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

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 46 focal events and 10 molecular subtypes across 90 patients, 155 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_4p16.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_4q35.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_5q35.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_6p21.31 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
amp_6q24.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_7p22.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_9q31.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_12q14.1 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_14q11.2 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_16p13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_16q22.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_16q24.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_17q25.3 cnv correlated to 'CN_CNMF'.
amp_19p13.12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_xp11.22 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
amp_xq28 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1q43 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_2q37.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_3q13.31 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_4q35.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_7q36.3 cnv correlated to 'CN_CNMF'.
del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_11q14.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_12q14.2 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF'.
del_14q21.2 cnv correlated to 'CN_CNMF'.
del_16p13.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_17q21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_17q24.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'CN_CNMF'.
del_20p12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_22q12.1 cnv correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 46 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, 155 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 14q11 2	27 (30%)	63	3e-05 (0.000862)	0.0124 (0.0603)	0.023 (0.0891)	0.0277 (0.101)	2e-05 (0.000613)	2e-05 (0.000613)	0.00023 (0.00441)	0.00669 (0.0427)	0.00059 (0.00875)	0.00085 (0.0105)
amp 5q35 3	63 (70%)	27	1e-05 (0.000418)	0.00125 (0.0135)	0.738 (0.856)	0.00663 (0.0427)	1e-05 (0.000418)	1e-05 (0.000418)	0.00702 (0.0431)	0.0467 (0.141)	0.0127 (0.0609)	0.29 (0.491)
del 9p23	24 (27%)	66	0.00971 (0.0502)	0.00806 (0.0463)	0.337 (0.525)	0.0493 (0.146)	1e-05 (0.000418)	0.00153 (0.016)	0.00761 (0.0455)	0.175 (0.372)	0.00779 (0.0459)	0.732 (0.856)
amp 16q24 2	49 (54%)	41	1e-05 (0.000418)	0.0261 (0.099)	1 (1.00)	0.319 (0.512)	0.00021 (0.0042)	2e-05 (0.000613)	0.0623 (0.176)	0.00273 (0.0228)	0.00564 (0.0387)	0.381 (0.57)
del 4q34 3	25 (28%)	65	0.00118 (0.0132)	0.0659 (0.182)	0.491 (0.674)	0.635 (0.779)	0.0213 (0.0857)	0.0392 (0.129)	0.0373 (0.125)	0.0421 (0.133)	5e-05 (0.00135)	0.247 (0.455)
del 9p21 3	27 (30%)	63	0.00658 (0.0427)	0.0035 (0.0287)	0.353 (0.537)	0.227 (0.436)	1e-05 (0.000418)	0.00036 (0.00637)	0.0175 (0.0761)	0.181 (0.377)	0.00952 (0.0501)	0.565 (0.724)
amp 1q22	17 (19%)	73	0.00817 (0.0464)	0.00038 (0.00647)	1 (1.00)	0.397 (0.587)	0.00252 (0.0219)	0.00014 (0.00307)	0.115 (0.277)	0.157 (0.346)	0.0137 (0.0635)	0.439 (0.632)
amp 5p15 33	65 (72%)	25	1e-05 (0.000418)	0.883 (0.953)	0.491 (0.674)	0.89 (0.959)	0.00958 (0.0501)	0.00075 (0.0101)	0.044 (0.137)	0.18 (0.377)	0.0156 (0.0698)	0.306 (0.505)
amp 9q31 3	34 (38%)	56	0.0005 (0.00782)	0.0204 (0.083)	0.0018 (0.0176)	0.14 (0.322)	0.0287 (0.103)	0.0182 (0.0784)	0.0548 (0.159)	0.2 (0.39)	0.252 (0.463)	0.13 (0.307)
amp 19p13 12	58 (64%)	32	0.00032 (0.00589)	0.034 (0.116)	0.189 (0.382)	0.00986 (0.0504)	0.00209 (0.0189)	0.00041 (0.00674)	0.328 (0.519)	0.478 (0.673)	0.582 (0.737)	0.171 (0.366)
amp xq28	46 (51%)	44	0.00051 (0.00782)	0.76 (0.862)	0.231 (0.44)	0.0436 (0.136)	0.00902 (0.049)	0.0119 (0.0585)	0.513 (0.691)	0.261 (0.465)	1 (1.00)	0.0292 (0.104)
del 17q21 31	26 (29%)	64	0.00418 (0.0326)	0.00902 (0.049)	0.353 (0.537)	0.544 (0.713)	0.0766 (0.207)	0.0472 (0.141)	0.0356 (0.12)	0.00482 (0.0346)	0.186 (0.38)	0.0621 (0.176)
del 20p12 1	12 (13%)	78	0.00464 (0.0339)	0.641 (0.78)	0.187 (0.38)	0.621 (0.769)	0.0413 (0.131)	0.0271 (0.0996)	0.00645 (0.0427)	0.516 (0.692)	0.00189 (0.0181)	1 (1.00)
amp 4p16 3	41 (46%)	49	0.00089 (0.0105)	0.548 (0.716)	1 (1.00)	0.191 (0.382)	0.0135 (0.0635)	0.00634 (0.0427)	0.486 (0.674)	0.0465 (0.141)	0.404 (0.589)	0.953 (1.00)
amp 4q35 1	29 (32%)	61	2e-05 (0.000613)	0.198 (0.39)	0.763 (0.862)	0.556 (0.718)	0.00066 (0.00949)	0.00098 (0.0113)	0.0553 (0.159)	0.00089 (0.0105)	0.066 (0.182)	0.294 (0.496)
amp 12q14 1	70 (78%)	20	1e-05 (0.000418)	0.281 (0.491)	0.284 (0.491)	0.0103 (0.0516)	0.0219 (0.087)	0.00209 (0.0189)	0.458 (0.653)	0.487 (0.674)	0.35 (0.537)	0.0889 (0.232)
