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

Skin Cutaneous Melanoma (Metastatic)

28 January 2016 | analyses__2016_01_28

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 (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1251HPZ

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 54 focal events and 10 molecular subtypes across 367 patients, 163 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p12 cnv correlated to 'MRNASEQ_CNMF'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_1q44 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q12 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
amp_5q35.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_6p24.3 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'.
amp_6q12 cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.
amp_7p22.1 cnv correlated to 'CN_CNMF'.
amp_7q34 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_11q13.3 cnv correlated to 'CN_CNMF'.
amp_12q14.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q31.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.2 cnv correlated to 'CN_CNMF'.
amp_17q25.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_20q13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_22q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_1p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3p25.1 cnv correlated to 'CN_CNMF'.
del_3q13.31 cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.
del_4p16.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5p15.31 cnv correlated to 'CN_CNMF'.
del_5q12.1 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
del_5q31.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
del_6q21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_6q26 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_8p23.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF'.
del_11q23.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
del_12q23.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_14q23.3 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_14q32.31 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q13.3 cnv correlated to 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_15q21.1 cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
del_16q12.1 cnv correlated to 'CN_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_16q24.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_17p13.3 cnv correlated to 'RPPA_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 54 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 163 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 6p24 3	211 (57%)	156	1e-05 (0.000245)	1e-05 (0.000245)	0.0268 (0.114)	0.05 (0.165)	0.00677 (0.043)	0.00421 (0.0316)	0.00414 (0.0316)	9e-05 (0.00157)	0.0002 (0.00292)	0.00014 (0.00236)
del xp21 1	86 (23%)	281	0.0301 (0.12)	2e-05 (0.000432)	0.141 (0.308)	0.249 (0.418)	0.00931 (0.0559)	0.0042 (0.0316)	0.00237 (0.0213)	0.0198 (0.095)	0.0437 (0.154)	0.00073 (0.00876)
amp 1q44	201 (55%)	166	2e-05 (0.000432)	0.0661 (0.195)	0.00067 (0.00822)	0.0846 (0.225)	0.00149 (0.0161)	0.072 (0.202)	0.00017 (0.00255)	0.0016 (0.0169)	0.00509 (0.0357)	0.0126 (0.0678)
del 2q37 3	93 (25%)	274	0.0163 (0.0823)	0.0106 (0.0607)	0.174 (0.346)	0.0233 (0.107)	0.0441 (0.154)	0.0018 (0.0183)	0.0124 (0.0678)	0.0343 (0.13)	0.241 (0.409)	0.647 (0.74)
del 9p21 3	278 (76%)	89	1e-05 (0.000245)	0.00061 (0.00766)	0.00821 (0.051)	0.206 (0.375)	0.00253 (0.0224)	0.00333 (0.0272)	0.0298 (0.12)	0.503 (0.636)	0.126 (0.286)	0.00262 (0.0224)
amp 1q21 3	203 (55%)	164	1e-05 (0.000245)	0.13 (0.293)	0.00117 (0.0132)	0.0979 (0.244)	0.00049 (0.00645)	0.357 (0.517)	0.0274 (0.115)	0.0127 (0.0678)	0.0389 (0.145)	0.0536 (0.169)
amp 13q31 3	104 (28%)	263	1e-05 (0.000245)	2e-05 (0.000432)	0.214 (0.382)	0.18 (0.352)	6e-05 (0.0012)	0.0105 (0.0607)	0.704 (0.784)	0.584 (0.698)	0.127 (0.286)	0.0128 (0.0678)
del 1p22 1	97 (26%)	270	0.00017 (0.00255)	0.00404 (0.0316)	0.303 (0.458)	0.0545 (0.169)	0.0175 (0.0866)	0.00672 (0.043)	0.113 (0.27)	0.646 (0.74)	0.042 (0.152)	0.694 (0.779)
del 4q34 3	110 (30%)	257	0.00685 (0.043)	0.371 (0.527)	0.748 (0.817)	0.722 (0.801)	0.0314 (0.123)	0.00476 (0.0338)	0.589 (0.698)	0.00313 (0.026)	0.17 (0.343)	0.0489 (0.164)
del 9p23	249 (68%)	118	0.00017 (0.00255)	0.0314 (0.123)	0.0422 (0.152)	0.252 (0.418)	0.0443 (0.154)	0.16 (0.331)	0.0916 (0.238)	0.0893 (0.235)	0.704 (0.784)	0.00127 (0.014)
amp 20q13 33	188 (51%)	179	1e-05 (0.000245)	0.0191 (0.093)	0.017 (0.085)	0.0984 (0.244)	0.118 (0.275)	0.0437 (0.154)	0.251 (0.418)	0.695 (0.779)	0.748 (0.817)	0.264 (0.429)
del 1p36 31	81 (22%)	286	0.00573 (0.0397)	0.00637 (0.0418)	0.071 (0.201)	0.801 (0.854)	0.107 (0.259)	0.0246 (0.109)	0.0115 (0.0643)	0.147 (0.317)	0.169 (0.342)	0.29 (0.447)
del 10p15 3	199 (54%)	168	1e-05 (0.000245)	0.00462 (0.0333)	0.739 (0.813)	0.585 (0.698)	0.00457 (0.0333)	0.00102 (0.0117)	0.9 (0.926)	0.195 (0.364)	0.3 (0.457)	0.111 (0.267)
del 10q23 31	230 (63%)	137	1e-05 (0.000245)	0.00227 (0.0208)	0.863 (0.896)	0.681 (0.769)	0.0342 (0.13)	0.0199 (0.095)	0.693 (0.779)	0.261 (0.426)	0.302 (0.458)	0.372 (0.527)
del 10q26 3	236 (64%)	131	1e-05 (0.000245)	0.00366 (0.0295)	0.982 (0.987)	1 (1.00)	0.00642 (0.0418)	0.00627 (0.0418)	0.67 (0.759)	0.19 (0.361)	0.117 (0.275)	0.225 (0.393)
del 14q23 3	120 (33%)	247	9e-05 (0.00157)	0.253 (0.418)	0.72 (0.8)	0.0138 (0.0717)	0.00602 (0.0411)	0.0302 (0.12)	0.0548 (0.169)	0.555 (0.685)	0.189 (0.361)	0.331 (0.489)
del 14q32 31	117 (32%)	250	8e-05 (0.00154)	0.0654 (0.194)	0.607 (0.712)	0.0294 (0.12)	0.0115 (0.0643)	0.0216 (0.102)	0.19 (0.361)	0.606 (0.712)	0.41 (0.558)	0.238 (0.406)
del 16q24 3	133 (36%)	234	1e-05 (0.000245)	0.096 (0.241)	0.0419 (0.152)	0.513 (0.645)	0.0254 (0.11)	0.0246 (0.109)	0.246 (0.414)	0.103 (0.252)	0.069 (0.2)	0.189 (0.361)
amp 8q24 21	192 (52%)	175	1e-05 (0.000245)	9e-05 (0.00157)	0.515 (0.645)	0.917 (0.939)	5e-05 (0.00104)	0.0541 (0.169)	0.93 (0.944)	0.125 (0.284)	0.371 (0.527)	0.275 (0.438)
