q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 11(6Q24.3) MUTATED	46	12	9	7
DEL PEAK 11(6Q24.3) WILD-TYPE	153	53	44	134

Figure S116. Get High-res Image Gene #30: 'del_6q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8q24.3' versus 'CN_CNMF'

P value = 2.83e-06 (Fisher's exact test), Q value = 0.0013

Table S117. Gene #32: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 13(8Q24.3) MUTATED	12	13	1
DEL PEAK 13(8Q24.3) WILD-TYPE	127	97	213

Figure S117. Get High-res Image Gene #32: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_8q24.3' versus 'METHLYATION_CNMF'

P value = 7.69e-06 (Fisher's exact test), Q value = 0.0034

Table S118. Gene #32: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 13(8Q24.3) MUTATED	14	11	1	0
DEL PEAK 13(8Q24.3) WILD-TYPE	185	54	52	141

Figure S118. Get High-res Image Gene #32: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 1.66e-08 (Fisher's exact test), Q value = 7.9e-06

Table S119. Gene #33: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 14(9P23) MUTATED	51	49	34
DEL PEAK 14(9P23) WILD-TYPE	88	61	180

Figure S119. Get High-res Image Gene #33: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0057

Table S120. Gene #33: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 14(9P23) MUTATED	70	29	9	24
DEL PEAK 14(9P23) WILD-TYPE	129	36	44	117

Figure S120. Get High-res Image Gene #33: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 6.16e-18 (Fisher's exact test), Q value = 3.2e-15

Table S121. Gene #34: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 15(9P21.3) MUTATED	55	70	33
DEL PEAK 15(9P21.3) WILD-TYPE	84	40	181

Figure S121. Get High-res Image Gene #34: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 4.21e-16 (Fisher's exact test), Q value = 2.2e-13

Table S122. Gene #34: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 15(9P21.3) MUTATED	71	50	11	24
DEL PEAK 15(9P21.3) WILD-TYPE	128	15	42	117

Figure S122. Get High-res Image Gene #34: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.0076

Table S123. Gene #34: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 15(9P21.3) MUTATED	12	38	26	18
DEL PEAK 15(9P21.3) WILD-TYPE	40	24	42	56

Figure S123. Get High-res Image Gene #34: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 4.94e-05 (Fisher's exact test), Q value = 0.021

Table S124. Gene #34: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	129	119
DEL PEAK 15(9P21.3) MUTATED	2	64	28
DEL PEAK 15(9P21.3) WILD-TYPE	6	65	91

Figure S124. Get High-res Image Gene #34: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1.09e-09 (Chi-square test), Q value = 5.3e-07

Table S125. Gene #34: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 15(9P21.3) MUTATED	33	52	16	43	9	5
DEL PEAK 15(9P21.3) WILD-TYPE	83	37	78	83	2	20

Figure S125. Get High-res Image Gene #34: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.52e-05 (Fisher's exact test), Q value = 0.015

Table S126. Gene #34: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 15(9P21.3) MUTATED	99	16	43
DEL PEAK 15(9P21.3) WILD-TYPE	125	64	114

Figure S126. Get High-res Image Gene #34: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1.05e-05 (Chi-square test), Q value = 0.0046

Table S127. Gene #34: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
DEL PEAK 15(9P21.3) MUTATED	15	44	13	8	38	25	5
DEL PEAK 15(9P21.3) WILD-TYPE	47	32	17	33	98	38	22

Figure S127. Get High-res Image Gene #34: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.96e-06 (Chi-square test), Q value = 0.00089

Table S128. Gene #34: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
DEL PEAK 15(9P21.3) MUTATED	24	48	12	37	13	8	6
DEL PEAK 15(9P21.3) WILD-TYPE	63	29	43	87	26	14	25

Figure S128. Get High-res Image Gene #34: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'CN_CNMF'