amp 16p13 3	50 (56%)	40	1e-05 (0.000418)	0.262 (0.465)	0.767 (0.862)	0.0528 (0.154)	0.00021 (0.0042)	1e-05 (0.000418)	0.0762 (0.207)	0.00946 (0.0501)	0.053 (0.154)	0.583 (0.737)
amp 16q22 1	56 (62%)	34	1e-05 (0.000418)	0.371 (0.558)	1 (1.00)	0.803 (0.893)	0.0286 (0.103)	8e-05 (0.00204)	0.0659 (0.182)	0.0225 (0.0883)	0.155 (0.346)	0.861 (0.934)
amp 19q12	56 (62%)	34	0.00086 (0.0105)	0.0196 (0.082)	0.353 (0.537)	0.167 (0.358)	0.00176 (0.0176)	0.00126 (0.0135)	0.197 (0.39)	0.256 (0.464)	0.514 (0.691)	0.0602 (0.172)
del 4q35 1	30 (33%)	60	0.00549 (0.0383)	0.013 (0.0617)	0.749 (0.858)	0.392 (0.584)	0.0952 (0.241)	0.04 (0.129)	0.191 (0.382)	0.167 (0.358)	0.00075 (0.0101)	0.682 (0.812)
del 16q23 1	11 (12%)	79	0.00906 (0.049)	0.504 (0.684)	0.414 (0.597)	0.234 (0.443)	0.041 (0.131)	0.0111 (0.0549)	0.274 (0.483)	0.138 (0.319)	0.0103 (0.0516)	0.538 (0.711)
del 17q24 2	24 (27%)	66	0.00195 (0.0183)	0.0139 (0.064)	0.749 (0.858)	0.29 (0.491)	0.16 (0.347)	0.0409 (0.131)	0.156 (0.346)	0.0269 (0.0996)	0.0525 (0.154)	0.239 (0.445)
amp 7p22 1	54 (60%)	36	0.00221 (0.0195)	0.482 (0.673)	1 (1.00)	0.674 (0.805)	0.00792 (0.0461)	0.0327 (0.115)	0.57 (0.727)	0.492 (0.674)	0.804 (0.893)	0.132 (0.311)
amp xp11 22	49 (54%)	41	0.00012 (0.00276)	0.921 (0.978)	0.758 (0.862)	0.0168 (0.0743)	0.0331 (0.115)	0.0947 (0.241)	0.765 (0.862)	0.144 (0.328)	0.739 (0.856)	0.0876 (0.23)
del 1p36 23	38 (42%)	52	0.0214 (0.0857)	0.00445 (0.0339)	0.767 (0.862)	0.149 (0.335)	0.0726 (0.199)	0.00405 (0.0321)	0.836 (0.918)	0.559 (0.718)	0.401 (0.589)	0.825 (0.912)
del 4q34 3	28 (31%)	62	0.00164 (0.0168)	0.00461 (0.0339)	0.53 (0.705)	0.145 (0.329)	0.186 (0.38)	0.187 (0.38)	0.09 (0.232)	0.191 (0.382)	0.00011 (0.00266)	0.262 (0.465)
del 11p15 5	27 (30%)	63	0.0073 (0.0442)	0.0204 (0.083)	1 (1.00)	0.673 (0.805)	0.0875 (0.23)	0.0332 (0.115)	0.124 (0.295)	0.598 (0.744)	0.392 (0.584)	0.511 (0.691)
del 16p13 3	7 (8%)	83	0.0817 (0.218)	0.558 (0.718)	0.665 (0.804)	0.345 (0.536)	0.54 (0.712)	0.00896 (0.049)	0.0246 (0.0942)	0.598 (0.744)	0.0201 (0.083)	0.761 (0.862)
del 17q11 2	24 (27%)	66	0.0151 (0.0682)	0.00534 (0.0378)	0.337 (0.525)	0.632 (0.777)	0.103 (0.255)	0.105 (0.259)	0.259 (0.465)	0.0173 (0.0757)	0.112 (0.272)	0.394 (0.584)
amp 6q24 3	19 (21%)	71	0.0228 (0.089)	0.91 (0.975)	0.738 (0.856)	0.641 (0.78)	0.0468 (0.141)	0.935 (0.989)	0.672 (0.805)	0.232 (0.44)	0.63 (0.777)	1 (1.00)
del 1q43	18 (20%)	72	0.0145 (0.0662)	0.0445 (0.137)	0.414 (0.597)	0.16 (0.347)	0.588 (0.739)	0.138 (0.319)	0.527 (0.703)	0.552 (0.717)	0.193 (0.385)	0.181 (0.377)
del 2q22 1	18 (20%)	72	0.038 (0.126)	0.00366 (0.0295)	0.722 (0.854)	0.796 (0.893)	0.239 (0.445)	0.0894 (0.232)	0.315 (0.512)	0.666 (0.804)	0.406 (0.589)	0.491 (0.674)
del 2q37 3	21 (23%)	69	0.0068 (0.0428)	0.0265 (0.099)	0.491 (0.674)	0.832 (0.915)	0.299 (0.501)	0.0911 (0.233)	0.481 (0.673)	0.526 (0.703)	0.57 (0.727)	0.939 (0.991)
del 3q13 31	25 (28%)	65	0.295 (0.496)	0.0465 (0.141)	0.314 (0.512)	0.472 (0.668)	0.157 (0.346)	0.0396 (0.129)	0.449 (0.644)	0.2 (0.39)	0.85 (0.929)	0.371 (0.558)
del 11q14 1	25 (28%)	65	0.0195 (0.082)	0.007 (0.0431)	0.738 (0.856)	0.552 (0.717)	0.218 (0.424)	0.349 (0.537)	0.281 (0.491)	0.745 (0.858)	0.326 (0.516)	0.587 (0.739)
amp 6p21 31	19 (21%)	71	0.0649 (0.182)	0.8 (0.893)	1 (1.00)	0.799 (0.893)	0.0814 (0.218)	1 (1.00)	0.143 (0.328)	0.0263 (0.099)	0.406 (0.589)	0.303 (0.503)
amp 17q25 3	18 (20%)	72	0.0342 (0.116)	0.687 (0.817)	0.284 (0.491)	0.1 (0.25)	0.124 (0.295)	0.671 (0.805)	0.402 (0.589)	0.696 (0.825)	0.303 (0.503)	0.467 (0.663)
del 7q36 3	11 (12%)	79	0.038 (0.126)	0.256 (0.464)	0.109 (0.266)	0.663 (0.804)	0.176 (0.372)	0.335 (0.525)	0.896 (0.963)	0.736 (0.856)	0.0963 (0.242)	0.245 (0.452)
del 12q14 2	5 (6%)	85	0.0903 (0.232)	0.224 (0.432)	1 (1.00)		0.177 (0.374)	0.00088 (0.0105)	0.593 (0.742)	0.304 (0.503)	0.855 (0.932)	0.149 (0.335)
del 13q14 2	42 (47%)	48	0.00264 (0.0225)	0.0866 (0.23)	0.236 (0.445)	0.838 (0.918)	0.332 (0.523)	0.555 (0.718)	1 (1.00)	0.533 (0.707)	0.404 (0.589)	0.827 (0.912)
del 14q21 2	20 (22%)	70	0.0192 (0.0819)	0.925 (0.981)	1 (1.00)	0.576 (0.732)	0.307 (0.505)	0.288 (0.491)	0.368 (0.557)	0.736 (0.856)	0.274 (0.483)	0.158 (0.347)
del 18q21 2	36 (40%)	54	0.0315 (0.111)	0.321 (0.513)	1 (1.00)	0.326 (0.516)	0.826 (0.912)	1 (1.00)	0.496 (0.678)	0.915 (0.978)	0.288 (0.491)	0.353 (0.537)
del 22q12 1	50 (56%)	40	0.00449 (0.0339)	0.138 (0.319)	0.542 (0.712)	0.289 (0.491)	0.748 (0.858)	0.185 (0.38)	0.637 (0.78)	0.88 (0.953)	0.918 (0.978)	0.2 (0.39)
del 6p24 3	20 (22%)	70	0.111 (0.27)	0.919 (0.978)	0.284 (0.491)	0.318 (0.512)	0.622 (0.769)	0.48 (0.673)	1 (1.00)	0.1 (0.25)	1 (1.00)	0.457 (0.653)
del 6q26	21 (23%)	69	0.119 (0.285)	0.86 (0.934)	0.738 (0.856)	0.318 (0.512)	0.319 (0.512)	0.309 (0.505)	0.504 (0.684)	0.348 (0.537)	0.223 (0.431)	0.593 (0.742)
del 10q23 1	11 (12%)	79	0.255 (0.464)	0.258 (0.465)	1 (1.00)	0.241 (0.447)	0.238 (0.445)	0.748 (0.858)	1 (1.00)	0.97 (1.00)	1 (1.00)	0.288 (0.491)