amp 22q13 2	152 (41%)	215	0.00217 (0.0202)	0.0442 (0.154)	0.222 (0.39)	0.273 (0.436)	0.277 (0.439)	0.535 (0.665)	0.419 (0.565)	0.0915 (0.238)	0.579 (0.698)	0.0108 (0.0614)
del 5q31 3	131 (36%)	236	1e-05 (0.000245)	0.03 (0.12)	0.026 (0.111)	0.651 (0.743)	0.244 (0.411)	0.37 (0.527)	0.845 (0.889)	0.609 (0.712)	0.589 (0.698)	0.788 (0.851)
del 6q21	214 (58%)	153	1e-05 (0.000245)	0.0017 (0.0177)	0.643 (0.739)	0.432 (0.572)	0.00192 (0.0185)	0.132 (0.295)	0.501 (0.636)	0.155 (0.326)	0.0993 (0.245)	0.41 (0.558)
del 6q26	221 (60%)	146	1e-05 (0.000245)	0.00417 (0.0316)	0.204 (0.374)	0.204 (0.374)	0.00634 (0.0418)	0.0509 (0.165)	0.399 (0.549)	0.189 (0.361)	0.315 (0.471)	0.278 (0.439)
del 8p23 3	89 (24%)	278	0.00028 (0.00398)	0.0821 (0.223)	0.0323 (0.126)	0.0217 (0.102)	0.0708 (0.201)	0.951 (0.96)	0.29 (0.447)	0.433 (0.572)	0.266 (0.43)	0.802 (0.854)
del 10q21 1	217 (59%)	150	1e-05 (0.000245)	0.0142 (0.0724)	0.885 (0.912)	0.913 (0.937)	0.0937 (0.239)	0.0346 (0.13)	0.502 (0.636)	0.136 (0.302)	0.15 (0.32)	0.653 (0.744)
del 15q13 3	84 (23%)	283	0.0846 (0.225)	0.0527 (0.168)	0.0224 (0.103)	0.203 (0.374)	0.29 (0.447)	0.0423 (0.152)	0.921 (0.942)	0.827 (0.876)	0.00832 (0.0511)	0.591 (0.698)
del 16p13 3	62 (17%)	305	0.00966 (0.0573)	0.00909 (0.0552)	0.192 (0.362)	0.0478 (0.162)	0.256 (0.422)	0.567 (0.688)	0.175 (0.347)	0.366 (0.525)	0.0506 (0.165)	0.418 (0.565)
del 16q23 1	120 (33%)	247	1e-05 (0.000245)	0.0412 (0.152)	0.0528 (0.168)	0.27 (0.434)	0.0178 (0.0874)	0.0679 (0.198)	0.273 (0.436)	0.0816 (0.223)	0.136 (0.302)	0.0928 (0.238)
amp 4q12	65 (18%)	302	0.124 (0.284)	0.407 (0.558)	0.209 (0.376)	0.385 (0.537)	0.489 (0.626)	0.0724 (0.202)	0.00456 (0.0333)	0.00091 (0.0107)	0.0617 (0.187)	0.306 (0.461)
amp 5p15 33	110 (30%)	257	1e-05 (0.000245)	0.284 (0.445)	0.405 (0.556)	0.352 (0.515)	0.149 (0.32)	0.191 (0.362)	0.00184 (0.0184)	0.179 (0.352)	0.0827 (0.223)	0.22 (0.388)
amp 5q35 3	59 (16%)	308	1e-05 (0.000245)	0.0302 (0.12)	0.46 (0.602)	0.0512 (0.166)	0.181 (0.353)	0.0926 (0.238)	0.394 (0.546)	0.149 (0.32)	0.053 (0.168)	0.583 (0.698)
amp 6q12	81 (22%)	286	0.386 (0.537)	0.463 (0.603)	0.613 (0.712)	0.0121 (0.0665)	0.258 (0.423)	0.242 (0.409)	0.613 (0.712)	0.0252 (0.11)	0.234 (0.404)	0.361 (0.521)
amp 7q34	225 (61%)	142	0.00192 (0.0185)	0.859 (0.894)	0.252 (0.418)	0.557 (0.685)	0.194 (0.364)	0.153 (0.322)	0.626 (0.724)	0.203 (0.374)	0.478 (0.616)	0.00201 (0.019)
amp 12q14 1	58 (16%)	309	0.0221 (0.103)	0.42 (0.565)	0.881 (0.912)	0.183 (0.355)	0.276 (0.438)	0.301 (0.457)	0.843 (0.889)	0.235 (0.404)	0.318 (0.474)	0.0251 (0.11)
amp 17q25 3	122 (33%)	245	0.00059 (0.00759)	0.076 (0.21)	0.197 (0.366)	0.342 (0.503)	0.802 (0.854)	0.0346 (0.13)	0.315 (0.471)	0.0714 (0.201)	0.484 (0.622)	0.064 (0.191)
del 3q13 31	62 (17%)	305	0.12 (0.278)	0.0568 (0.174)	0.174 (0.346)	0.063 (0.19)	0.0245 (0.109)	0.286 (0.445)	0.0495 (0.165)	0.0607 (0.185)	0.165 (0.336)	0.59 (0.698)
del 5q12 1	97 (26%)	270	1e-05 (0.000245)	0.165 (0.336)	0.00265 (0.0224)	0.163 (0.336)	0.339 (0.501)	0.108 (0.259)	0.846 (0.889)	0.59 (0.698)	0.608 (0.712)	0.944 (0.955)
del 11q23 3	204 (56%)	163	1e-05 (0.000245)	0.563 (0.687)	0.383 (0.537)	0.161 (0.333)	0.169 (0.342)	0.206 (0.375)	0.285 (0.445)	0.0709 (0.201)	0.0487 (0.164)	0.12 (0.278)
del 12q23 3	92 (25%)	275	0.0275 (0.115)	0.01 (0.059)	0.261 (0.426)	0.146 (0.316)	0.505 (0.637)	0.732 (0.807)	0.588 (0.698)	0.107 (0.259)	0.662 (0.752)	0.376 (0.53)
del 15q21 1	91 (25%)	276	0.0478 (0.162)	0.236 (0.404)	0.0839 (0.225)	0.0242 (0.109)	0.428 (0.57)	0.113 (0.27)	0.877 (0.909)	0.397 (0.548)	0.0906 (0.238)	0.853 (0.894)
del 19p13 3	104 (28%)	263	0.014 (0.072)	0.292 (0.448)	0.15 (0.32)	0.222 (0.39)	0.00015 (0.00245)	0.138 (0.304)	0.363 (0.523)	0.0958 (0.241)	0.546 (0.674)	0.233 (0.404)
amp 1p12	121 (33%)	246	0.135 (0.301)	0.963 (0.971)	0.252 (0.418)	0.93 (0.944)	0.0297 (0.12)	0.64 (0.739)	0.506 (0.637)	0.564 (0.687)	0.642 (0.739)	0.701 (0.784)
amp 7p22 1	209 (57%)	158	0.0004 (0.00553)	0.158 (0.331)	0.485 (0.622)	0.3 (0.457)	0.234 (0.404)	0.115 (0.273)	0.926 (0.944)	0.426 (0.569)	0.859 (0.894)	0.241 (0.409)
amp 11q13 3	69 (19%)	298	0.0136 (0.0714)	0.0729 (0.202)	0.787 (0.851)	0.449 (0.59)	0.53 (0.661)	0.795 (0.854)	0.573 (0.694)	0.0699 (0.201)	0.726 (0.804)	0.329 (0.488)
amp 15q26 2	120 (33%)	247	0.00265 (0.0224)	0.173 (0.346)	0.81 (0.861)	0.492 (0.629)	0.439 (0.579)	0.116 (0.273)	0.28 (0.44)	0.564 (0.687)	0.172 (0.345)	0.366 (0.525)
del 3p25 1	71 (19%)	296	0.0475 (0.162)	0.423 (0.567)	0.465 (0.603)	0.312 (0.469)	0.695 (0.779)	0.812 (0.861)	0.159 (0.331)	0.27 (0.434)	0.218 (0.386)	0.619 (0.717)
del 4p16 3	91 (25%)	276	0.562 (0.687)	0.0706 (0.201)	0.388 (0.538)	0.74 (0.813)	0.516 (0.645)	0.0457 (0.158)	0.988 (0.991)	0.21 (0.376)	0.532 (0.662)	0.942 (0.954)
del 5p15 31	79 (22%)	288	1e-05 (0.000245)	0.592 (0.698)	0.0945 (0.24)	0.796 (0.854)	0.439 (0.579)	0.28 (0.44)	0.991 (0.993)	0.43 (0.572)	0.19 (0.361)	0.669 (0.759)
del 11p15 5	114 (31%)	253	0.00041 (0.00553)	0.193 (0.363)	0.767 (0.833)	0.855 (0.894)	0.885 (0.912)	0.353 (0.515)	0.455 (0.596)	0.0827 (0.223)	0.208 (0.375)	0.408 (0.558)
del 16q12 1	117 (32%)	250	1e-05 (0.000245)	0.0665 (0.195)	0.0923 (0.238)	0.538 (0.666)	0.0507 (0.165)	0.197 (0.366)	0.16 (0.331)	0.0545 (0.169)	0.35 (0.514)	0.124 (0.284)
del 17p13 3	134 (37%)	233	0.749 (0.817)	0.262 (0.426)	0.0892 (0.235)	0.0329 (0.127)	0.216 (0.384)	0.386 (0.537)	0.847 (0.889)	0.355 (0.516)	0.354 (0.515)	0.226 (0.393)
amp 3p13	103 (28%)	264	0.151 (0.32)	0.799 (0.854)	0.289 (0.447)	0.76 (0.828)	0.731 (0.807)	0.42 (0.565)	0.93 (0.944)	0.107 (0.259)	0.797 (0.854)	0.859 (0.894)
amp 12q15	59 (16%)	308	0.208 (0.375)	0.494 (0.629)	0.12 (0.278)	0.137 (0.302)	0.214 (0.382)	0.0638 (0.191)	0.469 (0.608)	0.32 (0.477)	0.565 (0.687)	0.0984 (0.244)
del 13q34	85 (23%)	282	0.782 (0.848)	0.464 (0.603)	0.612 (0.712)	0.471 (0.608)	0.177 (0.348)	0.419 (0.565)	0.586 (0.698)	0.374 (0.529)	0.38 (0.534)	0.145 (0.316)