P value = 6.84e-36 (Fisher's exact test), Q value = 3.7e-33

Table S129. Gene #35: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 16(10Q26.3) MUTATED	46	80	13
DEL PEAK 16(10Q26.3) WILD-TYPE	93	30	201

Figure S129. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 4.29e-35 (Fisher's exact test), Q value = 2.3e-32

Table S130. Gene #35: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 16(10Q26.3) MUTATED	60	59	12	7
DEL PEAK 16(10Q26.3) WILD-TYPE	139	6	41	134

Figure S130. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 8.98e-07 (Fisher's exact test), Q value = 0.00041

Table S131. Gene #35: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 16(10Q26.3) MUTATED	13	35	14	11
DEL PEAK 16(10Q26.3) WILD-TYPE	39	27	54	63

Figure S131. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.000228 (Fisher's exact test), Q value = 0.091

Table S132. Gene #35: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	129	119
DEL PEAK 16(10Q26.3) MUTATED	2	51	20
DEL PEAK 16(10Q26.3) WILD-TYPE	6	78	99

Figure S132. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 5.82e-26 (Chi-square test), Q value = 3.1e-23

Table S133. Gene #35: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 16(10Q26.3) MUTATED	31	64	3	27	9	4
DEL PEAK 16(10Q26.3) WILD-TYPE	85	25	91	99	2	21

Figure S133. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.08e-18 (Fisher's exact test), Q value = 4.8e-15

Table S134. Gene #35: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 16(10Q26.3) MUTATED	107	3	28
DEL PEAK 16(10Q26.3) WILD-TYPE	117	77	129

Figure S134. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 1.18e-12 (Chi-square test), Q value = 6e-10

Table S135. Gene #35: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
DEL PEAK 16(10Q26.3) MUTATED	10	48	12	4	28	27	4
DEL PEAK 16(10Q26.3) WILD-TYPE	52	28	18	37	108	36	23

Figure S135. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.5e-06 (Fisher's exact test), Q value = 0.002

Table S136. Gene #35: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	16	225
DEL PEAK 16(10Q26.3) MUTATED	37	4	92
DEL PEAK 16(10Q26.3) WILD-TYPE	157	12	133

Figure S136. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.57e-17 (Chi-square test), Q value = 4.5e-14

Table S137. Gene #35: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
DEL PEAK 16(10Q26.3) MUTATED	18	56	7	22	15	7	8
DEL PEAK 16(10Q26.3) WILD-TYPE	69	21	48	102	24	15	23

Figure S137. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000307 (Fisher's exact test), Q value = 0.12

Table S138. Gene #35: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	196	234
DEL PEAK 16(10Q26.3) MUTATED	1	42	90
DEL PEAK 16(10Q26.3) WILD-TYPE	4	154	144

Figure S138. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1.16e-19 (Fisher's exact test), Q value = 6.1e-17

Table S139. Gene #36: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 17(11P15.5) MUTATED	65	18	12
DEL PEAK 17(11P15.5) WILD-TYPE	74	92	202

Figure S139. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 8.29e-22 (Fisher's exact test), Q value = 4.4e-19

Table S140. Gene #36: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 17(11P15.5) MUTATED	78	12	5	0
DEL PEAK 17(11P15.5) WILD-TYPE	121	53	48	141

Figure S140. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 3.62e-09 (Chi-square test), Q value = 1.8e-06

Table S141. Gene #36: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 17(11P15.5) MUTATED	34	24	0	21	7	8
DEL PEAK 17(11P15.5) WILD-TYPE	82	65	94	105	4	17

Figure S141. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.58e-11 (Fisher's exact test), Q value = 1.8e-08

Table S142. Gene #36: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 17(11P15.5) MUTATED	69	0	25
DEL PEAK 17(11P15.5) WILD-TYPE	155	80	132

Figure S142. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 1.5e-10 (Fisher's exact test), Q value = 7.5e-08