'amp_1q22' versus 'CN_CNMF'

P value = 0.00817 (Fisher's exact test), Q value = 0.046

Table S1. Gene #1: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 1(1Q22) MUTATED	13	2	2	0
AMP PEAK 1(1Q22) WILD-TYPE	23	24	14	12

Figure S1. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0065

Table S2. Gene #1: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
AMP PEAK 1(1Q22) MUTATED	9	2	0	4	0
AMP PEAK 1(1Q22) WILD-TYPE	9	9	20	14	11

Figure S2. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 0.00252 (Fisher's exact test), Q value = 0.022

Table S3. Gene #1: 'amp_1q22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 1(1Q22) MUTATED	11	1	1	2
AMP PEAK 1(1Q22) WILD-TYPE	13	12	16	21

Figure S3. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0031

Table S4. Gene #1: 'amp_1q22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 1(1Q22) MUTATED	11	1	2	1
AMP PEAK 1(1Q22) WILD-TYPE	12	22	5	23

Figure S4. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.064

Table S5. Gene #1: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
AMP PEAK 1(1Q22) MUTATED	4	9	2
AMP PEAK 1(1Q22) WILD-TYPE	24	13	25

Figure S5. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_4p16.3' versus 'CN_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.01

Table S6. Gene #2: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 2(4P16.3) MUTATED	8	13	11	9
AMP PEAK 2(4P16.3) WILD-TYPE	28	13	5	3

Figure S6. Get High-res Image Gene #2: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.064

Table S7. Gene #2: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 2(4P16.3) MUTATED	5	7	12	10
AMP PEAK 2(4P16.3) WILD-TYPE	19	6	5	13

Figure S7. Get High-res Image Gene #2: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00634 (Fisher's exact test), Q value = 0.043

Table S8. Gene #2: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 2(4P16.3) MUTATED	5	15	1	13
AMP PEAK 2(4P16.3) WILD-TYPE	18	8	6	11

Figure S8. Get High-res Image Gene #2: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.14

Table S9. Gene #2: 'amp_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
AMP PEAK 2(4P16.3) MUTATED	11	10	6	5	3
AMP PEAK 2(4P16.3) WILD-TYPE	5	17	5	15	1

Figure S9. Get High-res Image Gene #2: 'amp_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_4q35.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00061

Table S10. Gene #3: 'amp_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 3(4Q35.1) MUTATED	2	10	7	10
AMP PEAK 3(4Q35.1) WILD-TYPE	34	16	9	2

Figure S10. Get High-res Image Gene #3: 'amp_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q35.1' versus 'MRNASEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0095

Table S11. Gene #3: 'amp_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 3(4Q35.1) MUTATED	1	4	9	11
AMP PEAK 3(4Q35.1) WILD-TYPE	23	9	8	12

Figure S11. Get High-res Image Gene #3: 'amp_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.011

Table S12. Gene #3: 'amp_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 3(4Q35.1) MUTATED	2	10	0	13
AMP PEAK 3(4Q35.1) WILD-TYPE	21	13	7	11

Figure S12. Get High-res Image Gene #3: 'amp_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.01

Table S13. Gene #3: 'amp_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
AMP PEAK 3(4Q35.1) MUTATED	7	10	6	0	2
AMP PEAK 3(4Q35.1) WILD-TYPE	9	17	5	20	2

Figure S13. Get High-res Image Gene #3: 'amp_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S14. Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 4(5P15.33) MUTATED	14	25	15	11
AMP PEAK 4(5P15.33) WILD-TYPE	22	1	1	1

Figure S14. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00958 (Fisher's exact test), Q value = 0.05

Table S15. Gene #4: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 4(5P15.33) MUTATED	12	10	16	19
AMP PEAK 4(5P15.33) WILD-TYPE	12	3	1	4

Figure S15. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.01

Table S16. Gene #4: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 4(5P15.33) MUTATED	13	20	2	22
AMP PEAK 4(5P15.33) WILD-TYPE	10	3	5	2

Figure S16. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.14

Table S17. Gene #4: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	16	26
AMP PEAK 4(5P15.33) MUTATED	28	8	22
AMP PEAK 4(5P15.33) WILD-TYPE	8	8	4

Figure S17. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.07

Table S18. Gene #4: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
AMP PEAK 4(5P15.33) MUTATED	23	11	23
AMP PEAK 4(5P15.33) WILD-TYPE	5	11	4

Figure S18. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S19. Gene #5: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 5(5Q35.3) MUTATED	12	26	15	10
AMP PEAK 5(5Q35.3) WILD-TYPE	24	0	1	2

Figure S19. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.013

Table S20. Gene #5: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
AMP PEAK 5(5Q35.3) MUTATED	7	7	19	13	10
AMP PEAK 5(5Q35.3) WILD-TYPE	11	4	1	5	1

Figure S20. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00663 (Fisher's exact test), Q value = 0.043

Table S21. Gene #5: 'amp_5q35.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
AMP PEAK 5(5Q35.3) MUTATED	4	7	7	1	2	4	6	3
AMP PEAK 5(5Q35.3) WILD-TYPE	4	0	0	2	2	0	0	3

Figure S21. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S22. Gene #5: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 5(5Q35.3) MUTATED	7	12	16	20
AMP PEAK 5(5Q35.3) WILD-TYPE	17	1	1	3

Figure S22. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S23. Gene #5: 'amp_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 5(5Q35.3) MUTATED	8	22	2	23
AMP PEAK 5(5Q35.3) WILD-TYPE	15	1	5	1

Figure S23. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_CNMF'

P value = 0.00702 (Fisher's exact test), Q value = 0.043

Table S24. Gene #5: 'amp_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	16	26
AMP PEAK 5(5Q35.3) MUTATED	24	8	24
AMP PEAK 5(5Q35.3) WILD-TYPE	12	8	2

Figure S24. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0467 (Fisher's exact test), Q value = 0.14

Table S25. Gene #5: 'amp_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
AMP PEAK 5(5Q35.3) MUTATED	14	21	9	9	3
AMP PEAK 5(5Q35.3) WILD-TYPE	2	6	2	11	1

Figure S25. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.061

Table S26. Gene #5: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
AMP PEAK 5(5Q35.3) MUTATED	20	11	24
AMP PEAK 5(5Q35.3) WILD-TYPE	8	11	3

