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

Skin Cutaneous Melanoma (Metastatic)

02 April 2015 | analyses__2015_04_02

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 (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C14X56V6

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 55 focal events and 10 molecular subtypes across 366 patients, 151 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p12 cnv correlated to 'CN_CNMF'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
amp_1q44 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q12 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5q35.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
amp_6p24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p22.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_7q34 cnv correlated to 'CN_CNMF'.
amp_8q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_12q14.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_13q31.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_15q26.2 cnv correlated to 'CN_CNMF'.
amp_17q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_20q13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_22q13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_1p36.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_1p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_5q31.3 cnv correlated to 'METHLYATION_CNMF'.
del_6q22.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_6q26 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_8p23.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_9p23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_10q26.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
del_11q23.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_12q23.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_13q34 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_14q23.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q32.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_15q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_16p13.3 cnv correlated to 'RPPA_CNMF' and 'MIRSEQ_MATURE_CNMF'.
del_16q12.1 cnv correlated to 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_16q24.3 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.3 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 55 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, 151 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	210 (57%)	156	1e-05 (0.00025)	1e-05 (0.00025)	0.323 (0.525)	0.0159 (0.0868)	0.0349 (0.144)	0.00812 (0.0551)	0.00083 (0.0104)	0.0174 (0.0907)	0.0008 (0.0102)	0.00187 (0.019)
amp 1q44	201 (55%)	165	1e-05 (0.00025)	0.00882 (0.0577)	0.162 (0.367)	0.142 (0.336)	0.00872 (0.0577)	0.368 (0.561)	0.00437 (0.0358)	0.0062 (0.0449)	0.0199 (0.0975)	0.00221 (0.0217)
del xp21 1	87 (24%)	279	0.121 (0.301)	1e-05 (0.00025)	0.0469 (0.174)	0.11 (0.284)	0.00463 (0.0364)	0.00219 (0.0217)	0.00086 (0.0105)	0.048 (0.177)	0.00106 (0.0119)	0.239 (0.457)
del 2q37 3	93 (25%)	273	0.419 (0.611)	0.0963 (0.261)	0.165 (0.369)	0.0195 (0.0975)	0.00494 (0.0377)	0.0177 (0.091)	0.0305 (0.135)	0.0101 (0.0606)	0.264 (0.471)	0.308 (0.51)
del 9p21 3	278 (76%)	88	1e-05 (0.00025)	0.00792 (0.0544)	0.756 (0.846)	0.701 (0.813)	2e-05 (0.000423)	0.00741 (0.0516)	0.034 (0.144)	0.799 (0.87)	0.411 (0.603)	0.122 (0.301)
del 11q23 3	202 (55%)	164	1e-05 (0.00025)	0.336 (0.537)	0.904 (0.929)	0.261 (0.468)	0.043 (0.164)	0.00046 (0.00649)	0.444 (0.633)	0.0337 (0.144)	0.00986 (0.0606)	0.0845 (0.247)
del 14q23 3	120 (33%)	246	2e-05 (0.000423)	0.779 (0.856)	0.553 (0.705)	0.247 (0.463)	0.00592 (0.0434)	0.0354 (0.144)	0.00059 (0.00811)	0.178 (0.383)	0.112 (0.286)	0.0388 (0.154)
amp 5q35 3	59 (16%)	307	0.00021 (0.0035)	0.00032 (0.00489)	0.0913 (0.255)	0.0327 (0.143)	0.0142 (0.0782)	0.525 (0.693)	0.273 (0.479)	0.352 (0.551)	0.356 (0.554)	0.455 (0.638)
amp 8q11 21	163 (45%)	203	1e-05 (0.00025)	0.00145 (0.0153)	0.569 (0.713)	0.246 (0.463)	0.0181 (0.0921)	0.0105 (0.0616)	0.837 (0.886)	0.857 (0.896)	0.761 (0.847)	0.747 (0.846)
amp 13q31 3	104 (28%)	262	1e-05 (0.00025)	1e-05 (0.00025)	0.75 (0.846)	0.27 (0.477)	0.00021 (0.0035)	0.00121 (0.0133)	0.679 (0.796)	0.513 (0.686)	0.0585 (0.208)	0.789 (0.862)
amp 17q25 3	122 (33%)	244	0.00017 (0.00312)	0.0409 (0.16)	0.0296 (0.133)	0.0737 (0.234)	0.429 (0.62)	0.00729 (0.0516)	0.56 (0.706)	0.0656 (0.217)	0.239 (0.457)	0.194 (0.402)
del 1p22 1	97 (27%)	269	0.00096 (0.011)	1e-05 (0.00025)	0.591 (0.734)	0.211 (0.429)	0.00022 (0.00356)	0.023 (0.108)	0.0803 (0.243)	0.769 (0.849)	0.196 (0.406)	0.258 (0.467)
del 6q26	221 (60%)	145	1e-05 (0.00025)	0.00981 (0.0606)	0.841 (0.887)	0.537 (0.698)	9e-05 (0.00171)	0.0487 (0.179)	0.324 (0.525)	0.602 (0.744)	0.837 (0.886)	0.458 (0.64)
del 10p15 3	199 (54%)	167	1e-05 (0.00025)	0.0448 (0.17)	0.886 (0.914)	0.221 (0.438)	0.00064 (0.00859)	0.00094 (0.011)	0.0714 (0.23)	0.453 (0.638)	0.327 (0.529)	0.275 (0.481)
del 10q23 31	230 (63%)	136	1e-05 (0.00025)	0.125 (0.306)	0.881 (0.912)	0.206 (0.421)	0.00394 (0.0333)	0.0172 (0.0907)	0.0299 (0.134)	0.688 (0.803)	0.342 (0.539)	0.776 (0.855)
del 14q32 31	117 (32%)	249	1e-05 (0.00025)	0.622 (0.753)	0.588 (0.733)	0.186 (0.391)	0.00449 (0.0358)	0.0344 (0.144)	0.00372 (0.0325)	0.188 (0.391)	0.42 (0.611)	0.187 (0.391)
del 15q13 3	84 (23%)	282	0.0496 (0.181)	0.0101 (0.0606)	0.0897 (0.254)	0.306 (0.509)	0.4 (0.593)	0.0175 (0.0907)	0.651 (0.775)	0.869 (0.905)	0.0162 (0.0874)	0.762 (0.847)
del 16q24 3	133 (36%)	233	0.113 (0.286)	0.62 (0.753)	0.146 (0.344)	0.906 (0.929)	0.00945 (0.0597)	0.0024 (0.0228)	0.0821 (0.243)	0.0944 (0.258)	0.0128 (0.0726)	0.0413 (0.16)
del 19p13 3	104 (28%)	262	0.0215 (0.104)	0.705 (0.815)	0.00236 (0.0228)	0.0623 (0.214)	0.00079 (0.0102)	0.00124 (0.0134)	0.785 (0.86)	0.101 (0.269)	0.186 (0.391)	0.462 (0.643)
amp 1q21 3	203 (55%)	163	1e-05 (0.00025)	0.0741 (0.234)	0.339 (0.538)	0.523 (0.693)	0.00393 (0.0333)	0.47 (0.648)	0.0228 (0.108)	0.0631 (0.215)	0.173 (0.378)	0.0829 (0.244)