Table S143. Gene #38: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 19(12Q12) MUTATED	43	5	16
DEL PEAK 19(12Q12) WILD-TYPE	96	105	198

Figure S143. Get High-res Image Gene #38: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 9.81e-09 (Fisher's exact test), Q value = 4.7e-06

Table S144. Gene #38: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 19(12Q12) MUTATED	51	3	4	6
DEL PEAK 19(12Q12) WILD-TYPE	148	62	49	135

Figure S144. Get High-res Image Gene #38: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.029

Table S145. Gene #38: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 19(12Q12) MUTATED	45	2	17
DEL PEAK 19(12Q12) WILD-TYPE	179	78	140

Figure S145. Get High-res Image Gene #38: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.000618 (Fisher's exact test), Q value = 0.23

Table S146. Gene #39: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	6	10	4
DEL PEAK 20(13Q14.2) MUTATED	0	0	5	4
DEL PEAK 20(13Q14.2) WILD-TYPE	7	6	5	0

Figure S146. Get High-res Image Gene #39: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 2.16e-13 (Fisher's exact test), Q value = 1.1e-10

Table S147. Gene #39: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 20(13Q14.2) MUTATED	71	29	29
DEL PEAK 20(13Q14.2) WILD-TYPE	68	81	185

Figure S147. Get High-res Image Gene #39: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.000484 (Fisher's exact test), Q value = 0.18

Table S148. Gene #39: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 20(13Q14.2) MUTATED	73	21	10	25
DEL PEAK 20(13Q14.2) WILD-TYPE	126	44	43	116

Figure S148. Get High-res Image Gene #39: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.000605 (Chi-square test), Q value = 0.23

Table S149. Gene #39: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 20(13Q14.2) MUTATED	39	31	17	28	8	6
DEL PEAK 20(13Q14.2) WILD-TYPE	77	58	77	98	3	19

Figure S149. Get High-res Image Gene #39: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000282 (Fisher's exact test), Q value = 0.11

Table S150. Gene #39: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 20(13Q14.2) MUTATED	82	14	33
DEL PEAK 20(13Q14.2) WILD-TYPE	142	66	124

Figure S150. Get High-res Image Gene #39: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.000618 (Fisher's exact test), Q value = 0.23

Table S151. Gene #40: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	6	10	4
DEL PEAK 21(13Q14.2) MUTATED	0	0	5	4
DEL PEAK 21(13Q14.2) WILD-TYPE	7	6	5	0

Figure S151. Get High-res Image Gene #40: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 8.51e-14 (Fisher's exact test), Q value = 4.4e-11

Table S152. Gene #40: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 21(13Q14.2) MUTATED	72	30	29
DEL PEAK 21(13Q14.2) WILD-TYPE	67	80	185

Figure S152. Get High-res Image Gene #40: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.000272 (Fisher's exact test), Q value = 0.11

Table S153. Gene #40: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 21(13Q14.2) MUTATED	74	22	10	25
DEL PEAK 21(13Q14.2) WILD-TYPE	125	43	43	116

Figure S153. Get High-res Image Gene #40: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.000377 (Chi-square test), Q value = 0.15

Table S154. Gene #40: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 21(13Q14.2) MUTATED	40	32	17	28	8	6
DEL PEAK 21(13Q14.2) WILD-TYPE	76	57	77	98	3	19

Figure S154. Get High-res Image Gene #40: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000131 (Fisher's exact test), Q value = 0.054

Table S155. Gene #40: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 21(13Q14.2) MUTATED	84	14	33
DEL PEAK 21(13Q14.2) WILD-TYPE	140	66	124

Figure S155. Get High-res Image Gene #40: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

P value = 4.7e-07 (Fisher's exact test), Q value = 0.00022

Table S156. Gene #41: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 22(13Q34) MUTATED	50	23	25
DEL PEAK 22(13Q34) WILD-TYPE	89	87	189

Figure S156. Get High-res Image Gene #41: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q24.3' versus 'MRNASEQ_CNMF'