Figure S26. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0263 (Fisher's exact test), Q value = 0.099

Table S27. Gene #6: 'amp_6p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
AMP PEAK 6(6P21.31) MUTATED	5	2	5	2	0
AMP PEAK 6(6P21.31) WILD-TYPE	11	25	6	18	4

Figure S27. Get High-res Image Gene #6: 'amp_6p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q24.3' versus 'CN_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.089

Table S28. Gene #7: 'amp_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 7(6Q24.3) MUTATED	9	1	4	5
AMP PEAK 7(6Q24.3) WILD-TYPE	27	25	12	7

Figure S28. Get High-res Image Gene #7: 'amp_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0468 (Fisher's exact test), Q value = 0.14

Table S29. Gene #7: 'amp_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 7(6Q24.3) MUTATED	5	0	7	4
AMP PEAK 7(6Q24.3) WILD-TYPE	19	13	10	19

Figure S29. Get High-res Image Gene #7: 'amp_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'CN_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.02

Table S30. Gene #8: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 8(7P22.1) MUTATED	13	20	13	8
AMP PEAK 8(7P22.1) WILD-TYPE	23	6	3	4

Figure S30. Get High-res Image Gene #8: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.00792 (Fisher's exact test), Q value = 0.046

Table S31. Gene #8: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 8(7P22.1) MUTATED	10	12	13	12
AMP PEAK 8(7P22.1) WILD-TYPE	14	1	4	11

Figure S31. Get High-res Image Gene #8: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.11

Table S32. Gene #8: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 8(7P22.1) MUTATED	12	19	2	14
AMP PEAK 8(7P22.1) WILD-TYPE	11	4	5	10

Figure S32. Get High-res Image Gene #8: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9q31.3' versus 'CN_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0078

Table S33. Gene #9: 'amp_9q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 9(9Q31.3) MUTATED	11	5	13	5
AMP PEAK 9(9Q31.3) WILD-TYPE	25	21	3	7

Figure S33. Get High-res Image Gene #9: 'amp_9q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q31.3' versus 'METHLYATION_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.083

Table S34. Gene #9: 'amp_9q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
AMP PEAK 9(9Q31.3) MUTATED	9	5	9	2	1
AMP PEAK 9(9Q31.3) WILD-TYPE	9	6	11	16	10

Figure S34. Get High-res Image Gene #9: 'amp_9q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q31.3' versus 'RPPA_CNMF'

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

Table S35. Gene #9: 'amp_9q31.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	23	22
AMP PEAK 9(9Q31.3) MUTATED	3	13
AMP PEAK 9(9Q31.3) WILD-TYPE	20	9

Figure S35. Get High-res Image Gene #9: 'amp_9q31.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_9q31.3' versus 'MRNASEQ_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 0.1

Table S36. Gene #9: 'amp_9q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 9(9Q31.3) MUTATED	8	8	6	3
AMP PEAK 9(9Q31.3) WILD-TYPE	16	5	11	20

Figure S36. Get High-res Image Gene #9: 'amp_9q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.078

Table S37. Gene #9: 'amp_9q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 9(9Q31.3) MUTATED	9	12	1	3
AMP PEAK 9(9Q31.3) WILD-TYPE	14	11	6	21

Figure S37. Get High-res Image Gene #9: 'amp_9q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S38. Gene #10: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 10(12Q14.1) MUTATED	19	26	16	9
AMP PEAK 10(12Q14.1) WILD-TYPE	17	0	0	3

Figure S38. Get High-res Image Gene #10: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q14.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.052

Table S39. Gene #10: 'amp_12q14.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
AMP PEAK 10(12Q14.1) MUTATED	7	6	7	3	3	4	5	1
AMP PEAK 10(12Q14.1) WILD-TYPE	1	1	0	0	1	0	1	5

Figure S39. Get High-res Image Gene #10: 'amp_12q14.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.087

Table S40. Gene #10: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 10(12Q14.1) MUTATED	14	13	14	19
AMP PEAK 10(12Q14.1) WILD-TYPE	10	0	3	4

Figure S40. Get High-res Image Gene #10: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00209 (Fisher's exact test), Q value = 0.019

Table S41. Gene #10: 'amp_12q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 10(12Q14.1) MUTATED	14	20	3	23
AMP PEAK 10(12Q14.1) WILD-TYPE	9	3	4	1

Figure S41. Get High-res Image Gene #10: 'amp_12q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q11.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00086

Table S42. Gene #11: 'amp_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 11(14Q11.2) MUTATED	7	5	13	2
AMP PEAK 11(14Q11.2) WILD-TYPE	29	21	3	10

Figure S42. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q11.2' versus 'METHLYATION_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.06

Table S43. Gene #11: 'amp_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
AMP PEAK 11(14Q11.2) MUTATED	6	4	11	1	2
AMP PEAK 11(14Q11.2) WILD-TYPE	12	7	9	17	9

Figure S43. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_14q11.2' versus 'RPPA_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.089

Table S44. Gene #11: 'amp_14q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	23	22
AMP PEAK 11(14Q11.2) MUTATED	3	10
AMP PEAK 11(14Q11.2) WILD-TYPE	20	12

Figure S44. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_14q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.1

Table S45. Gene #11: 'amp_14q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
AMP PEAK 11(14Q11.2) MUTATED	3	5	0	2	0	0	1	2
AMP PEAK 11(14Q11.2) WILD-TYPE	5	2	7	1	4	4	5	4

Figure S45. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_14q11.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00061

Table S46. Gene #11: 'amp_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 11(14Q11.2) MUTATED	4	7	11	1
AMP PEAK 11(14Q11.2) WILD-TYPE	20	6	6	22

Figure S46. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00061

Table S47. Gene #11: 'amp_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 11(14Q11.2) MUTATED	5	16	0	2
AMP PEAK 11(14Q11.2) WILD-TYPE	18	7	7	22

Figure S47. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0044

Table S48. Gene #11: 'amp_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	16	26
AMP PEAK 11(14Q11.2) MUTATED	19	3	2
AMP PEAK 11(14Q11.2) WILD-TYPE	17	13	24

Figure S48. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_14q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00669 (Fisher's exact test), Q value = 0.043

Table S49. Gene #11: 'amp_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
AMP PEAK 11(14Q11.2) MUTATED	9	3	3	6	3
AMP PEAK 11(14Q11.2) WILD-TYPE	7	24	8	14	1

Figure S49. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_14q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0088

Table S50. Gene #11: 'amp_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
AMP PEAK 11(14Q11.2) MUTATED	15	6	2
AMP PEAK 11(14Q11.2) WILD-TYPE	13	16	25

Figure S50. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_14q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.01

Table S51. Gene #11: 'amp_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	24	14
AMP PEAK 11(14Q11.2) MUTATED	19	3	1
AMP PEAK 11(14Q11.2) WILD-TYPE	20	21	13