amp 5p15 33	110 (30%)	256	1e-05 (0.00025)	0.134 (0.321)	0.693 (0.808)	0.74 (0.84)	0.0617 (0.214)	0.563 (0.707)	0.00546 (0.0411)	0.739 (0.84)	0.246 (0.463)	0.0235 (0.109)
amp 8q24 21	191 (52%)	175	1e-05 (0.00025)	0.00401 (0.0334)	0.754 (0.846)	0.939 (0.953)	0.00999 (0.0606)	0.314 (0.515)	0.806 (0.874)	0.753 (0.846)	0.616 (0.753)	0.768 (0.849)
amp 20q13 33	187 (51%)	179	1e-05 (0.00025)	0.00148 (0.0154)	0.828 (0.884)	0.989 (0.989)	0.00584 (0.0434)	0.0756 (0.236)	0.181 (0.387)	0.589 (0.733)	0.795 (0.868)	0.367 (0.561)
del 1p36 31	81 (22%)	285	0.0377 (0.151)	2e-05 (0.000423)	0.579 (0.724)	0.209 (0.426)	0.0332 (0.144)	0.0895 (0.254)	0.0641 (0.216)	0.0595 (0.208)	0.403 (0.596)	0.857 (0.896)
del 6q22 31	215 (59%)	151	1e-05 (0.00025)	0.00482 (0.0373)	0.959 (0.966)	0.445 (0.633)	0.0003 (0.00471)	0.165 (0.369)	0.479 (0.654)	0.533 (0.698)	0.467 (0.647)	0.267 (0.474)
del 9p23	249 (68%)	117	3e-05 (0.000611)	0.103 (0.272)	0.455 (0.638)	0.612 (0.752)	0.00874 (0.0577)	0.158 (0.364)	0.035 (0.144)	0.169 (0.374)	0.825 (0.883)	0.153 (0.359)
del 10q21 1	217 (59%)	149	1e-05 (0.00025)	0.466 (0.647)	0.715 (0.819)	0.148 (0.349)	0.0133 (0.0749)	0.0317 (0.14)	0.0606 (0.211)	0.25 (0.463)	0.225 (0.441)	0.761 (0.847)
del 10q26 3	236 (64%)	130	1e-05 (0.00025)	0.393 (0.587)	0.833 (0.886)	0.309 (0.51)	0.0002 (0.0035)	0.00444 (0.0358)	0.079 (0.242)	0.513 (0.686)	0.185 (0.391)	0.394 (0.587)
del 16q12 1	117 (32%)	249	0.26 (0.468)	0.306 (0.509)	0.0217 (0.104)	0.68 (0.796)	0.0387 (0.154)	0.0709 (0.23)	0.186 (0.391)	0.0217 (0.104)	0.267 (0.474)	0.059 (0.208)
amp 4q12	65 (18%)	301	0.00277 (0.025)	0.223 (0.439)	0.0823 (0.243)	0.539 (0.699)	0.757 (0.846)	0.103 (0.272)	0.0634 (0.215)	0.0276 (0.127)	0.279 (0.483)	0.503 (0.677)
amp 7p22 1	208 (57%)	158	1e-05 (0.00025)	0.814 (0.878)	0.628 (0.759)	0.214 (0.431)	0.0238 (0.11)	0.131 (0.315)	0.075 (0.236)	0.408 (0.602)	0.913 (0.932)	0.475 (0.651)
amp 12q14 1	58 (16%)	308	0.00285 (0.0253)	0.332 (0.534)	0.871 (0.905)	0.285 (0.49)	0.0461 (0.173)	0.485 (0.657)	0.768 (0.849)	0.216 (0.431)	0.171 (0.376)	0.644 (0.771)
amp 19p13 2	69 (19%)	297	0.00091 (0.0109)	0.0934 (0.257)	0.442 (0.633)	0.959 (0.966)	0.00254 (0.0233)	0.137 (0.325)	0.95 (0.961)	0.29 (0.495)	0.129 (0.312)	0.738 (0.84)
amp 22q13 2	151 (41%)	215	7e-05 (0.00137)	0.0419 (0.161)	0.974 (0.978)	0.715 (0.819)	0.234 (0.453)	0.133 (0.32)	0.807 (0.874)	0.0856 (0.248)	0.261 (0.468)	0.317 (0.519)
del 4q34 3	110 (30%)	256	0.268 (0.474)	0.0659 (0.217)	0.515 (0.687)	0.551 (0.703)	0.0766 (0.238)	0.011 (0.0635)	0.678 (0.796)	0.00935 (0.0597)	0.124 (0.303)	0.173 (0.378)
del 8p23 3	89 (24%)	277	0.00908 (0.0588)	0.107 (0.278)	0.203 (0.418)	0.16 (0.366)	0.0394 (0.155)	0.278 (0.483)	0.374 (0.566)	0.253 (0.463)	0.0858 (0.248)	0.0816 (0.243)
del 11p15 5	114 (31%)	252	0.0198 (0.0975)	0.0503 (0.182)	0.618 (0.753)	0.712 (0.819)	0.535 (0.698)	0.255 (0.465)	0.482 (0.656)	0.247 (0.463)	0.0288 (0.131)	0.338 (0.537)
del 12q23 3	92 (25%)	274	0.0137 (0.0761)	0.0361 (0.146)	0.965 (0.971)	0.819 (0.879)	0.302 (0.506)	0.368 (0.561)	0.301 (0.506)	0.245 (0.463)	0.47 (0.648)	0.455 (0.638)
del 13q34	85 (23%)	281	0.951 (0.961)	0.0105 (0.0616)	0.066 (0.217)	0.74 (0.84)	0.817 (0.879)	0.00733 (0.0516)	0.642 (0.771)	0.0974 (0.261)	0.292 (0.495)	0.697 (0.811)
del 16p13 3	62 (17%)	304	0.561 (0.706)	0.0907 (0.255)	0.0121 (0.0693)	0.336 (0.537)	0.161 (0.366)	0.108 (0.28)	0.366 (0.561)	0.33 (0.532)	0.0454 (0.171)	0.091 (0.255)
del 17p13 3	135 (37%)	231	0.252 (0.463)	0.00034 (0.00505)	0.366 (0.561)	0.636 (0.768)	0.0918 (0.255)	0.0183 (0.0923)	0.85 (0.892)	0.359 (0.557)	0.387 (0.583)	0.215 (0.431)
amp 1p12	121 (33%)	245	0.0354 (0.144)	0.911 (0.932)	0.708 (0.816)	0.883 (0.913)	0.371 (0.563)	0.251 (0.463)	0.62 (0.753)	0.525 (0.693)	0.777 (0.855)	0.612 (0.752)
amp 7q34	224 (61%)	142	2e-05 (0.000423)	0.479 (0.654)	0.234 (0.453)	0.939 (0.953)	0.157 (0.364)	0.252 (0.463)	0.0974 (0.261)	0.258 (0.467)	0.082 (0.243)	0.418 (0.611)
amp 15q26 2	119 (33%)	247	0.00042 (0.00608)	0.204 (0.418)	0.939 (0.953)	0.81 (0.875)	0.159 (0.366)	0.455 (0.638)	0.805 (0.874)	0.237 (0.457)	0.163 (0.367)	0.442 (0.633)
del 4p16 3	91 (25%)	275	0.544 (0.701)	0.111 (0.284)	0.649 (0.775)	0.705 (0.815)	0.176 (0.381)	0.0173 (0.0907)	0.666 (0.788)	0.253 (0.463)	0.432 (0.622)	0.981 (0.983)
del 5q12 1	97 (27%)	269	0.233 (0.453)	0.221 (0.438)	0.39 (0.585)	0.115 (0.289)	0.494 (0.667)	0.0344 (0.144)	0.302 (0.506)	0.522 (0.693)	0.34 (0.538)	0.653 (0.775)
del 5q31 3	131 (36%)	235	0.274 (0.479)	0.00249 (0.0232)	0.616 (0.753)	0.306 (0.509)	0.736 (0.84)	0.176 (0.381)	0.832 (0.886)	0.638 (0.768)	0.39 (0.585)	0.475 (0.651)
amp 3p13	103 (28%)	263	0.122 (0.301)	0.534 (0.698)	0.065 (0.217)	0.052 (0.186)	0.601 (0.744)	0.294 (0.497)	0.484 (0.657)	0.671 (0.792)	0.841 (0.887)	0.872 (0.905)
amp 6q12	80 (22%)	286	0.55 (0.703)	0.561 (0.706)	0.528 (0.693)	0.0815 (0.243)	0.456 (0.638)	0.0695 (0.228)	0.214 (0.431)	0.169 (0.374)	0.347 (0.546)	0.106 (0.278)
amp 11q13 3	69 (19%)	297	0.128 (0.31)	0.0863 (0.249)	0.907 (0.929)	0.838 (0.886)	0.283 (0.487)	0.446 (0.634)	0.157 (0.364)	0.109 (0.282)	0.557 (0.706)	0.249 (0.463)
amp 12q15	59 (16%)	307	0.0729 (0.233)	0.228 (0.446)	0.607 (0.748)	0.427 (0.618)	0.0965 (0.261)	0.184 (0.391)	0.658 (0.78)	0.291 (0.495)	0.366 (0.561)	0.314 (0.515)
del 3p25 1	71 (19%)	295	0.174 (0.378)	0.238 (0.457)	0.427 (0.618)	0.216 (0.431)	0.528 (0.693)	0.751 (0.846)	0.353 (0.551)	0.398 (0.592)	0.324 (0.525)	0.169 (0.374)
del 3q13 31	62 (17%)	304	0.163 (0.367)	0.0926 (0.256)	0.411 (0.603)	0.115 (0.289)	0.0522 (0.186)	0.555 (0.705)	0.253 (0.463)	0.279 (0.483)	0.0777 (0.239)	0.55 (0.703)
del 5p15 31	79 (22%)	287	0.651 (0.775)	0.376 (0.568)	0.545 (0.701)	0.541 (0.699)	0.819 (0.879)	0.071 (0.23)	0.678 (0.796)	0.363 (0.561)	0.0893 (0.254)	0.905 (0.929)
del 15q21 1	91 (25%)	275	0.0778 (0.239)	0.103 (0.272)	0.541 (0.699)	0.338 (0.537)	0.5 (0.675)	0.291 (0.495)	0.864 (0.902)	0.518 (0.69)	0.115 (0.289)	0.846 (0.889)