P value = 0.000322 (Chi-square test), Q value = 0.13

Table S157. Gene #42: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 23(14Q24.3) MUTATED	20	34	20	21	6	5
DEL PEAK 23(14Q24.3) WILD-TYPE	96	55	74	105	5	20

Figure S157. Get High-res Image Gene #42: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q24.3' versus 'MIRSEQ_CNMF'

P value = 4.07e-05 (Chi-square test), Q value = 0.017

Table S158. Gene #42: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
DEL PEAK 23(14Q24.3) MUTATED	10	36	3	8	28	13	6
DEL PEAK 23(14Q24.3) WILD-TYPE	52	40	27	33	108	50	21

Figure S158. Get High-res Image Gene #42: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000175 (Chi-square test), Q value = 0.071

Table S159. Gene #42: 'del_14q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
DEL PEAK 23(14Q24.3) MUTATED	19	35	10	21	6	4	9
DEL PEAK 23(14Q24.3) WILD-TYPE	68	42	45	103	33	18	22

Figure S159. Get High-res Image Gene #42: 'del_14q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000288 (Fisher's exact test), Q value = 0.11

Table S160. Gene #42: 'del_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	196	234
DEL PEAK 23(14Q24.3) MUTATED	3	31	70
DEL PEAK 23(14Q24.3) WILD-TYPE	2	165	164

Figure S160. Get High-res Image Gene #42: 'del_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.42' versus 'CN_CNMF'

P value = 3.99e-30 (Fisher's exact test), Q value = 2.1e-27

Table S161. Gene #44: 'del_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 25(19Q13.42) MUTATED	43	31	176
DEL PEAK 25(19Q13.42) WILD-TYPE	96	79	38

Figure S161. Get High-res Image Gene #44: 'del_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.42' versus 'METHLYATION_CNMF'

P value = 2.68e-52 (Fisher's exact test), Q value = 1.5e-49

Table S162. Gene #44: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 25(19Q13.42) MUTATED	80	8	18	141
DEL PEAK 25(19Q13.42) WILD-TYPE	119	57	35	0

Figure S162. Get High-res Image Gene #44: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.42' versus 'MRNASEQ_CNMF'

P value = 8.21e-25 (Chi-square test), Q value = 4.4e-22

Table S163. Gene #44: 'del_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 25(19Q13.42) MUTATED	42	22	93	73	6	13
DEL PEAK 25(19Q13.42) WILD-TYPE	74	67	1	53	5	12

Figure S163. Get High-res Image Gene #44: 'del_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.28e-32 (Fisher's exact test), Q value = 6.9e-30

Table S164. Gene #44: 'del_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 25(19Q13.42) MUTATED	70	80	99
DEL PEAK 25(19Q13.42) WILD-TYPE	154	0	58

Figure S164. Get High-res Image Gene #44: 'del_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_CNMF'

P value = 1.3e-10 (Chi-square test), Q value = 6.5e-08

Table S165. Gene #44: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	62	76	30	41	136	63	27
DEL PEAK 25(19Q13.42) MUTATED	23	26	12	40	85	33	17
DEL PEAK 25(19Q13.42) WILD-TYPE	39	50	18	1	51	30	10

Figure S165. Get High-res Image Gene #44: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.42' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-11 (Chi-square test), Q value = 5.1e-09

Table S166. Gene #44: 'del_19q13.42' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	87	77	55	124	39	22	31
DEL PEAK 25(19Q13.42) MUTATED	37	22	52	75	21	12	17
DEL PEAK 25(19Q13.42) WILD-TYPE	50	55	3	49	18	10	14

Figure S166. Get High-res Image Gene #44: 'del_19q13.42' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 2.01e-14 (Fisher's exact test), Q value = 1e-11

Table S167. Gene #45: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 26(22Q13.31) MUTATED	33	31	4
DEL PEAK 26(22Q13.31) WILD-TYPE	106	79	210