Figure S51. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S52. Gene #12: 'amp_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 12(16P13.3) MUTATED	6	26	11	7
AMP PEAK 12(16P13.3) WILD-TYPE	30	0	5	5

Figure S52. Get High-res Image Gene #12: 'amp_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0042

Table S53. Gene #12: 'amp_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 12(16P13.3) MUTATED	5	9	14	16
AMP PEAK 12(16P13.3) WILD-TYPE	19	4	3	7

Figure S53. Get High-res Image Gene #12: 'amp_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S54. Gene #12: 'amp_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 12(16P13.3) MUTATED	6	19	0	19
AMP PEAK 12(16P13.3) WILD-TYPE	17	4	7	5

Figure S54. Get High-res Image Gene #12: 'amp_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00946 (Fisher's exact test), Q value = 0.05

Table S55. Gene #12: 'amp_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
AMP PEAK 12(16P13.3) MUTATED	14	16	7	6	2
AMP PEAK 12(16P13.3) WILD-TYPE	2	11	4	14	2

Figure S55. Get High-res Image Gene #12: 'amp_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S56. Gene #13: 'amp_16q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 13(16Q22.1) MUTATED	10	26	14	6
AMP PEAK 13(16Q22.1) WILD-TYPE	26	0	2	6

Figure S56. Get High-res Image Gene #13: 'amp_16q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.1

Table S57. Gene #13: 'amp_16q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 13(16Q22.1) MUTATED	9	10	13	16
AMP PEAK 13(16Q22.1) WILD-TYPE	15	3	4	7

Figure S57. Get High-res Image Gene #13: 'amp_16q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.002

Table S58. Gene #13: 'amp_16q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 13(16Q22.1) MUTATED	9	20	1	18
AMP PEAK 13(16Q22.1) WILD-TYPE	14	3	6	6

Figure S58. Get High-res Image Gene #13: 'amp_16q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.088

Table S59. Gene #13: 'amp_16q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
AMP PEAK 13(16Q22.1) MUTATED	15	17	6	9	2
AMP PEAK 13(16Q22.1) WILD-TYPE	1	10	5	11	2

Figure S59. Get High-res Image Gene #13: 'amp_16q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16q24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S60. Gene #14: 'amp_16q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 14(16Q24.2) MUTATED	6	26	11	6
AMP PEAK 14(16Q24.2) WILD-TYPE	30	0	5	6

Figure S60. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q24.2' versus 'METHLYATION_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.099

Table S61. Gene #14: 'amp_16q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
AMP PEAK 14(16Q24.2) MUTATED	5	6	16	11	6
AMP PEAK 14(16Q24.2) WILD-TYPE	13	5	4	7	5

Figure S61. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_16q24.2' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0042

Table S62. Gene #14: 'amp_16q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 14(16Q24.2) MUTATED	5	10	13	16
AMP PEAK 14(16Q24.2) WILD-TYPE	19	3	4	7

Figure S62. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00061

Table S63. Gene #14: 'amp_16q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 14(16Q24.2) MUTATED	5	20	1	18
AMP PEAK 14(16Q24.2) WILD-TYPE	18	3	6	6

Figure S63. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16q24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00273 (Fisher's exact test), Q value = 0.023

Table S64. Gene #14: 'amp_16q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
AMP PEAK 14(16Q24.2) MUTATED	14	17	6	5	2
AMP PEAK 14(16Q24.2) WILD-TYPE	2	10	5	15	2

Figure S64. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16q24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00564 (Fisher's exact test), Q value = 0.039

Table S65. Gene #14: 'amp_16q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
AMP PEAK 14(16Q24.2) MUTATED	18	6	19
AMP PEAK 14(16Q24.2) WILD-TYPE	10	16	8

Figure S65. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.12

Table S66. Gene #15: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 15(17Q25.3) MUTATED	12	2	1	3
AMP PEAK 15(17Q25.3) WILD-TYPE	24	24	15	9

Figure S66. Get High-res Image Gene #15: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.12' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0059

Table S67. Gene #16: 'amp_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 16(19P13.12) MUTATED	16	17	16	9
AMP PEAK 16(19P13.12) WILD-TYPE	20	9	0	3

Figure S67. Get High-res Image Gene #16: 'amp_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.12

Table S68. Gene #16: 'amp_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
AMP PEAK 16(19P13.12) MUTATED	14	8	16	7	5
AMP PEAK 16(19P13.12) WILD-TYPE	4	3	4	11	6

Figure S68. Get High-res Image Gene #16: 'amp_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00986 (Fisher's exact test), Q value = 0.05

Table S69. Gene #16: 'amp_19p13.12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
AMP PEAK 16(19P13.12) MUTATED	8	7	4	3	1	3	4	2
AMP PEAK 16(19P13.12) WILD-TYPE	0	0	3	0	3	1	2	4

Figure S69. Get High-res Image Gene #16: 'amp_19p13.12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.019

Table S70. Gene #16: 'amp_19p13.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 16(19P13.12) MUTATED	12	13	13	11
AMP PEAK 16(19P13.12) WILD-TYPE	12	0	4	12

Figure S70. Get High-res Image Gene #16: 'amp_19p13.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0067

Table S71. Gene #16: 'amp_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 16(19P13.12) MUTATED	15	21	1	12
AMP PEAK 16(19P13.12) WILD-TYPE	8	2	6	12

Figure S71. Get High-res Image Gene #16: 'amp_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.01

Table S72. Gene #17: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 17(19Q12) MUTATED	17	15	16	8
AMP PEAK 17(19Q12) WILD-TYPE	19	11	0	4

Figure S72. Get High-res Image Gene #17: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.082

Table S73. Gene #17: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
AMP PEAK 17(19Q12) MUTATED	14	7	16	7	4
AMP PEAK 17(19Q12) WILD-TYPE	4	4	4	11	7

Figure S73. Get High-res Image Gene #17: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.018

Table S74. Gene #17: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 17(19Q12) MUTATED	12	13	12	10
AMP PEAK 17(19Q12) WILD-TYPE	12	0	5	13

Figure S74. Get High-res Image Gene #17: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.013

Table S75. Gene #17: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 17(19Q12) MUTATED	15	20	1	11
AMP PEAK 17(19Q12) WILD-TYPE	8	3	6	13

Figure S75. Get High-res Image Gene #17: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0028

Table S76. Gene #18: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 18(XP11.22) MUTATED	11	22	11	5
AMP PEAK 18(XP11.22) WILD-TYPE	25	4	5	7

Figure S76. Get High-res Image Gene #18: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp11.22' versus 'RPPA_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.074

Table S77. Gene #18: 'amp_xp11.22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
AMP PEAK 18(XP11.22) MUTATED	7	6	5	1	3	3	4	0
AMP PEAK 18(XP11.22) WILD-TYPE	1	1	2	2	1	1	2	6

Figure S77. Get High-res Image Gene #18: 'amp_xp11.22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.11

Table S78. Gene #18: 'amp_xp11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 18(XP11.22) MUTATED	8	10	12	12
AMP PEAK 18(XP11.22) WILD-TYPE	16	3	5	11