'amp_1p12' versus 'CN_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.14

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 1(1P12) MUTATED	43	37	41
AMP PEAK 1(1P12) WILD-TYPE	58	102	85

Figure S1. Get High-res Image Gene #1: 'amp_1p12' versus Molecular Subtype #1: 'CN_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	101	139	126
AMP PEAK 2(1Q21.3) MUTATED	92	51	60
AMP PEAK 2(1Q21.3) WILD-TYPE	9	88	66

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

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00393 (Fisher's exact test), Q value = 0.033

Table S3. Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 2(1Q21.3) MUTATED	87	44	72
AMP PEAK 2(1Q21.3) WILD-TYPE	50	60	53

Figure S3. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.11

Table S4. Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	102	79	114	8
AMP PEAK 2(1Q21.3) MUTATED	32	55	35	69	2
AMP PEAK 2(1Q21.3) WILD-TYPE	15	47	44	45	6

Figure S4. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q44' versus 'CN_CNMF'

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

Table S5. Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 3(1Q44) MUTATED	90	50	61
AMP PEAK 3(1Q44) WILD-TYPE	11	89	65

Figure S5. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q44' versus 'METHLYATION_CNMF'

P value = 0.00882 (Fisher's exact test), Q value = 0.058

Table S6. Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 3(1Q44) MUTATED	74	66	61
AMP PEAK 3(1Q44) WILD-TYPE	55	78	32

Figure S6. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q44' versus 'MRNASEQ_CNMF'

P value = 0.00872 (Fisher's exact test), Q value = 0.058

Table S7. Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 3(1Q44) MUTATED	83	44	74
AMP PEAK 3(1Q44) WILD-TYPE	54	60	51

Figure S7. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q44' versus 'MIRSEQ_CNMF'

P value = 0.00437 (Fisher's exact test), Q value = 0.036

Table S8. Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	102	79	114	8
AMP PEAK 3(1Q44) MUTATED	34	52	33	70	3
AMP PEAK 3(1Q44) WILD-TYPE	13	50	46	44	5

Figure S8. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0062 (Fisher's exact test), Q value = 0.045

Table S9. Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	147	74	38
AMP PEAK 3(1Q44) MUTATED	49	83	31	29
AMP PEAK 3(1Q44) WILD-TYPE	42	64	43	9