'amp_1p12' versus 'MRNASEQ_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.12

Table S1. Gene #1: 'amp_1p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
AMP PEAK 1(1P12) MUTATED	46	18	40	17
AMP PEAK 1(1P12) WILD-TYPE	70	55	65	56

Figure S1. Get High-res Image Gene #1: 'amp_1p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S2. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 2(1Q21.3) MUTATED	98	71	34
AMP PEAK 2(1Q21.3) WILD-TYPE	56	39	69

Figure S2. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'RPPA_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.013

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	78	43	69	32
AMP PEAK 2(1Q21.3) MUTATED	13	43	19	44	25
AMP PEAK 2(1Q21.3) WILD-TYPE	26	35	24	25	7

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

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0065

Table S4. Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
AMP PEAK 2(1Q21.3) MUTATED	72	26	56	49
AMP PEAK 2(1Q21.3) WILD-TYPE	44	47	49	24

Figure S4. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.12

Table S5. Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	97	103	97	54
AMP PEAK 2(1Q21.3) MUTATED	44	62	50	37
AMP PEAK 2(1Q21.3) WILD-TYPE	53	41	47	17

Figure S5. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.068

Table S6. Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	88	38
AMP PEAK 2(1Q21.3) MUTATED	80	39	48	26
AMP PEAK 2(1Q21.3) WILD-TYPE	52	54	40	12

Figure S6. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.14

Table S7. Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	119	133
AMP PEAK 2(1Q21.3) MUTATED	38	65	83
AMP PEAK 2(1Q21.3) WILD-TYPE	47	54	50

Figure S7. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q44' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00043

Table S8. Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 3(1Q44) MUTATED	96	70	35
AMP PEAK 3(1Q44) WILD-TYPE	58	40	68

Figure S8. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q44' versus 'RPPA_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0082

Table S9. Gene #3: 'amp_1q44' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	78	43	69	32
AMP PEAK 3(1Q44) MUTATED	14	40	21	41	27
AMP PEAK 3(1Q44) WILD-TYPE	25	38	22	28	5

Figure S9. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_1q44' versus 'MRNASEQ_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.016

Table S10. Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
AMP PEAK 3(1Q44) MUTATED	71	28	53	49
AMP PEAK 3(1Q44) WILD-TYPE	45	45	52	24

Figure S10. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q44' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0025

Table S11. Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	97	103	97	54
AMP PEAK 3(1Q44) MUTATED	40	63	48	41
AMP PEAK 3(1Q44) WILD-TYPE	57	40	49	13

Figure S11. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0016 (Fisher's exact test), Q value = 0.017

Table S12. Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	88	38
AMP PEAK 3(1Q44) MUTATED	77	38	48	29
AMP PEAK 3(1Q44) WILD-TYPE	55	55	40	9

Figure S12. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00509 (Fisher's exact test), Q value = 0.036

Table S13. Gene #3: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	119	133
AMP PEAK 3(1Q44) MUTATED	36	64	86
AMP PEAK 3(1Q44) WILD-TYPE	49	55	47

Figure S13. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q44' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.068

Table S14. Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	36	24	51	63	38	17	64	29	15
AMP PEAK 3(1Q44) MUTATED	16	11	23	40	21	6	38	24	7
AMP PEAK 3(1Q44) WILD-TYPE	20	13	28	23	17	11	26	5	8

Figure S14. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_CNMF'

P value = 0.00456 (Fisher's exact test), Q value = 0.033

Table S15. Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	97	103	97	54
AMP PEAK 5(4Q12) MUTATED	12	29	11	13
AMP PEAK 5(4Q12) WILD-TYPE	85	74	86	41

Figure S15. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.011

Table S16. Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	88	38
AMP PEAK 5(4Q12) MUTATED	38	8	14	5
AMP PEAK 5(4Q12) WILD-TYPE	94	85	74	33

Figure S16. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S17. Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 6(5P15.33) MUTATED	72	23	15
AMP PEAK 6(5P15.33) WILD-TYPE	82	87	88

Figure S17. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.018

Table S18. Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	97	103	97	54
AMP PEAK 6(5P15.33) MUTATED	30	38	15	21
AMP PEAK 6(5P15.33) WILD-TYPE	67	65	82	33

Figure S18. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S19. Gene #7: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 7(5Q35.3) MUTATED	46	8	5
AMP PEAK 7(5Q35.3) WILD-TYPE	108	102	98