Figure S78. Get High-res Image Gene #18: 'amp_xp11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0078

Table S79. Gene #19: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
AMP PEAK 19(XQ28) MUTATED	10	21	9	6
AMP PEAK 19(XQ28) WILD-TYPE	26	5	7	6

Figure S79. Get High-res Image Gene #19: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'RPPA_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.14

Table S80. Gene #19: 'amp_xq28' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
AMP PEAK 19(XQ28) MUTATED	6	5	6	1	2	3	4	0
AMP PEAK 19(XQ28) WILD-TYPE	2	2	1	2	2	1	2	6

Figure S80. Get High-res Image Gene #19: 'amp_xq28' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 0.00902 (Fisher's exact test), Q value = 0.049

Table S81. Gene #19: 'amp_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
AMP PEAK 19(XQ28) MUTATED	6	10	11	13
AMP PEAK 19(XQ28) WILD-TYPE	18	3	6	10

Figure S81. Get High-res Image Gene #19: 'amp_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.058

Table S82. Gene #19: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
AMP PEAK 19(XQ28) MUTATED	8	14	1	17
AMP PEAK 19(XQ28) WILD-TYPE	15	9	6	7

Figure S82. Get High-res Image Gene #19: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.1

Table S83. Gene #19: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	24	14
AMP PEAK 19(XQ28) MUTATED	18	17	4
AMP PEAK 19(XQ28) WILD-TYPE	21	7	10

Figure S83. Get High-res Image Gene #19: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.23' versus 'CN_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.086

Table S84. Gene #20: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 1(1P36.23) MUTATED	17	5	8	8
DEL PEAK 1(1P36.23) WILD-TYPE	19	21	8	4

Figure S84. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.23' versus 'METHLYATION_CNMF'

P value = 0.00445 (Fisher's exact test), Q value = 0.034

Table S85. Gene #20: 'del_1p36.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 1(1P36.23) MUTATED	13	5	10	2	4
DEL PEAK 1(1P36.23) WILD-TYPE	5	6	10	16	7

Figure S85. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00405 (Fisher's exact test), Q value = 0.032

Table S86. Gene #20: 'del_1p36.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 1(1P36.23) MUTATED	16	9	0	8
DEL PEAK 1(1P36.23) WILD-TYPE	7	14	7	16

Figure S86. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1q43' versus 'CN_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.066

Table S87. Gene #21: 'del_1q43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 2(1Q43) MUTATED	4	3	5	6
DEL PEAK 2(1Q43) WILD-TYPE	32	23	11	6

Figure S87. Get High-res Image Gene #21: 'del_1q43' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q43' versus 'METHLYATION_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.14

Table S88. Gene #21: 'del_1q43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 2(1Q43) MUTATED	2	0	8	2	3
DEL PEAK 2(1Q43) WILD-TYPE	16	11	12	16	8

Figure S88. Get High-res Image Gene #21: 'del_1q43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.13

Table S89. Gene #22: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 3(2Q22.1) MUTATED	5	3	4	6
DEL PEAK 3(2Q22.1) WILD-TYPE	31	23	12	6

Figure S89. Get High-res Image Gene #22: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.00366 (Fisher's exact test), Q value = 0.03

Table S90. Gene #22: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 3(2Q22.1) MUTATED	1	0	8	2	5
DEL PEAK 3(2Q22.1) WILD-TYPE	17	11	12	16	6

Figure S90. Get High-res Image Gene #22: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 0.0068 (Fisher's exact test), Q value = 0.043

Table S91. Gene #23: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 4(2Q37.3) MUTATED	5	3	7	6
DEL PEAK 4(2Q37.3) WILD-TYPE	31	23	9	6

Figure S91. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.099

Table S92. Gene #23: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 4(2Q37.3) MUTATED	4	0	8	2	5
DEL PEAK 4(2Q37.3) WILD-TYPE	14	11	12	16	6

Figure S92. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.14

Table S93. Gene #24: 'del_3q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 5(3Q13.31) MUTATED	6	1	10	3	1
DEL PEAK 5(3Q13.31) WILD-TYPE	12	10	10	15	10

Figure S93. Get High-res Image Gene #24: 'del_3q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 0.13

Table S94. Gene #24: 'del_3q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 5(3Q13.31) MUTATED	7	10	2	2
DEL PEAK 5(3Q13.31) WILD-TYPE	16	13	5	22

Figure S94. Get High-res Image Gene #24: 'del_3q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.013

Table S95. Gene #25: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 6(4Q34.3) MUTATED	17	3	5	0
DEL PEAK 6(4Q34.3) WILD-TYPE	19	23	11	12

Figure S95. Get High-res Image Gene #25: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.086

Table S96. Gene #25: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
DEL PEAK 6(4Q34.3) MUTATED	11	2	3	2
DEL PEAK 6(4Q34.3) WILD-TYPE	13	11	14	21

Figure S96. Get High-res Image Gene #25: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0392 (Fisher's exact test), Q value = 0.13

Table S97. Gene #25: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 6(4Q34.3) MUTATED	10	5	1	2
DEL PEAK 6(4Q34.3) WILD-TYPE	13	18	6	22

Figure S97. Get High-res Image Gene #25: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.13

Table S98. Gene #25: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	16	26
DEL PEAK 6(4Q34.3) MUTATED	11	6	2
DEL PEAK 6(4Q34.3) WILD-TYPE	25	10	24

Figure S98. Get High-res Image Gene #25: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0421 (Fisher's exact test), Q value = 0.13

Table S99. Gene #25: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
DEL PEAK 6(4Q34.3) MUTATED	2	7	0	9	1
DEL PEAK 6(4Q34.3) WILD-TYPE	14	20	11	11	3

Figure S99. Get High-res Image Gene #25: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0014

Table S100. Gene #25: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
DEL PEAK 6(4Q34.3) MUTATED	4	13	2
DEL PEAK 6(4Q34.3) WILD-TYPE	24	9	25

Figure S100. Get High-res Image Gene #25: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.017

Table S101. Gene #26: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 7(4Q34.3) MUTATED	15	2	9	2
DEL PEAK 7(4Q34.3) WILD-TYPE	21	24	7	10

Figure S101. Get High-res Image Gene #26: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.00461 (Fisher's exact test), Q value = 0.034

Table S102. Gene #26: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 7(4Q34.3) MUTATED	11	0	7	3	3
DEL PEAK 7(4Q34.3) WILD-TYPE	7	11	13	15	8

Figure S102. Get High-res Image Gene #26: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0027

Table S103. Gene #26: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
DEL PEAK 7(4Q34.3) MUTATED	5	15	4
DEL PEAK 7(4Q34.3) WILD-TYPE	23	7	23

Figure S103. Get High-res Image Gene #26: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'CN_CNMF'

P value = 0.00549 (Fisher's exact test), Q value = 0.038

Table S104. Gene #27: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 8(4Q35.1) MUTATED	17	4	8	1
DEL PEAK 8(4Q35.1) WILD-TYPE	19	22	8	11