Figure S9. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.098

Table S10. Gene #3: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	105	139
AMP PEAK 3(1Q44) MUTATED	41	57	88
AMP PEAK 3(1Q44) WILD-TYPE	51	48	51

Figure S10. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q44' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00221 (Fisher's exact test), Q value = 0.022

Table S11. Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	169	137	30
AMP PEAK 3(1Q44) MUTATED	93	68	25
AMP PEAK 3(1Q44) WILD-TYPE	76	69	5

Figure S11. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.025

Table S12. Gene #5: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 5(4Q12) MUTATED	22	13	30
AMP PEAK 5(4Q12) WILD-TYPE	79	126	96

Figure S12. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.13

Table S13. Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	147	74	38
AMP PEAK 5(4Q12) MUTATED	14	38	8	5
AMP PEAK 5(4Q12) WILD-TYPE	77	109	66	33

Figure S13. 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 S14. Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 6(5P15.33) MUTATED	31	24	55
AMP PEAK 6(5P15.33) WILD-TYPE	70	115	71

Figure S14. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00546 (Fisher's exact test), Q value = 0.041

Table S15. Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	102	79	114	8
AMP PEAK 6(5P15.33) MUTATED	18	17	24	41	4
AMP PEAK 6(5P15.33) WILD-TYPE	29	85	55	73	4

Figure S15. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.11

Table S16. Gene #6: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	169	137	30
AMP PEAK 6(5P15.33) MUTATED	58	30	12
AMP PEAK 6(5P15.33) WILD-TYPE	111	107	18

Figure S16. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.3' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0035

Table S17. Gene #7: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 7(5Q35.3) MUTATED	21	9	29
AMP PEAK 7(5Q35.3) WILD-TYPE	80	130	97

Figure S17. Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0049

Table S18. Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 7(5Q35.3) MUTATED	19	13	27
AMP PEAK 7(5Q35.3) WILD-TYPE	110	131	66

Figure S18. Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.14

Table S19. Gene #7: 'amp_5q35.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	58	35	49
AMP PEAK 7(5Q35.3) MUTATED	3	4	7	13
AMP PEAK 7(5Q35.3) WILD-TYPE	24	54	28	36

Figure S19. Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.078

Table S20. Gene #7: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 7(5Q35.3) MUTATED	26	8	25
AMP PEAK 7(5Q35.3) WILD-TYPE	111	96	100

Figure S20. Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_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	101	139	126
AMP PEAK 8(6P24.3) MUTATED	78	57	75
AMP PEAK 8(6P24.3) WILD-TYPE	23	82	51

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
ALL	129	144	93
AMP PEAK 8(6P24.3) MUTATED	79	61	70
AMP PEAK 8(6P24.3) WILD-TYPE	50	83	23

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

'amp_6p24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.087

Table S23. Gene #8: 'amp_6p24.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	58	35	49
AMP PEAK 8(6P24.3) MUTATED	12	38	13	32
AMP PEAK 8(6P24.3) WILD-TYPE	15	20	22	17

Figure S23. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6p24.3' versus 'MRNASEQ_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.14

Table S24. Gene #8: 'amp_6p24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 8(6P24.3) MUTATED	87	49	74
AMP PEAK 8(6P24.3) WILD-TYPE	50	55	51

Figure S24. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00812 (Fisher's exact test), Q value = 0.055

Table S25. Gene #8: 'amp_6p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
AMP PEAK 8(6P24.3) MUTATED	71	65	42	32
AMP PEAK 8(6P24.3) WILD-TYPE	36	40	54	26

Figure S25. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.01

Table S26. Gene #8: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	102	79	114	8
AMP PEAK 8(6P24.3) MUTATED	29	51	40	80	1
AMP PEAK 8(6P24.3) WILD-TYPE	18	51	39	34	7

Figure S26. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.091

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	147	74	38
AMP PEAK 8(6P24.3) MUTATED	59	90	31	21
AMP PEAK 8(6P24.3) WILD-TYPE	32	57	43	17

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

'amp_6p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.01

Table S28. Gene #8: 'amp_6p24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	105	139
AMP PEAK 8(6P24.3) MUTATED	44	52	96
AMP PEAK 8(6P24.3) WILD-TYPE	48	53	43

Figure S28. 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 = 0.00187 (Fisher's exact test), Q value = 0.019

Table S29. Gene #8: 'amp_6p24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	169	137	30
AMP PEAK 8(6P24.3) MUTATED	112	63	17
AMP PEAK 8(6P24.3) WILD-TYPE	57	74	13

Figure S29. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p22.1' versus 'CN_CNMF'

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

Table S30. Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 10(7P22.1) MUTATED	62	55	91
AMP PEAK 10(7P22.1) WILD-TYPE	39	84	35

Figure S30. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.11

Table S31. Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 10(7P22.1) MUTATED	73	52	83
AMP PEAK 10(7P22.1) WILD-TYPE	64	52	42

Figure S31. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q34' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S32. Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 11(7Q34) MUTATED	64	66	94
AMP PEAK 11(7Q34) WILD-TYPE	37	73	32

Figure S32. Get High-res Image Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'CN_CNMF'

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

Table S33. Gene #12: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 12(8Q11.21) MUTATED	35	39	89
AMP PEAK 12(8Q11.21) WILD-TYPE	66	100	37

Figure S33. Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'METHLYATION_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.015

Table S34. Gene #12: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 12(8Q11.21) MUTATED	47	60	56
AMP PEAK 12(8Q11.21) WILD-TYPE	82	84	37

Figure S34. Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.092

Table S35. Gene #12: 'amp_8q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 12(8Q11.21) MUTATED	57	38	68
AMP PEAK 12(8Q11.21) WILD-TYPE	80	66	57

Figure S35. Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.062

Table S36. Gene #12: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
AMP PEAK 12(8Q11.21) MUTATED	56	43	48	16
AMP PEAK 12(8Q11.21) WILD-TYPE	51	62	48	42

Figure S36. Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

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

Table S37. Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 13(8Q24.21) MUTATED	47	48	96
AMP PEAK 13(8Q24.21) WILD-TYPE	54	91	30

Figure S37. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.033

Table S38. Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 13(8Q24.21) MUTATED	58	71	62
AMP PEAK 13(8Q24.21) WILD-TYPE	71	73	31

Figure S38. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.00999 (Fisher's exact test), Q value = 0.061

Table S39. Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 13(8Q24.21) MUTATED	71	43	77
AMP PEAK 13(8Q24.21) WILD-TYPE	66	61	48

Figure S39. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'CN_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.025

Table S40. Gene #15: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 15(12Q14.1) MUTATED	16	12	30
AMP PEAK 15(12Q14.1) WILD-TYPE	85	127	96

Figure S40. Get High-res Image Gene #15: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 0.0461 (Fisher's exact test), Q value = 0.17