Figure S19. Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.12

Table S20. Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
AMP PEAK 7(5Q35.3) MUTATED	24	11	8	16
AMP PEAK 7(5Q35.3) WILD-TYPE	87	111	26	83

Figure S20. Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S21. Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 8(6P24.3) MUTATED	105	71	35
AMP PEAK 8(6P24.3) WILD-TYPE	49	39	68

Figure S21. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S22. Gene #8: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
AMP PEAK 8(6P24.3) MUTATED	71	48	21	70
AMP PEAK 8(6P24.3) WILD-TYPE	40	74	13	29

Figure S22. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p24.3' versus 'RPPA_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.11

Table S23. Gene #8: 'amp_6p24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	78	43	69	32
AMP PEAK 8(6P24.3) MUTATED	17	45	22	50	16
AMP PEAK 8(6P24.3) WILD-TYPE	22	33	21	19	16

Figure S23. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6p24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.05 (Fisher's exact test), Q value = 0.17

Table S24. Gene #8: 'amp_6p24.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	84	91
AMP PEAK 8(6P24.3) MUTATED	57	40	53
AMP PEAK 8(6P24.3) WILD-TYPE	29	44	38

Figure S24. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6p24.3' versus 'MRNASEQ_CNMF'

P value = 0.00677 (Fisher's exact test), Q value = 0.043

Table S25. Gene #8: 'amp_6p24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
AMP PEAK 8(6P24.3) MUTATED	72	35	52	52
AMP PEAK 8(6P24.3) WILD-TYPE	44	38	53	21

Figure S25. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00421 (Fisher's exact test), Q value = 0.032

Table S26. Gene #8: 'amp_6p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
AMP PEAK 8(6P24.3) MUTATED	72	95	44
AMP PEAK 8(6P24.3) WILD-TYPE	33	70	53

Figure S26. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.032

Table S27. Gene #8: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	97	103	97	54
AMP PEAK 8(6P24.3) MUTATED	48	73	48	33
AMP PEAK 8(6P24.3) WILD-TYPE	49	30	49	21

Figure S27. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016

Table S28. Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	88	38
AMP PEAK 8(6P24.3) MUTATED	91	35	55	21
AMP PEAK 8(6P24.3) WILD-TYPE	41	58	33	17

Figure S28. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0029

Table S29. Gene #8: 'amp_6p24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	119	133
AMP PEAK 8(6P24.3) MUTATED	36	64	93
AMP PEAK 8(6P24.3) WILD-TYPE	49	55	40

Figure S29. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0024

Table S30. Gene #8: 'amp_6p24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	36	24	51	63	38	17	64	29	15
AMP PEAK 8(6P24.3) MUTATED	17	14	25	51	15	5	39	16	11
AMP PEAK 8(6P24.3) WILD-TYPE	19	10	26	12	23	12	25	13	4

Figure S30. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.067

Table S31. Gene #9: 'amp_6q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	84	91
AMP PEAK 9(6Q12) MUTATED	26	10	20
AMP PEAK 9(6Q12) WILD-TYPE	60	74	71

Figure S31. Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.11

Table S32. Gene #9: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	88	38
AMP PEAK 9(6Q12) MUTATED	35	14	25	4
AMP PEAK 9(6Q12) WILD-TYPE	97	79	63	34

Figure S32. Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0055

Table S33. Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 10(7P22.1) MUTATED	103	63	43
AMP PEAK 10(7P22.1) WILD-TYPE	51	47	60

Figure S33. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q34' versus 'CN_CNMF'

P value = 0.00192 (Fisher's exact test), Q value = 0.019

Table S34. Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 11(7Q34) MUTATED	110	63	52
AMP PEAK 11(7Q34) WILD-TYPE	44	47	51

Figure S34. Get High-res Image Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00201 (Fisher's exact test), Q value = 0.019

Table S35. Gene #11: 'amp_7q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	36	24	51	63	38	17	64	29	15
AMP PEAK 11(7Q34) MUTATED	18	13	42	32	23	15	36	20	7
AMP PEAK 11(7Q34) WILD-TYPE	18	11	9	31	15	2	28	9	8

Figure S35. Get High-res Image Gene #11: 'amp_7q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S36. Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 12(8Q24.21) MUTATED	91	68	33
AMP PEAK 12(8Q24.21) WILD-TYPE	63	42	70

Figure S36. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016

Table S37. Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
AMP PEAK 12(8Q24.21) MUTATED	44	59	26	62
AMP PEAK 12(8Q24.21) WILD-TYPE	67	63	8	37

Figure S37. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.001

Table S38. Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
AMP PEAK 12(8Q24.21) MUTATED	51	29	57	55
AMP PEAK 12(8Q24.21) WILD-TYPE	65	44	48	18

Figure S38. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.071

Table S39. Gene #13: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 13(11Q13.3) MUTATED	40	15	14
AMP PEAK 13(11Q13.3) WILD-TYPE	114	95	89

Figure S39. Get High-res Image Gene #13: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q14.1' versus 'CN_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.1

Table S40. Gene #14: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 14(12Q14.1) MUTATED	30	20	8
AMP PEAK 14(12Q14.1) WILD-TYPE	124	90	95

Figure S40. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.11

Table S41. Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	36	24	51	63	38	17	64	29	15
AMP PEAK 14(12Q14.1) MUTATED	1	2	14	9	9	3	14	5	0
AMP PEAK 14(12Q14.1) WILD-TYPE	35	22	37	54	29	14	50	24	15

Figure S41. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S42. Gene #16: 'amp_13q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 16(13Q31.3) MUTATED	51	41	12
AMP PEAK 16(13Q31.3) WILD-TYPE	103	69	91

Figure S42. Get High-res Image Gene #16: 'amp_13q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q31.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00043

Table S43. Gene #16: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
AMP PEAK 16(13Q31.3) MUTATED	29	18	11	45
AMP PEAK 16(13Q31.3) WILD-TYPE	82	104	23	54

Figure S43. Get High-res Image Gene #16: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q31.3' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0012

Table S44. Gene #16: 'amp_13q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
AMP PEAK 16(13Q31.3) MUTATED	24	11	36	33
AMP PEAK 16(13Q31.3) WILD-TYPE	92	62	69	40

Figure S44. Get High-res Image Gene #16: 'amp_13q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.061

Table S45. Gene #16: 'amp_13q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
AMP PEAK 16(13Q31.3) MUTATED	36	34	34
AMP PEAK 16(13Q31.3) WILD-TYPE	69	131	63

Figure S45. Get High-res Image Gene #16: 'amp_13q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q31.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.068

Table S46. Gene #16: 'amp_13q31.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	36	24	51	63	38	17	64	29	15
AMP PEAK 16(13Q31.3) MUTATED	6	3	8	26	13	6	24	6	4
AMP PEAK 16(13Q31.3) WILD-TYPE	30	21	43	37	25	11	40	23	11

Figure S46. Get High-res Image Gene #16: 'amp_13q31.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.2' versus 'CN_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.022

Table S47. Gene #17: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 17(15Q26.2) MUTATED	65	32	23
AMP PEAK 17(15Q26.2) WILD-TYPE	89	78	80

Figure S47. Get High-res Image Gene #17: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0076

Table S48. Gene #18: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 18(17Q25.3) MUTATED	67	33	22
AMP PEAK 18(17Q25.3) WILD-TYPE	87	77	81

Figure S48. Get High-res Image Gene #18: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.13