Figure S167. Get High-res Image Gene #45: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 1.61e-09 (Fisher's exact test), Q value = 7.8e-07

Table S168. Gene #45: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 26(22Q13.31) MUTATED	34	23	7	3
DEL PEAK 26(22Q13.31) WILD-TYPE	165	42	46	138

Figure S168. Get High-res Image Gene #45: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.31' versus 'RPPA_CNMF'

P value = 0.000215 (Fisher's exact test), Q value = 0.087

Table S169. Gene #45: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 26(22Q13.31) MUTATED	4	21	8	6
DEL PEAK 26(22Q13.31) WILD-TYPE	48	41	60	68

Figure S169. Get High-res Image Gene #45: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 3.59e-10 (Chi-square test), Q value = 1.8e-07

Table S170. Gene #45: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 26(22Q13.31) MUTATED	14	31	2	13	5	2
DEL PEAK 26(22Q13.31) WILD-TYPE	102	58	92	113	6	23

Figure S170. Get High-res Image Gene #45: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.38e-07 (Fisher's exact test), Q value = 0.00016

Table S171. Gene #45: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 26(22Q13.31) MUTATED	52	2	13
DEL PEAK 26(22Q13.31) WILD-TYPE	172	78	144

Figure S171. Get High-res Image Gene #45: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 2.01e-14 (Fisher's exact test), Q value = 1e-11

Table S172. Gene #46: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 27(22Q13.31) MUTATED	33	31	4
DEL PEAK 27(22Q13.31) WILD-TYPE	106	79	210

Figure S172. Get High-res Image Gene #46: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 1.61e-09 (Fisher's exact test), Q value = 7.8e-07

Table S173. Gene #46: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	199	65	53	141
DEL PEAK 27(22Q13.31) MUTATED	34	23	7	3
DEL PEAK 27(22Q13.31) WILD-TYPE	165	42	46	138

Figure S173. Get High-res Image Gene #46: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.31' versus 'RPPA_CNMF'

P value = 0.000215 (Fisher's exact test), Q value = 0.087

Table S174. Gene #46: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 27(22Q13.31) MUTATED	4	21	8	6
DEL PEAK 27(22Q13.31) WILD-TYPE	48	41	60	68

Figure S174. Get High-res Image Gene #46: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 3.59e-10 (Chi-square test), Q value = 1.8e-07

Table S175. Gene #46: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 27(22Q13.31) MUTATED	14	31	2	13	5	2
DEL PEAK 27(22Q13.31) WILD-TYPE	102	58	92	113	6	23

Figure S175. Get High-res Image Gene #46: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.38e-07 (Fisher's exact test), Q value = 0.00016

Table S176. Gene #46: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	80	157
DEL PEAK 27(22Q13.31) MUTATED	52	2	13
DEL PEAK 27(22Q13.31) WILD-TYPE	172	78	144

Figure S176. Get High-res Image Gene #46: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 7.65e-05 (Fisher's exact test), Q value = 0.032

Table S177. Gene #47: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	139	110	214
DEL PEAK 28(XP21.1) MUTATED	44	11	38
DEL PEAK 28(XP21.1) WILD-TYPE	95	99	176

Figure S177. Get High-res Image Gene #47: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_xq21.1' versus 'MRNASEQ_CNMF'

P value = 2.1e-05 (Chi-square test), Q value = 0.0091

Table S178. Gene #48: 'del_xq21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	89	94	126	11	25
DEL PEAK 29(XQ21.1) MUTATED	10	15	22	14	6	0
DEL PEAK 29(XQ21.1) WILD-TYPE	106	74	72	112	5	25

Figure S178. Get High-res Image Gene #48: 'del_xq21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = LGG-TP.transferedmergedcluster.txt
Number of patients = 463
Number of significantly focal cnvs = 48
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

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

Q value calculation

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

Download Results

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

References

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

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[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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