Figure S104. Get High-res Image Gene #27: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.062

Table S105. Gene #27: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 8(4Q35.1) MUTATED	11	1	8	3	2
DEL PEAK 8(4Q35.1) WILD-TYPE	7	10	12	15	9

Figure S105. Get High-res Image Gene #27: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.13

Table S106. Gene #27: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 8(4Q35.1) MUTATED	10	10	1	3
DEL PEAK 8(4Q35.1) WILD-TYPE	13	13	6	21

Figure S106. Get High-res Image Gene #27: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.01

Table S107. Gene #27: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
DEL PEAK 8(4Q35.1) MUTATED	5	14	5
DEL PEAK 8(4Q35.1) WILD-TYPE	23	8	22

Figure S107. Get High-res Image Gene #27: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_7q36.3' versus 'CN_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.13

Table S108. Gene #30: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 11(7Q36.3) MUTATED	8	0	2	1
DEL PEAK 11(7Q36.3) WILD-TYPE	28	26	14	11

Figure S108. Get High-res Image Gene #30: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 0.00971 (Fisher's exact test), Q value = 0.05

Table S109. Gene #31: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 12(9P23) MUTATED	16	2	4	2
DEL PEAK 12(9P23) WILD-TYPE	20	24	12	10

Figure S109. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 0.00806 (Fisher's exact test), Q value = 0.046

Table S110. Gene #31: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 12(9P23) MUTATED	11	2	2	4	2
DEL PEAK 12(9P23) WILD-TYPE	7	9	18	14	9

Figure S110. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.0493 (Fisher's exact test), Q value = 0.15

Table S111. Gene #31: 'del_9p23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	8	7	7	3	4	4	6	6
DEL PEAK 12(9P23) MUTATED	3	1	0	2	3	0	3	1
DEL PEAK 12(9P23) WILD-TYPE	5	6	7	1	1	4	3	5

Figure S111. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S112. Gene #31: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
DEL PEAK 12(9P23) MUTATED	15	1	4	1
DEL PEAK 12(9P23) WILD-TYPE	9	12	13	22

Figure S112. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00153 (Fisher's exact test), Q value = 0.016

Table S113. Gene #31: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 12(9P23) MUTATED	13	4	2	2
DEL PEAK 12(9P23) WILD-TYPE	10	19	5	22

Figure S113. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.00761 (Fisher's exact test), Q value = 0.045

Table S114. Gene #31: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	16	26
DEL PEAK 12(9P23) MUTATED	11	8	2
DEL PEAK 12(9P23) WILD-TYPE	25	8	24

Figure S114. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00779 (Fisher's exact test), Q value = 0.046

Table S115. Gene #31: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
DEL PEAK 12(9P23) MUTATED	6	11	3
DEL PEAK 12(9P23) WILD-TYPE	22	11	24

Figure S115. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.00658 (Fisher's exact test), Q value = 0.043

Table S116. Gene #32: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 13(9P21.3) MUTATED	18	3	4	2
DEL PEAK 13(9P21.3) WILD-TYPE	18	23	12	10

Figure S116. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.0035 (Fisher's exact test), Q value = 0.029

Table S117. Gene #32: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 13(9P21.3) MUTATED	12	3	2	5	2
DEL PEAK 13(9P21.3) WILD-TYPE	6	8	18	13	9

Figure S117. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S118. Gene #32: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
DEL PEAK 13(9P21.3) MUTATED	17	1	4	2
DEL PEAK 13(9P21.3) WILD-TYPE	7	12	13	21

Figure S118. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0064

Table S119. Gene #32: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 13(9P21.3) MUTATED	15	4	2	3
DEL PEAK 13(9P21.3) WILD-TYPE	8	19	5	21

Figure S119. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.076

Table S120. Gene #32: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	16	26
DEL PEAK 13(9P21.3) MUTATED	13	8	3
DEL PEAK 13(9P21.3) WILD-TYPE	23	8	23

Figure S120. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00952 (Fisher's exact test), Q value = 0.05

Table S121. Gene #32: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
DEL PEAK 13(9P21.3) MUTATED	7	12	4
DEL PEAK 13(9P21.3) WILD-TYPE	21	10	23

Figure S121. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'CN_CNMF'

P value = 0.0073 (Fisher's exact test), Q value = 0.044

Table S122. Gene #34: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 15(11P15.5) MUTATED	7	5	7	8
DEL PEAK 15(11P15.5) WILD-TYPE	29	21	9	4

Figure S122. Get High-res Image Gene #34: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.083

Table S123. Gene #34: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 15(11P15.5) MUTATED	4	3	12	2	4
DEL PEAK 15(11P15.5) WILD-TYPE	14	8	8	16	7

Figure S123. Get High-res Image Gene #34: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 0.11

Table S124. Gene #34: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 15(11P15.5) MUTATED	4	11	0	9
DEL PEAK 15(11P15.5) WILD-TYPE	19	12	7	15

Figure S124. Get High-res Image Gene #34: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q14.1' versus 'CN_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.082

Table S125. Gene #35: 'del_11q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 16(11Q14.1) MUTATED	9	3	6	7
DEL PEAK 16(11Q14.1) WILD-TYPE	27	23	10	5

Figure S125. Get High-res Image Gene #35: 'del_11q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q14.1' versus 'METHLYATION_CNMF'

P value = 0.007 (Fisher's exact test), Q value = 0.043

Table S126. Gene #35: 'del_11q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 16(11Q14.1) MUTATED	2	1	11	3	5
DEL PEAK 16(11Q14.1) WILD-TYPE	16	10	9	15	6

Figure S126. Get High-res Image Gene #35: 'del_11q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.01

Table S127. Gene #36: 'del_12q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 17(12Q14.2) MUTATED	2	0	3	0
DEL PEAK 17(12Q14.2) WILD-TYPE	21	23	4	24

Figure S127. Get High-res Image Gene #36: 'del_12q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 0.00264 (Fisher's exact test), Q value = 0.022

Table S128. Gene #37: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 18(13Q14.2) MUTATED	21	5	7	9
DEL PEAK 18(13Q14.2) WILD-TYPE	15	21	9	3

Figure S128. Get High-res Image Gene #37: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q21.2' versus 'CN_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.082

Table S129. Gene #38: 'del_14q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 19(14Q21.2) MUTATED	7	3	3	7
DEL PEAK 19(14Q21.2) WILD-TYPE	29	23	13	5

Figure S129. Get High-res Image Gene #38: 'del_14q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00896 (Fisher's exact test), Q value = 0.049

Table S130. Gene #39: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 20(16P13.3) MUTATED	2	2	3	0
DEL PEAK 20(16P13.3) WILD-TYPE	21	21	4	24

Figure S130. Get High-res Image Gene #39: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.094

Table S131. Gene #39: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	16	26
DEL PEAK 20(16P13.3) MUTATED	3	4	0
DEL PEAK 20(16P13.3) WILD-TYPE	33	12	26

Figure S131. Get High-res Image Gene #39: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.083