Table S49. Gene #18: 'amp_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
AMP PEAK 18(17Q25.3) MUTATED	32	66	24
AMP PEAK 18(17Q25.3) WILD-TYPE	73	99	73

Figure S49. Get High-res Image Gene #18: 'amp_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S50. Gene #19: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 19(20Q13.33) MUTATED	100	60	28
AMP PEAK 19(20Q13.33) WILD-TYPE	54	50	75

Figure S50. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.093

Table S51. Gene #19: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
AMP PEAK 19(20Q13.33) MUTATED	53	52	21	61
AMP PEAK 19(20Q13.33) WILD-TYPE	58	70	13	38

Figure S51. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'RPPA_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.085

Table S52. Gene #19: 'amp_20q13.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	78	43	69	32
AMP PEAK 19(20Q13.33) MUTATED	13	33	24	44	15
AMP PEAK 19(20Q13.33) WILD-TYPE	26	45	19	25	17

Figure S52. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.15

Table S53. Gene #19: 'amp_20q13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
AMP PEAK 19(20Q13.33) MUTATED	55	74	59
AMP PEAK 19(20Q13.33) WILD-TYPE	50	91	38

Figure S53. Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_22q13.2' versus 'CN_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.02

Table S54. Gene #20: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
AMP PEAK 20(22Q13.2) MUTATED	72	52	28
AMP PEAK 20(22Q13.2) WILD-TYPE	82	58	75

Figure S54. Get High-res Image Gene #20: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q13.2' versus 'METHLYATION_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.15

Table S55. Gene #20: 'amp_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
AMP PEAK 20(22Q13.2) MUTATED	45	40	15	51
AMP PEAK 20(22Q13.2) WILD-TYPE	66	82	19	48

Figure S55. Get High-res Image Gene #20: 'amp_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_22q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.061

Table S56. Gene #20: 'amp_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	36	24	51	63	38	17	64	29	15
AMP PEAK 20(22Q13.2) MUTATED	7	7	30	24	14	5	31	15	5
AMP PEAK 20(22Q13.2) WILD-TYPE	29	17	21	39	24	12	33	14	10

Figure S56. Get High-res Image Gene #20: 'amp_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'CN_CNMF'

P value = 0.00573 (Fisher's exact test), Q value = 0.04

Table S57. Gene #21: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 1(1P36.31) MUTATED	43	26	12
DEL PEAK 1(1P36.31) WILD-TYPE	111	84	91

Figure S57. Get High-res Image Gene #21: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 0.00637 (Fisher's exact test), Q value = 0.042

Table S58. Gene #21: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 1(1P36.31) MUTATED	21	18	13	29
DEL PEAK 1(1P36.31) WILD-TYPE	90	104	21	70

Figure S58. Get High-res Image Gene #21: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.11

Table S59. Gene #21: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 1(1P36.31) MUTATED	30	26	25
DEL PEAK 1(1P36.31) WILD-TYPE	75	139	72

Figure S59. Get High-res Image Gene #21: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.064

Table S60. Gene #21: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	97	103	97	54
DEL PEAK 1(1P36.31) MUTATED	13	23	23	20
DEL PEAK 1(1P36.31) WILD-TYPE	84	80	74	34

Figure S60. Get High-res Image Gene #21: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p22.1' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0025

Table S61. Gene #22: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 2(1P22.1) MUTATED	48	37	12
DEL PEAK 2(1P22.1) WILD-TYPE	106	73	91

Figure S61. Get High-res Image Gene #22: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 0.00404 (Fisher's exact test), Q value = 0.032

Table S62. Gene #22: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 2(1P22.1) MUTATED	20	29	16	32
DEL PEAK 2(1P22.1) WILD-TYPE	91	93	18	67

Figure S62. Get High-res Image Gene #22: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.087

Table S63. Gene #22: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 2(1P22.1) MUTATED	30	10	36	21
DEL PEAK 2(1P22.1) WILD-TYPE	86	63	69	52

Figure S63. Get High-res Image Gene #22: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00672 (Fisher's exact test), Q value = 0.043

Table S64. Gene #22: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 2(1P22.1) MUTATED	27	33	37
DEL PEAK 2(1P22.1) WILD-TYPE	78	132	60

Figure S64. Get High-res Image Gene #22: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.042 (Fisher's exact test), Q value = 0.15

Table S65. Gene #22: 'del_1p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	119	133
DEL PEAK 2(1P22.1) MUTATED	16	41	35
DEL PEAK 2(1P22.1) WILD-TYPE	69	78	98

Figure S65. Get High-res Image Gene #22: 'del_1p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.082

Table S66. Gene #23: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 3(2Q37.3) MUTATED	51	21	21
DEL PEAK 3(2Q37.3) WILD-TYPE	103	89	82

Figure S66. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.061

Table S67. Gene #23: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 3(2Q37.3) MUTATED	38	21	12	22
DEL PEAK 3(2Q37.3) WILD-TYPE	73	101	22	77

Figure S67. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.11

Table S68. Gene #23: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	84	91
DEL PEAK 3(2Q37.3) MUTATED	19	16	33
DEL PEAK 3(2Q37.3) WILD-TYPE	67	68	58

Figure S68. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.15

Table S69. Gene #23: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 3(2Q37.3) MUTATED	39	15	19	20
DEL PEAK 3(2Q37.3) WILD-TYPE	77	58	86	53

Figure S69. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.018

Table S70. Gene #23: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 3(2Q37.3) MUTATED	38	41	14
DEL PEAK 3(2Q37.3) WILD-TYPE	67	124	83

Figure S70. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.068

Table S71. Gene #23: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	97	103	97	54
DEL PEAK 3(2Q37.3) MUTATED	19	37	18	17
DEL PEAK 3(2Q37.3) WILD-TYPE	78	66	79	37

Figure S71. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 0.13

Table S72. Gene #23: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	88	38
DEL PEAK 3(2Q37.3) MUTATED	44	15	23	9
DEL PEAK 3(2Q37.3) WILD-TYPE	88	78	65	29

Figure S72. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.1' versus 'CN_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.16

Table S73. Gene #24: 'del_3p25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 4(3P25.1) MUTATED	24	30	17
DEL PEAK 4(3P25.1) WILD-TYPE	130	80	86

Figure S73. Get High-res Image Gene #24: 'del_3p25.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q13.31' versus 'MRNASEQ_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.11

Table S74. Gene #25: 'del_3q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 5(3Q13.31) MUTATED	24	6	14	18
DEL PEAK 5(3Q13.31) WILD-TYPE	92	67	91	55

Figure S74. Get High-res Image Gene #25: 'del_3q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q13.31' versus 'MIRSEQ_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.16

Table S75. Gene #25: 'del_3q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	97	103	97	54
DEL PEAK 5(3Q13.31) MUTATED	14	25	17	4
DEL PEAK 5(3Q13.31) WILD-TYPE	83	78	80	50

Figure S75. Get High-res Image Gene #25: 'del_3q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0457 (Fisher's exact test), Q value = 0.16

Table S76. Gene #26: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 6(4P16.3) MUTATED	30	31	30
DEL PEAK 6(4P16.3) WILD-TYPE	75	134	67

Figure S76. Get High-res Image Gene #26: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.00685 (Fisher's exact test), Q value = 0.043

Table S77. Gene #27: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 7(4Q34.3) MUTATED	59	30	21
DEL PEAK 7(4Q34.3) WILD-TYPE	95	80	82