Table S41. Gene #15: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 15(12Q14.1) MUTATED	25	9	24
AMP PEAK 15(12Q14.1) WILD-TYPE	112	95	101

Figure S41. Get High-res Image Gene #15: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q31.3' versus 'CN_CNMF'

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

Table S42. Gene #17: 'amp_13q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 17(13Q31.3) MUTATED	34	19	51
AMP PEAK 17(13Q31.3) WILD-TYPE	67	120	75

Figure S42. Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q31.3' versus 'METHLYATION_CNMF'

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

Table S43. Gene #17: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 17(13Q31.3) MUTATED	37	23	44
AMP PEAK 17(13Q31.3) WILD-TYPE	92	121	49

Figure S43. Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q31.3' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0035

Table S44. Gene #17: 'amp_13q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 17(13Q31.3) MUTATED	31	21	52
AMP PEAK 17(13Q31.3) WILD-TYPE	106	83	73

Figure S44. Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.013

Table S45. Gene #17: 'amp_13q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
AMP PEAK 17(13Q31.3) MUTATED	35	31	33	5
AMP PEAK 17(13Q31.3) WILD-TYPE	72	74	63	53

Figure S45. Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.2' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0061

Table S46. Gene #18: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 18(15Q26.2) MUTATED	30	32	57
AMP PEAK 18(15Q26.2) WILD-TYPE	71	107	69

Figure S46. Get High-res Image Gene #18: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0031

Table S47. Gene #19: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 19(17Q25.3) MUTATED	50	33	39
AMP PEAK 19(17Q25.3) WILD-TYPE	51	106	87

Figure S47. Get High-res Image Gene #19: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'METHLYATION_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.16

Table S48. Gene #19: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 19(17Q25.3) MUTATED	43	39	40
AMP PEAK 19(17Q25.3) WILD-TYPE	86	105	53

Figure S48. Get High-res Image Gene #19: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.3' versus 'RPPA_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.13

Table S49. Gene #19: 'amp_17q25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	58	26	38
AMP PEAK 19(17Q25.3) MUTATED	11	24	15	16
AMP PEAK 19(17Q25.3) WILD-TYPE	36	34	11	22

Figure S49. Get High-res Image Gene #19: 'amp_17q25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_17q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00729 (Fisher's exact test), Q value = 0.052

Table S50. Gene #19: 'amp_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
AMP PEAK 19(17Q25.3) MUTATED	32	40	22	28
AMP PEAK 19(17Q25.3) WILD-TYPE	75	65	74	30

Figure S50. Get High-res Image Gene #19: 'amp_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

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

Table S51. Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 20(19P13.2) MUTATED	16	16	37
AMP PEAK 20(19P13.2) WILD-TYPE	85	123	89

Figure S51. Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.023

Table S52. Gene #20: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 20(19P13.2) MUTATED	25	10	34
AMP PEAK 20(19P13.2) WILD-TYPE	112	94	91

Figure S52. Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

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

Table S53. Gene #21: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 21(20Q13.33) MUTATED	64	41	82
AMP PEAK 21(20Q13.33) WILD-TYPE	37	98	44

Figure S53. Get High-res Image Gene #21: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.015

Table S54. Gene #21: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 21(20Q13.33) MUTATED	63	62	62
AMP PEAK 21(20Q13.33) WILD-TYPE	66	82	31

Figure S54. Get High-res Image Gene #21: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 0.00584 (Fisher's exact test), Q value = 0.043

Table S55. Gene #21: 'amp_20q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
AMP PEAK 21(20Q13.33) MUTATED	65	44	78
AMP PEAK 21(20Q13.33) WILD-TYPE	72	60	47

Figure S55. Get High-res Image Gene #21: 'amp_20q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_22q13.2' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0014

Table S56. Gene #22: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
AMP PEAK 22(22Q13.2) MUTATED	54	37	60
AMP PEAK 22(22Q13.2) WILD-TYPE	47	102	66

Figure S56. Get High-res Image Gene #22: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q13.2' versus 'METHLYATION_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.16

Table S57. Gene #22: 'amp_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
AMP PEAK 22(22Q13.2) MUTATED	58	48	45
AMP PEAK 22(22Q13.2) WILD-TYPE	71	96	48

Figure S57. Get High-res Image Gene #22: 'amp_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'CN_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.15

Table S58. Gene #23: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 1(1P36.31) MUTATED	30	22	29
DEL PEAK 1(1P36.31) WILD-TYPE	71	117	97

Figure S58. Get High-res Image Gene #23: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S59. Gene #23: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 1(1P36.31) MUTATED	20	22	39
DEL PEAK 1(1P36.31) WILD-TYPE	109	122	54

Figure S59. Get High-res Image Gene #23: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.14

Table S60. Gene #23: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 1(1P36.31) MUTATED	30	15	36
DEL PEAK 1(1P36.31) WILD-TYPE	107	89	89

Figure S60. Get High-res Image Gene #23: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'CN_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.011

Table S61. Gene #24: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 2(1P22.1) MUTATED	32	22	43
DEL PEAK 2(1P22.1) WILD-TYPE	69	117	83

Figure S61. Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

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

Table S62. Gene #24: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 2(1P22.1) MUTATED	22	31	44
DEL PEAK 2(1P22.1) WILD-TYPE	107	113	49

Figure S62. Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0036

Table S63. Gene #24: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 2(1P22.1) MUTATED	36	14	47
DEL PEAK 2(1P22.1) WILD-TYPE	101	90	78

Figure S63. Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.11

Table S64. Gene #24: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 2(1P22.1) MUTATED	26	22	37	12
DEL PEAK 2(1P22.1) WILD-TYPE	81	83	59	46

Figure S64. Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.097

Table S65. Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	58	35	49
DEL PEAK 3(2Q37.3) MUTATED	4	11	8	21
DEL PEAK 3(2Q37.3) WILD-TYPE	23	47	27	28

Figure S65. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.00494 (Fisher's exact test), Q value = 0.038

Table S66. Gene #25: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 3(2Q37.3) MUTATED	48	19	26
DEL PEAK 3(2Q37.3) WILD-TYPE	89	85	99

Figure S66. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.091

Table S67. Gene #25: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 3(2Q37.3) MUTATED	37	28	15	13
DEL PEAK 3(2Q37.3) WILD-TYPE	70	77	81	45

Figure S67. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.14

Table S68. Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	102	79	114	8
DEL PEAK 3(2Q37.3) MUTATED	11	21	15	42	2
DEL PEAK 3(2Q37.3) WILD-TYPE	36	81	64	72	6

Figure S68. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.061

Table S69. Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	147	74	38
DEL PEAK 3(2Q37.3) MUTATED	22	50	10	9
DEL PEAK 3(2Q37.3) WILD-TYPE	69	97	64	29