Table S132. Gene #39: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
DEL PEAK 20(16P13.3) MUTATED	2	5	0
DEL PEAK 20(16P13.3) WILD-TYPE	26	17	27

Figure S132. Get High-res Image Gene #39: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00906 (Fisher's exact test), Q value = 0.049

Table S133. Gene #40: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 21(16Q23.1) MUTATED	9	0	2	0
DEL PEAK 21(16Q23.1) WILD-TYPE	27	26	14	12

Figure S133. Get High-res Image Gene #40: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.13

Table S134. Gene #40: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
DEL PEAK 21(16Q23.1) MUTATED	6	1	0	1
DEL PEAK 21(16Q23.1) WILD-TYPE	18	12	17	22

Figure S134. Get High-res Image Gene #40: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.055

Table S135. Gene #40: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 21(16Q23.1) MUTATED	5	1	2	0
DEL PEAK 21(16Q23.1) WILD-TYPE	18	22	5	24

Figure S135. Get High-res Image Gene #40: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.052

Table S136. Gene #40: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
DEL PEAK 21(16Q23.1) MUTATED	1	6	1
DEL PEAK 21(16Q23.1) WILD-TYPE	27	16	26

Figure S136. Get High-res Image Gene #40: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17q11.2' versus 'CN_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.068

Table S137. Gene #41: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 22(17Q11.2) MUTATED	12	3	8	1
DEL PEAK 22(17Q11.2) WILD-TYPE	24	23	8	11

Figure S137. Get High-res Image Gene #41: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00534 (Fisher's exact test), Q value = 0.038

Table S138. Gene #41: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 22(17Q11.2) MUTATED	7	0	11	4	1
DEL PEAK 22(17Q11.2) WILD-TYPE	11	11	9	14	10

Figure S138. Get High-res Image Gene #41: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.076

Table S139. Gene #41: 'del_17q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
DEL PEAK 22(17Q11.2) MUTATED	4	7	0	11	1
DEL PEAK 22(17Q11.2) WILD-TYPE	12	20	11	9	3

Figure S139. Get High-res Image Gene #41: 'del_17q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 0.00418 (Fisher's exact test), Q value = 0.033

Table S140. Gene #42: 'del_17q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 23(17Q21.31) MUTATED	13	3	9	1
DEL PEAK 23(17Q21.31) WILD-TYPE	23	23	7	11

Figure S140. Get High-res Image Gene #42: 'del_17q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 0.00902 (Fisher's exact test), Q value = 0.049

Table S141. Gene #42: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 23(17Q21.31) MUTATED	7	1	12	4	1
DEL PEAK 23(17Q21.31) WILD-TYPE	11	10	8	14	10

Figure S141. Get High-res Image Gene #42: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.14

Table S142. Gene #42: 'del_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 23(17Q21.31) MUTATED	9	11	2	3
DEL PEAK 23(17Q21.31) WILD-TYPE	14	12	5	21

Figure S142. Get High-res Image Gene #42: 'del_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.12

Table S143. Gene #42: 'del_17q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	16	26
DEL PEAK 23(17Q21.31) MUTATED	17	3	5
DEL PEAK 23(17Q21.31) WILD-TYPE	19	13	21

Figure S143. Get High-res Image Gene #42: 'del_17q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00482 (Fisher's exact test), Q value = 0.035

Table S144. Gene #42: 'del_17q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
DEL PEAK 23(17Q21.31) MUTATED	6	6	0	12	1
DEL PEAK 23(17Q21.31) WILD-TYPE	10	21	11	8	3

Figure S144. Get High-res Image Gene #42: 'del_17q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q24.2' versus 'CN_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.018

Table S145. Gene #43: 'del_17q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 24(17Q24.2) MUTATED	10	3	10	1
DEL PEAK 24(17Q24.2) WILD-TYPE	26	23	6	11

Figure S145. Get High-res Image Gene #43: 'del_17q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q24.2' versus 'METHLYATION_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.064

Table S146. Gene #43: 'del_17q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
DEL PEAK 24(17Q24.2) MUTATED	6	2	12	3	1
DEL PEAK 24(17Q24.2) WILD-TYPE	12	9	8	15	10

Figure S146. Get High-res Image Gene #43: 'del_17q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0409 (Fisher's exact test), Q value = 0.13

Table S147. Gene #43: 'del_17q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 24(17Q24.2) MUTATED	8	11	1	3
DEL PEAK 24(17Q24.2) WILD-TYPE	15	12	6	21

Figure S147. Get High-res Image Gene #43: 'del_17q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.1

Table S148. Gene #43: 'del_17q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
DEL PEAK 24(17Q24.2) MUTATED	6	7	0	8	3
DEL PEAK 24(17Q24.2) WILD-TYPE	10	20	11	12	1

Figure S148. Get High-res Image Gene #43: 'del_17q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 0.0315 (Fisher's exact test), Q value = 0.11

Table S149. Gene #44: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 25(18Q21.2) MUTATED	16	5	7	8
DEL PEAK 25(18Q21.2) WILD-TYPE	20	21	9	4

Figure S149. Get High-res Image Gene #44: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'CN_CNMF'

P value = 0.00464 (Fisher's exact test), Q value = 0.034

Table S150. Gene #45: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 26(20P12.1) MUTATED	10	0	2	0
DEL PEAK 26(20P12.1) WILD-TYPE	26	26	14	12

Figure S150. Get High-res Image Gene #45: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.13

Table S151. Gene #45: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
DEL PEAK 26(20P12.1) MUTATED	6	1	2	0
DEL PEAK 26(20P12.1) WILD-TYPE	18	12	15	23

Figure S151. Get High-res Image Gene #45: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.1

Table S152. Gene #45: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
DEL PEAK 26(20P12.1) MUTATED	6	2	1	0
DEL PEAK 26(20P12.1) WILD-TYPE	17	21	6	24

Figure S152. Get High-res Image Gene #45: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00645 (Fisher's exact test), Q value = 0.043

Table S153. Gene #45: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	16	26
DEL PEAK 26(20P12.1) MUTATED	4	5	0
DEL PEAK 26(20P12.1) WILD-TYPE	32	11	26

Figure S153. Get High-res Image Gene #45: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.018

Table S154. Gene #45: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	22	27
DEL PEAK 26(20P12.1) MUTATED	2	7	0
DEL PEAK 26(20P12.1) WILD-TYPE	26	15	27

Figure S154. Get High-res Image Gene #45: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q12.1' versus 'CN_CNMF'

P value = 0.00449 (Fisher's exact test), Q value = 0.034

Table S155. Gene #46: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	26	16	12
DEL PEAK 27(22Q12.1) MUTATED	22	7	12	9
DEL PEAK 27(22Q12.1) WILD-TYPE	14	19	4	3

Figure S155. Get High-res Image Gene #46: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

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/ACC-TP/19778622/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ACC-TP/20124001/ACC-TP.transferedmergedcluster.txt
Number of patients = 90
Number of significantly focal cnvs = 46
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.

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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