Figure S77. Get High-res Image Gene #27: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.12

Table S78. Gene #27: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 7(4Q34.3) MUTATED	32	16	43	19
DEL PEAK 7(4Q34.3) WILD-TYPE	84	57	62	54

Figure S78. Get High-res Image Gene #27: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00476 (Fisher's exact test), Q value = 0.034

Table S79. Gene #27: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 7(4Q34.3) MUTATED	27	41	42
DEL PEAK 7(4Q34.3) WILD-TYPE	78	124	55

Figure S79. Get High-res Image Gene #27: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00313 (Fisher's exact test), Q value = 0.026

Table S80. Gene #27: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	88	38
DEL PEAK 7(4Q34.3) MUTATED	26	38	28	15
DEL PEAK 7(4Q34.3) WILD-TYPE	106	55	60	23

Figure S80. Get High-res Image Gene #27: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0489 (Fisher's exact test), Q value = 0.16

Table S81. Gene #27: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	36	24	51	63	38	17	64	29	15
DEL PEAK 7(4Q34.3) MUTATED	9	5	17	14	20	8	17	10	3
DEL PEAK 7(4Q34.3) WILD-TYPE	27	19	34	49	18	9	47	19	12

Figure S81. Get High-res Image Gene #27: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S82. Gene #28: 'del_5p15.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 8(5P15.31) MUTATED	16	49	14
DEL PEAK 8(5P15.31) WILD-TYPE	138	61	89

Figure S82. Get High-res Image Gene #28: 'del_5p15.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S83. Gene #29: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 9(5Q12.1) MUTATED	26	57	14
DEL PEAK 9(5Q12.1) WILD-TYPE	128	53	89

Figure S83. Get High-res Image Gene #29: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.022

Table S84. Gene #29: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	78	43	69	32
DEL PEAK 9(5Q12.1) MUTATED	2	18	11	20	14
DEL PEAK 9(5Q12.1) WILD-TYPE	37	60	32	49	18

Figure S84. Get High-res Image Gene #29: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S85. Gene #30: 'del_5q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 10(5Q31.3) MUTATED	33	72	26
DEL PEAK 10(5Q31.3) WILD-TYPE	121	38	77

Figure S85. Get High-res Image Gene #30: 'del_5q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q31.3' versus 'METHLYATION_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.12

Table S86. Gene #30: 'del_5q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 10(5Q31.3) MUTATED	43	42	5	41
DEL PEAK 10(5Q31.3) WILD-TYPE	68	80	29	58

Figure S86. Get High-res Image Gene #30: 'del_5q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q31.3' versus 'RPPA_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.11

Table S87. Gene #30: 'del_5q31.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	78	43	69	32
DEL PEAK 10(5Q31.3) MUTATED	5	26	14	25	15
DEL PEAK 10(5Q31.3) WILD-TYPE	34	52	29	44	17

Figure S87. Get High-res Image Gene #30: 'del_5q31.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S88. Gene #31: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 11(6Q21) MUTATED	132	54	28
DEL PEAK 11(6Q21) WILD-TYPE	22	56	75

Figure S88. Get High-res Image Gene #31: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q21' versus 'METHLYATION_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.018

Table S89. Gene #31: 'del_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 11(6Q21) MUTATED	72	55	19	68
DEL PEAK 11(6Q21) WILD-TYPE	39	67	15	31

Figure S89. Get High-res Image Gene #31: 'del_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q21' versus 'MRNASEQ_CNMF'

P value = 0.00192 (Fisher's exact test), Q value = 0.019

Table S90. Gene #31: 'del_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 11(6Q21) MUTATED	78	29	65	42
DEL PEAK 11(6Q21) WILD-TYPE	38	44	40	31

Figure S90. Get High-res Image Gene #31: 'del_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S91. Gene #32: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 12(6Q26) MUTATED	135	57	29
DEL PEAK 12(6Q26) WILD-TYPE	19	53	74

Figure S91. Get High-res Image Gene #32: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00417 (Fisher's exact test), Q value = 0.032

Table S92. Gene #32: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 12(6Q26) MUTATED	71	59	20	71
DEL PEAK 12(6Q26) WILD-TYPE	40	63	14	28

Figure S92. Get High-res Image Gene #32: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00634 (Fisher's exact test), Q value = 0.042

Table S93. Gene #32: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 12(6Q26) MUTATED	78	31	67	45
DEL PEAK 12(6Q26) WILD-TYPE	38	42	38	28

Figure S93. Get High-res Image Gene #32: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.004

Table S94. Gene #33: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 13(8P23.3) MUTATED	54	17	18
DEL PEAK 13(8P23.3) WILD-TYPE	100	93	85

Figure S94. Get High-res Image Gene #33: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'RPPA_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.13

Table S95. Gene #33: 'del_8p23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	78	43	69	32
DEL PEAK 13(8P23.3) MUTATED	4	19	10	26	9
DEL PEAK 13(8P23.3) WILD-TYPE	35	59	33	43	23

Figure S95. Get High-res Image Gene #33: 'del_8p23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_8p23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.1

Table S96. Gene #33: 'del_8p23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	84	91
DEL PEAK 13(8P23.3) MUTATED	27	13	28
DEL PEAK 13(8P23.3) WILD-TYPE	59	71	63

Figure S96. Get High-res Image Gene #33: 'del_8p23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0025

Table S97. Gene #34: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 14(9P23) MUTATED	112	84	53
DEL PEAK 14(9P23) WILD-TYPE	42	26	50

Figure S97. Get High-res Image Gene #34: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.12

Table S98. Gene #34: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 14(9P23) MUTATED	80	71	23	75
DEL PEAK 14(9P23) WILD-TYPE	31	51	11	24

Figure S98. Get High-res Image Gene #34: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.15

Table S99. Gene #34: 'del_9p23' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	78	43	69	32
DEL PEAK 14(9P23) MUTATED	24	58	30	38	26
DEL PEAK 14(9P23) WILD-TYPE	15	20	13	31	6

Figure S99. Get High-res Image Gene #34: 'del_9p23' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.15

Table S100. Gene #34: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 14(9P23) MUTATED	77	41	80	51
DEL PEAK 14(9P23) WILD-TYPE	39	32	25	22

Figure S100. Get High-res Image Gene #34: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.014

Table S101. Gene #34: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	36	24	51	63	38	17	64	29	15
DEL PEAK 14(9P23) MUTATED	19	18	31	36	27	16	47	17	15
DEL PEAK 14(9P23) WILD-TYPE	17	6	20	27	11	1	17	12	0

Figure S101. Get High-res Image Gene #34: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S102. Gene #35: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 15(9P21.3) MUTATED	130	90	58
DEL PEAK 15(9P21.3) WILD-TYPE	24	20	45

Figure S102. Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0077

Table S103. Gene #35: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 15(9P21.3) MUTATED	89	78	25	86
DEL PEAK 15(9P21.3) WILD-TYPE	22	44	9	13

Figure S103. Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 0.00821 (Fisher's exact test), Q value = 0.051

Table S104. Gene #35: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	78	43	69	32
DEL PEAK 15(9P21.3) MUTATED	24	65	35	45	28
DEL PEAK 15(9P21.3) WILD-TYPE	15	13	8	24	4