Figure S69. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.091

Table S70. Gene #28: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 6(4P16.3) MUTATED	33	16	30	12
DEL PEAK 6(4P16.3) WILD-TYPE	74	89	66	46

Figure S70. Get High-res Image Gene #28: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.064

Table S71. Gene #29: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 7(4Q34.3) MUTATED	27	26	42	15
DEL PEAK 7(4Q34.3) WILD-TYPE	80	79	54	43

Figure S71. Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00935 (Fisher's exact test), Q value = 0.06

Table S72. Gene #29: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	147	74	38
DEL PEAK 7(4Q34.3) MUTATED	29	32	31	15
DEL PEAK 7(4Q34.3) WILD-TYPE	62	115	43	23

Figure S72. Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.14

Table S73. Gene #31: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 9(5Q12.1) MUTATED	32	17	30	18
DEL PEAK 9(5Q12.1) WILD-TYPE	75	88	66	40

Figure S73. Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.3' versus 'METHLYATION_CNMF'

P value = 0.00249 (Fisher's exact test), Q value = 0.023

Table S74. Gene #32: 'del_5q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 10(5Q31.3) MUTATED	58	52	21
DEL PEAK 10(5Q31.3) WILD-TYPE	71	92	72

Figure S74. Get High-res Image Gene #32: 'del_5q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q22.31' versus 'CN_CNMF'

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

Table S75. Gene #33: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 11(6Q22.31) MUTATED	81	47	87
DEL PEAK 11(6Q22.31) WILD-TYPE	20	92	39

Figure S75. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 0.00482 (Fisher's exact test), Q value = 0.037

Table S76. Gene #33: 'del_6q22.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 11(6Q22.31) MUTATED	87	70	58
DEL PEAK 11(6Q22.31) WILD-TYPE	42	74	35

Figure S76. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0047

Table S77. Gene #33: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 11(6Q22.31) MUTATED	87	44	84
DEL PEAK 11(6Q22.31) WILD-TYPE	50	60	41

Figure S77. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'CN_CNMF'

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

Table S78. Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 12(6Q26) MUTATED	82	50	89
DEL PEAK 12(6Q26) WILD-TYPE	19	89	37

Figure S78. Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00981 (Fisher's exact test), Q value = 0.061

Table S79. Gene #34: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 12(6Q26) MUTATED	87	73	61
DEL PEAK 12(6Q26) WILD-TYPE	42	71	32

Figure S79. Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0017

Table S80. Gene #34: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 12(6Q26) MUTATED	90	45	86
DEL PEAK 12(6Q26) WILD-TYPE	47	59	39

Figure S80. Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0487 (Fisher's exact test), Q value = 0.18

Table S81. Gene #34: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 12(6Q26) MUTATED	72	52	62	35
DEL PEAK 12(6Q26) WILD-TYPE	35	53	34	23

Figure S81. Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 0.00908 (Fisher's exact test), Q value = 0.059

Table S82. Gene #35: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 13(8P23.3) MUTATED	35	24	30
DEL PEAK 13(8P23.3) WILD-TYPE	66	115	96

Figure S82. Get High-res Image Gene #35: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.15

Table S83. Gene #35: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 13(8P23.3) MUTATED	38	16	35
DEL PEAK 13(8P23.3) WILD-TYPE	99	88	90

Figure S83. Get High-res Image Gene #35: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S84. Gene #36: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 14(9P23) MUTATED	63	80	106
DEL PEAK 14(9P23) WILD-TYPE	38	59	20

Figure S84. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.00874 (Fisher's exact test), Q value = 0.058

Table S85. Gene #36: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 14(9P23) MUTATED	93	60	96
DEL PEAK 14(9P23) WILD-TYPE	44	44	29

Figure S85. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.14

Table S86. Gene #36: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	102	79	114	8
DEL PEAK 14(9P23) MUTATED	28	75	46	79	8
DEL PEAK 14(9P23) WILD-TYPE	19	27	33	35	0

Figure S86. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'CN_CNMF'

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

Table S87. Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 15(9P21.3) MUTATED	77	86	115
DEL PEAK 15(9P21.3) WILD-TYPE	24	53	11

Figure S87. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00792 (Fisher's exact test), Q value = 0.054

Table S88. Gene #37: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 15(9P21.3) MUTATED	107	97	74
DEL PEAK 15(9P21.3) WILD-TYPE	22	47	19

Figure S88. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S89. Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 15(9P21.3) MUTATED	102	65	111
DEL PEAK 15(9P21.3) WILD-TYPE	35	39	14

Figure S89. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00741 (Fisher's exact test), Q value = 0.052

Table S90. Gene #37: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 15(9P21.3) MUTATED	83	75	83	37
DEL PEAK 15(9P21.3) WILD-TYPE	24	30	13	21

Figure S90. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.14

Table S91. Gene #37: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	102	79	114	8
DEL PEAK 15(9P21.3) MUTATED	34	84	51	87	8
DEL PEAK 15(9P21.3) WILD-TYPE	13	18	28	27	0

Figure S91. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'CN_CNMF'

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

Table S92. Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 16(10P15.3) MUTATED	54	48	97
DEL PEAK 16(10P15.3) WILD-TYPE	47	91	29

Figure S92. Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.17

Table S93. Gene #38: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 16(10P15.3) MUTATED	70	69	60
DEL PEAK 16(10P15.3) WILD-TYPE	59	75	33

Figure S93. Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0086

Table S94. Gene #38: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 16(10P15.3) MUTATED	66	48	85
DEL PEAK 16(10P15.3) WILD-TYPE	71	56	40

Figure S94. Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.011

Table S95. Gene #38: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 16(10P15.3) MUTATED	57	50	68	24
DEL PEAK 16(10P15.3) WILD-TYPE	50	55	28	34

Figure S95. Get High-res Image Gene #38: '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 S96. Gene #39: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 17(10Q21.1) MUTATED	48	61	108
DEL PEAK 17(10Q21.1) WILD-TYPE	53	78	18

Figure S96. Get High-res Image Gene #39: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.075

Table S97. Gene #39: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 17(10Q21.1) MUTATED	75	55	87
DEL PEAK 17(10Q21.1) WILD-TYPE	62	49	38

Figure S97. Get High-res Image Gene #39: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.14

Table S98. Gene #39: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 17(10Q21.1) MUTATED	59	58	69	31
DEL PEAK 17(10Q21.1) WILD-TYPE	48	47	27	27

Figure S98. Get High-res Image Gene #39: '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 S99. Gene #40: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 18(10Q23.31) MUTATED	53	66	111
DEL PEAK 18(10Q23.31) WILD-TYPE	48	73	15

Figure S99. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.033

Table S100. Gene #40: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 18(10Q23.31) MUTATED	79	58	93
DEL PEAK 18(10Q23.31) WILD-TYPE	58	46	32

Figure S100. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.091

Table S101. Gene #40: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 18(10Q23.31) MUTATED	63	60	73	34
DEL PEAK 18(10Q23.31) WILD-TYPE	44	45	23	24

Figure S101. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.13

Table S102. Gene #40: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	102	79	114	8
DEL PEAK 18(10Q23.31) MUTATED	30	64	41	78	8
DEL PEAK 18(10Q23.31) WILD-TYPE	17	38	38	36	0

Figure S102. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'CN_CNMF'

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

Table S103. Gene #41: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 19(10Q26.3) MUTATED	51	71	114
DEL PEAK 19(10Q26.3) WILD-TYPE	50	68	12

Figure S103. Get High-res Image Gene #41: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0035

Table S104. Gene #41: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 19(10Q26.3) MUTATED	78	60	98
DEL PEAK 19(10Q26.3) WILD-TYPE	59	44	27

Figure S104. Get High-res Image Gene #41: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00444 (Fisher's exact test), Q value = 0.036

Table S105. Gene #41: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 19(10Q26.3) MUTATED	63	64	76	33
DEL PEAK 19(10Q26.3) WILD-TYPE	44	41	20	25

Figure S105. Get High-res Image Gene #41: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.098

Table S106. Gene #42: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 20(11P15.5) MUTATED	41	33	40
DEL PEAK 20(11P15.5) WILD-TYPE	60	106	86

Figure S106. Get High-res Image Gene #42: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.13

Table S107. Gene #42: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	105	139
DEL PEAK 20(11P15.5) MUTATED	23	28	55
DEL PEAK 20(11P15.5) WILD-TYPE	69	77	84

Figure S107. Get High-res Image Gene #42: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q23.3' versus 'CN_CNMF'

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

Table S108. Gene #43: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 21(11Q23.3) MUTATED	77	63	62
DEL PEAK 21(11Q23.3) WILD-TYPE	24	76	64

Figure S108. Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'MRNASEQ_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 0.16

Table S109. Gene #43: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 21(11Q23.3) MUTATED	87	51	64
DEL PEAK 21(11Q23.3) WILD-TYPE	50	53	61

Figure S109. Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0065

Table S110. Gene #43: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 21(11Q23.3) MUTATED	62	49	46	45
DEL PEAK 21(11Q23.3) WILD-TYPE	45	56	50	13

Figure S110. Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.14

Table S111. Gene #43: 'del_11q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	147	74	38
DEL PEAK 21(11Q23.3) MUTATED	58	87	31	21
DEL PEAK 21(11Q23.3) WILD-TYPE	33	60	43	17

Figure S111. Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00986 (Fisher's exact test), Q value = 0.061

Table S112. Gene #43: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	105	139
DEL PEAK 21(11Q23.3) MUTATED	49	50	92
DEL PEAK 21(11Q23.3) WILD-TYPE	43	55	47

Figure S112. Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12q23.3' versus 'CN_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.076

Table S113. Gene #44: 'del_12q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 22(12Q23.3) MUTATED	23	26	43
DEL PEAK 22(12Q23.3) WILD-TYPE	78	113	83

Figure S113. Get High-res Image Gene #44: 'del_12q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q23.3' versus 'METHLYATION_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.15

Table S114. Gene #44: 'del_12q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 22(12Q23.3) MUTATED	40	26	26
DEL PEAK 22(12Q23.3) WILD-TYPE	89	118	67

Figure S114. Get High-res Image Gene #44: 'del_12q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q34' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.062

Table S115. Gene #45: 'del_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 23(13Q34) MUTATED	28	44	13
DEL PEAK 23(13Q34) WILD-TYPE	101	100	80

Figure S115. Get High-res Image Gene #45: 'del_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00733 (Fisher's exact test), Q value = 0.052

Table S116. Gene #45: 'del_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 23(13Q34) MUTATED	21	16	26	22
DEL PEAK 23(13Q34) WILD-TYPE	86	89	70	36

Figure S116. Get High-res Image Gene #45: 'del_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S117. Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 24(14Q23.3) MUTATED	30	29	61
DEL PEAK 24(14Q23.3) WILD-TYPE	71	110	65

Figure S117. Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00592 (Fisher's exact test), Q value = 0.043

Table S118. Gene #46: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 24(14Q23.3) MUTATED	32	36	52
DEL PEAK 24(14Q23.3) WILD-TYPE	105	68	73

Figure S118. Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0354 (Fisher's exact test), Q value = 0.14

Table S119. Gene #46: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 24(14Q23.3) MUTATED	32	35	41	12
DEL PEAK 24(14Q23.3) WILD-TYPE	75	70	55	46

Figure S119. Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0081

Table S120. Gene #46: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	102	79	114	8
DEL PEAK 24(14Q23.3) MUTATED	17	39	24	24	7
DEL PEAK 24(14Q23.3) WILD-TYPE	30	63	55	90	1

Figure S120. Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.15

Table S121. Gene #46: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	169	137	30
DEL PEAK 24(14Q23.3) MUTATED	43	53	11
DEL PEAK 24(14Q23.3) WILD-TYPE	126	84	19

Figure S121. Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.31' versus 'CN_CNMF'

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

Table S122. Gene #47: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 25(14Q32.31) MUTATED	28	27	62
DEL PEAK 25(14Q32.31) WILD-TYPE	73	112	64

Figure S122. Get High-res Image Gene #47: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'MRNASEQ_CNMF'

P value = 0.00449 (Fisher's exact test), Q value = 0.036

Table S123. Gene #47: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 25(14Q32.31) MUTATED	31	34	52
DEL PEAK 25(14Q32.31) WILD-TYPE	106	70	73

Figure S123. Get High-res Image Gene #47: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.14

Table S124. Gene #47: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 25(14Q32.31) MUTATED	32	32	41	12
DEL PEAK 25(14Q32.31) WILD-TYPE	75	73	55	46

Figure S124. Get High-res Image Gene #47: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.31' versus 'MIRSEQ_CNMF'

P value = 0.00372 (Fisher's exact test), Q value = 0.032

Table S125. Gene #47: 'del_14q32.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	102	79	114	8
DEL PEAK 25(14Q32.31) MUTATED	16	34	25	26	7
DEL PEAK 25(14Q32.31) WILD-TYPE	31	68	54	88	1

Figure S125. Get High-res Image Gene #47: 'del_14q32.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q13.3' versus 'CN_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 0.18

Table S126. Gene #48: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 26(15Q13.3) MUTATED	31	24	29
DEL PEAK 26(15Q13.3) WILD-TYPE	70	115	97

Figure S126. Get High-res Image Gene #48: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q13.3' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.061