Figure S104. Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.022

Table S105. Gene #35: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 15(9P21.3) MUTATED	87	44	89	58
DEL PEAK 15(9P21.3) WILD-TYPE	29	29	16	15

Figure S105. Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00333 (Fisher's exact test), Q value = 0.027

Table S106. Gene #35: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 15(9P21.3) MUTATED	81	113	84
DEL PEAK 15(9P21.3) WILD-TYPE	24	52	13

Figure S106. Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.12

Table S107. Gene #35: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	97	103	97	54
DEL PEAK 15(9P21.3) MUTATED	66	73	82	43
DEL PEAK 15(9P21.3) WILD-TYPE	31	30	15	11

Figure S107. Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00262 (Fisher's exact test), Q value = 0.022

Table S108. Gene #35: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	36	24	51	63	38	17	64	29	15
DEL PEAK 15(9P21.3) MUTATED	23	19	33	41	34	16	51	21	15
DEL PEAK 15(9P21.3) WILD-TYPE	13	5	18	22	4	1	13	8	0

Figure S108. Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S109. Gene #36: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 16(10P15.3) MUTATED	90	84	25
DEL PEAK 16(10P15.3) WILD-TYPE	64	26	78

Figure S109. Get High-res Image Gene #36: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.033

Table S110. Gene #36: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 16(10P15.3) MUTATED	57	55	19	68
DEL PEAK 16(10P15.3) WILD-TYPE	54	67	15	31

Figure S110. Get High-res Image Gene #36: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00457 (Fisher's exact test), Q value = 0.033

Table S111. Gene #36: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 16(10P15.3) MUTATED	52	35	71	41
DEL PEAK 16(10P15.3) WILD-TYPE	64	38	34	32

Figure S111. Get High-res Image Gene #36: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.012

Table S112. Gene #36: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 16(10P15.3) MUTATED	57	75	67
DEL PEAK 16(10P15.3) WILD-TYPE	48	90	30

Figure S112. Get High-res Image Gene #36: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S113. Gene #37: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 17(10Q21.1) MUTATED	96	93	28
DEL PEAK 17(10Q21.1) WILD-TYPE	58	17	75

Figure S113. Get High-res Image Gene #37: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.072

Table S114. Gene #37: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 17(10Q21.1) MUTATED	66	63	17	71
DEL PEAK 17(10Q21.1) WILD-TYPE	45	59	17	28

Figure S114. Get High-res Image Gene #37: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.13

Table S115. Gene #37: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 17(10Q21.1) MUTATED	59	90	68
DEL PEAK 17(10Q21.1) WILD-TYPE	46	75	29

Figure S115. Get High-res Image Gene #37: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S116. Gene #38: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 18(10Q23.31) MUTATED	103	93	34
DEL PEAK 18(10Q23.31) WILD-TYPE	51	17	69

Figure S116. Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.021

Table S117. Gene #38: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 18(10Q23.31) MUTATED	70	64	20	76
DEL PEAK 18(10Q23.31) WILD-TYPE	41	58	14	23

Figure S117. Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.13

Table S118. Gene #38: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 18(10Q23.31) MUTATED	63	42	73	52
DEL PEAK 18(10Q23.31) WILD-TYPE	53	31	32	21

Figure S118. Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.095

Table S119. Gene #38: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 18(10Q23.31) MUTATED	63	95	72
DEL PEAK 18(10Q23.31) WILD-TYPE	42	70	25

Figure S119. Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S120. Gene #39: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 19(10Q26.3) MUTATED	103	95	38
DEL PEAK 19(10Q26.3) WILD-TYPE	51	15	65

Figure S120. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 0.00366 (Fisher's exact test), Q value = 0.029

Table S121. Gene #39: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 19(10Q26.3) MUTATED	69	69	20	78
DEL PEAK 19(10Q26.3) WILD-TYPE	42	53	14	21

Figure S121. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 0.00642 (Fisher's exact test), Q value = 0.042

Table S122. Gene #39: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 19(10Q26.3) MUTATED	62	44	77	53
DEL PEAK 19(10Q26.3) WILD-TYPE	54	29	28	20

Figure S122. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00627 (Fisher's exact test), Q value = 0.042

Table S123. Gene #39: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 19(10Q26.3) MUTATED	64	97	75
DEL PEAK 19(10Q26.3) WILD-TYPE	41	68	22

Figure S123. Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0055

Table S124. Gene #40: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 20(11P15.5) MUTATED	50	46	18
DEL PEAK 20(11P15.5) WILD-TYPE	104	64	85

Figure S124. Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S125. Gene #41: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 21(11Q23.3) MUTATED	101	67	36
DEL PEAK 21(11Q23.3) WILD-TYPE	53	43	67

Figure S125. Get High-res Image Gene #41: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.16

Table S126. Gene #41: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	119	133
DEL PEAK 21(11Q23.3) MUTATED	45	61	87
DEL PEAK 21(11Q23.3) WILD-TYPE	40	58	46

Figure S126. Get High-res Image Gene #41: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12q23.3' versus 'CN_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.12

Table S127. Gene #42: 'del_12q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 22(12Q23.3) MUTATED	44	32	16
DEL PEAK 22(12Q23.3) WILD-TYPE	110	78	87

Figure S127. Get High-res Image Gene #42: 'del_12q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q23.3' versus 'METHLYATION_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.059

Table S128. Gene #42: 'del_12q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 22(12Q23.3) MUTATED	38	21	5	28
DEL PEAK 22(12Q23.3) WILD-TYPE	73	101	29	71

Figure S128. Get High-res Image Gene #42: 'del_12q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016

Table S129. Gene #44: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 24(14Q23.3) MUTATED	58	45	17
DEL PEAK 24(14Q23.3) WILD-TYPE	96	65	86

Figure S129. Get High-res Image Gene #44: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.072

Table S130. Gene #44: 'del_14q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	84	91
DEL PEAK 24(14Q23.3) MUTATED	37	19	26
DEL PEAK 24(14Q23.3) WILD-TYPE	49	65	65

Figure S130. Get High-res Image Gene #44: 'del_14q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00602 (Fisher's exact test), Q value = 0.041

Table S131. Gene #44: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 24(14Q23.3) MUTATED	28	26	47	19
DEL PEAK 24(14Q23.3) WILD-TYPE	88	47	58	54

Figure S131. Get High-res Image Gene #44: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.12

Table S132. Gene #44: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 24(14Q23.3) MUTATED	28	50	42
DEL PEAK 24(14Q23.3) WILD-TYPE	77	115	55

Figure S132. Get High-res Image Gene #44: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.31' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S133. Gene #45: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 25(14Q32.31) MUTATED	57	44	16
DEL PEAK 25(14Q32.31) WILD-TYPE	97	66	87

Figure S133. Get High-res Image Gene #45: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.12

Table S134. Gene #45: 'del_14q32.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	84	91
DEL PEAK 25(14Q32.31) MUTATED	37	21	26
DEL PEAK 25(14Q32.31) WILD-TYPE	49	63	65

Figure S134. Get High-res Image Gene #45: 'del_14q32.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_14q32.31' versus 'MRNASEQ_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.064

Table S135. Gene #45: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 25(14Q32.31) MUTATED	28	24	46	19
DEL PEAK 25(14Q32.31) WILD-TYPE	88	49	59	54

Figure S135. Get High-res Image Gene #45: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.1

Table S136. Gene #45: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 25(14Q32.31) MUTATED	29	46	42
DEL PEAK 25(14Q32.31) WILD-TYPE	76	119	55