Table S127. Gene #48: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 26(15Q13.3) MUTATED	33	22	29
DEL PEAK 26(15Q13.3) WILD-TYPE	96	122	64

Figure S127. Get High-res Image Gene #48: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.091

Table S128. Gene #48: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 26(15Q13.3) MUTATED	35	21	21	7
DEL PEAK 26(15Q13.3) WILD-TYPE	72	84	75	51

Figure S128. Get High-res Image Gene #48: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.087

Table S129. Gene #48: 'del_15q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	105	139
DEL PEAK 26(15Q13.3) MUTATED	12	30	37
DEL PEAK 26(15Q13.3) WILD-TYPE	80	75	102

Figure S129. Get High-res Image Gene #48: 'del_15q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'RPPA_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.069

Table S130. Gene #50: 'del_16p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	58	26	38
DEL PEAK 28(16P13.3) MUTATED	9	16	0	8
DEL PEAK 28(16P13.3) WILD-TYPE	38	42	26	30

Figure S130. Get High-res Image Gene #50: 'del_16p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0454 (Fisher's exact test), Q value = 0.17

Table S131. Gene #50: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	105	139
DEL PEAK 28(16P13.3) MUTATED	18	11	31
DEL PEAK 28(16P13.3) WILD-TYPE	74	94	108

Figure S131. Get High-res Image Gene #50: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q12.1' versus 'RPPA_CNMF'

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

Table S132. Gene #51: 'del_16q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	58	26	38
DEL PEAK 29(16Q12.1) MUTATED	15	24	3	17
DEL PEAK 29(16Q12.1) WILD-TYPE	32	34	23	21

Figure S132. Get High-res Image Gene #51: 'del_16q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16q12.1' versus 'MRNASEQ_CNMF'

P value = 0.0387 (Fisher's exact test), Q value = 0.15

Table S133. Gene #51: 'del_16q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 29(16Q12.1) MUTATED	55	29	33
DEL PEAK 29(16Q12.1) WILD-TYPE	82	75	92

Figure S133. Get High-res Image Gene #51: 'del_16q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q12.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S134. Gene #51: 'del_16q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	147	74	38
DEL PEAK 29(16Q12.1) MUTATED	39	48	17	8
DEL PEAK 29(16Q12.1) WILD-TYPE	52	99	57	30

Figure S134. Get High-res Image Gene #51: 'del_16q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00945 (Fisher's exact test), Q value = 0.06

Table S135. Gene #52: 'del_16q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 30(16Q24.3) MUTATED	63	35	35
DEL PEAK 30(16Q24.3) WILD-TYPE	74	69	90

Figure S135. Get High-res Image Gene #52: 'del_16q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0024 (Fisher's exact test), Q value = 0.023

Table S136. Gene #52: 'del_16q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 30(16Q24.3) MUTATED	41	36	24	32
DEL PEAK 30(16Q24.3) WILD-TYPE	66	69	72	26

Figure S136. Get High-res Image Gene #52: 'del_16q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.073

Table S137. Gene #52: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	105	139
DEL PEAK 30(16Q24.3) MUTATED	40	26	54
DEL PEAK 30(16Q24.3) WILD-TYPE	52	79	85

Figure S137. Get High-res Image Gene #52: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0413 (Fisher's exact test), Q value = 0.16

Table S138. Gene #52: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	169	137	30
DEL PEAK 30(16Q24.3) MUTATED	71	42	7
DEL PEAK 30(16Q24.3) WILD-TYPE	98	95	23

Figure S138. Get High-res Image Gene #52: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0051

Table S139. Gene #53: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 31(17P13.3) MUTATED	59	57	19
DEL PEAK 31(17P13.3) WILD-TYPE	70	87	74

Figure S139. Get High-res Image Gene #53: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.092

Table S140. Gene #53: 'del_17p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 31(17P13.3) MUTATED	44	33	28	30
DEL PEAK 31(17P13.3) WILD-TYPE	63	72	68	28

Figure S140. Get High-res Image Gene #53: 'del_17p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.1

Table S141. Gene #54: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	139	126
DEL PEAK 32(19P13.3) MUTATED	39	31	34
DEL PEAK 32(19P13.3) WILD-TYPE	62	108	92

Figure S141. Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.023

Table S142. Gene #54: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	58	26	38
DEL PEAK 32(19P13.3) MUTATED	15	12	16	9
DEL PEAK 32(19P13.3) WILD-TYPE	32	46	10	29

Figure S142. Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.01

Table S143. Gene #54: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 32(19P13.3) MUTATED	55	22	27
DEL PEAK 32(19P13.3) WILD-TYPE	82	82	98

Figure S143. Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.013

Table S144. Gene #54: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 32(19P13.3) MUTATED	37	21	20	26
DEL PEAK 32(19P13.3) WILD-TYPE	70	84	76	32

Figure S144. Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'METHLYATION_CNMF'

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

Table S145. Gene #55: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	144	93
DEL PEAK 33(XP21.1) MUTATED	47	16	24
DEL PEAK 33(XP21.1) WILD-TYPE	82	128	69

Figure S145. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'RPPA_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.17

Table S146. Gene #55: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	58	26	38
DEL PEAK 33(XP21.1) MUTATED	4	17	7	8
DEL PEAK 33(XP21.1) WILD-TYPE	43	41	19	30

Figure S146. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.00463 (Fisher's exact test), Q value = 0.036

Table S147. Gene #55: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	104	125
DEL PEAK 33(XP21.1) MUTATED	39	13	35
DEL PEAK 33(XP21.1) WILD-TYPE	98	91	90

Figure S147. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00219 (Fisher's exact test), Q value = 0.022

Table S148. Gene #55: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	105	96	58
DEL PEAK 33(XP21.1) MUTATED	36	13	26	12
DEL PEAK 33(XP21.1) WILD-TYPE	71	92	70	46

Figure S148. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.011

Table S149. Gene #55: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	102	79	114	8
DEL PEAK 33(XP21.1) MUTATED	7	16	15	41	4
DEL PEAK 33(XP21.1) WILD-TYPE	40	86	64	73	4

Figure S149. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.048 (Fisher's exact test), Q value = 0.18

Table S150. Gene #55: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	147	74	38
DEL PEAK 33(XP21.1) MUTATED	23	43	13	4
DEL PEAK 33(XP21.1) WILD-TYPE	68	104	61	34

Figure S150. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.012

Table S151. Gene #55: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	105	139
DEL PEAK 33(XP21.1) MUTATED	17	15	46
DEL PEAK 33(XP21.1) WILD-TYPE	75	90	93

Figure S151. Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_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/SKCM-TM/15098585/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SKCM-TM/15111349/SKCM-TM.transferedmergedcluster.txt
Number of patients = 366
Number of significantly focal cnvs = 55
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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