Figure S136. Get High-res Image Gene #45: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.3' versus 'RPPA_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.1

Table S137. Gene #46: 'del_15q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	78	43	69	32
DEL PEAK 26(15Q13.3) MUTATED	4	16	11	25	5
DEL PEAK 26(15Q13.3) WILD-TYPE	35	62	32	44	27

Figure S137. Get High-res Image Gene #46: 'del_15q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.15

Table S138. Gene #46: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 26(15Q13.3) MUTATED	33	30	21
DEL PEAK 26(15Q13.3) WILD-TYPE	72	135	76

Figure S138. Get High-res Image Gene #46: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00832 (Fisher's exact test), Q value = 0.051

Table S139. Gene #46: 'del_15q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	119	133
DEL PEAK 26(15Q13.3) MUTATED	10	34	35
DEL PEAK 26(15Q13.3) WILD-TYPE	75	85	98

Figure S139. Get High-res Image Gene #46: 'del_15q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q21.1' versus 'CN_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.16

Table S140. Gene #47: 'del_15q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 27(15Q21.1) MUTATED	46	28	17
DEL PEAK 27(15Q21.1) WILD-TYPE	108	82	86

Figure S140. Get High-res Image Gene #47: 'del_15q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.11

Table S141. Gene #47: 'del_15q21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	84	91
DEL PEAK 27(15Q21.1) MUTATED	30	14	26
DEL PEAK 27(15Q21.1) WILD-TYPE	56	70	65

Figure S141. Get High-res Image Gene #47: 'del_15q21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 0.00966 (Fisher's exact test), Q value = 0.057

Table S142. Gene #48: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 28(16P13.3) MUTATED	37	12	13
DEL PEAK 28(16P13.3) WILD-TYPE	117	98	90

Figure S142. Get High-res Image Gene #48: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.00909 (Fisher's exact test), Q value = 0.055

Table S143. Gene #48: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 28(16P13.3) MUTATED	26	16	10	10
DEL PEAK 28(16P13.3) WILD-TYPE	85	106	24	89

Figure S143. Get High-res Image Gene #48: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.16

Table S144. Gene #48: 'del_16p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	84	91
DEL PEAK 28(16P13.3) MUTATED	22	10	13
DEL PEAK 28(16P13.3) WILD-TYPE	64	74	78

Figure S144. Get High-res Image Gene #48: 'del_16p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_16q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S145. Gene #49: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 29(16Q12.1) MUTATED	78	16	23
DEL PEAK 29(16Q12.1) WILD-TYPE	76	94	80

Figure S145. Get High-res Image Gene #49: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S146. Gene #50: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 30(16Q23.1) MUTATED	79	16	25
DEL PEAK 30(16Q23.1) WILD-TYPE	75	94	78

Figure S146. Get High-res Image Gene #50: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.15

Table S147. Gene #50: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 30(16Q23.1) MUTATED	47	34	13	26
DEL PEAK 30(16Q23.1) WILD-TYPE	64	88	21	73

Figure S147. Get High-res Image Gene #50: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.087

Table S148. Gene #50: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 30(16Q23.1) MUTATED	48	23	23	26
DEL PEAK 30(16Q23.1) WILD-TYPE	68	50	82	47

Figure S148. Get High-res Image Gene #50: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S149. Gene #51: 'del_16q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 31(16Q24.3) MUTATED	85	19	29
DEL PEAK 31(16Q24.3) WILD-TYPE	69	91	74

Figure S149. Get High-res Image Gene #51: 'del_16q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q24.3' versus 'RPPA_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.15

Table S150. Gene #51: 'del_16q24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	78	43	69	32
DEL PEAK 31(16Q24.3) MUTATED	9	25	22	30	9
DEL PEAK 31(16Q24.3) WILD-TYPE	30	53	21	39	23

Figure S150. Get High-res Image Gene #51: 'del_16q24.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.11

Table S151. Gene #51: 'del_16q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 31(16Q24.3) MUTATED	52	25	27	29
DEL PEAK 31(16Q24.3) WILD-TYPE	64	48	78	44

Figure S151. Get High-res Image Gene #51: 'del_16q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.11

Table S152. Gene #51: 'del_16q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 31(16Q24.3) MUTATED	38	70	25
DEL PEAK 31(16Q24.3) WILD-TYPE	67	95	72

Figure S152. Get High-res Image Gene #51: 'del_16q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.13

Table S153. Gene #52: 'del_17p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	84	91
DEL PEAK 32(17P13.3) MUTATED	28	43	33
DEL PEAK 32(17P13.3) WILD-TYPE	58	41	58

Figure S153. Get High-res Image Gene #52: 'del_17p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.072

Table S154. Gene #53: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 33(19P13.3) MUTATED	50	36	18
DEL PEAK 33(19P13.3) WILD-TYPE	104	74	85

Figure S154. Get High-res Image Gene #53: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0025

Table S155. Gene #53: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 33(19P13.3) MUTATED	51	16	18	19
DEL PEAK 33(19P13.3) WILD-TYPE	65	57	87	54

Figure S155. Get High-res Image Gene #53: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'CN_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.12

Table S156. Gene #54: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	110	103
DEL PEAK 34(XP21.1) MUTATED	34	35	17
DEL PEAK 34(XP21.1) WILD-TYPE	120	75	86

Figure S156. Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00043

Table S157. Gene #54: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	111	122	34	99
DEL PEAK 34(XP21.1) MUTATED	38	12	11	25
DEL PEAK 34(XP21.1) WILD-TYPE	73	110	23	74

Figure S157. Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.00931 (Fisher's exact test), Q value = 0.056

Table S158. Gene #54: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	73	105	73
DEL PEAK 34(XP21.1) MUTATED	34	7	27	18
DEL PEAK 34(XP21.1) WILD-TYPE	82	66	78	55

Figure S158. Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0042 (Fisher's exact test), Q value = 0.032

Table S159. Gene #54: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	165	97
DEL PEAK 34(XP21.1) MUTATED	34	26	26
DEL PEAK 34(XP21.1) WILD-TYPE	71	139	71

Figure S159. Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.021

Table S160. Gene #54: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	97	103	97	54
DEL PEAK 34(XP21.1) MUTATED	22	37	16	7
DEL PEAK 34(XP21.1) WILD-TYPE	75	66	81	47

Figure S160. Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 0.095

Table S161. Gene #54: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	132	93	88	38
DEL PEAK 34(XP21.1) MUTATED	39	15	24	4
DEL PEAK 34(XP21.1) WILD-TYPE	93	78	64	34

Figure S161. Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.15

Table S162. Gene #54: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	119	133
DEL PEAK 34(XP21.1) MUTATED	16	21	40
DEL PEAK 34(XP21.1) WILD-TYPE	69	98	93

Figure S162. Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0088

Table S163. Gene #54: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	36	24	51	63	38	17	64	29	15
DEL PEAK 34(XP21.1) MUTATED	6	8	8	23	3	9	11	4	5
DEL PEAK 34(XP21.1) WILD-TYPE	30	16	43	40	35	8	53	25	10

Figure S163. Get High-res Image Gene #54: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/22533834/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SKCM-TM/22546664/SKCM-TM.transferedmergedcluster.txt
Number of patients = 367
Number of significantly focal cnvs = 54
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

Download Results

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

References

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

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

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