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

Kidney Renal Clear Cell Carcinoma (Primary solid tumor)

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/C1TH8KQ5

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 30 focal events and 12 molecular subtypes across 528 patients, 221 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q24.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_1q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_3q26.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_4q32.1 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_5q35.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_7q36.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_8q24.22 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_10p14 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_xp22.2 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_xp11.4 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_xq11.2 cnv correlated to 'RPPA_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_1p36.23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_1p31.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_1q43 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_3p26.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p22.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_3p12.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_3q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_6q26 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_9p23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_9p21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_14q31.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 30 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 221 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 3p26 3	455 (86%)	73	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	3e-05 (0.000112)	0.0332 (0.0577)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	0.00011 (0.000354)	5e-05 (0.000173)	0.00287 (0.00689)	0.00971 (0.0199)
del 9p21 3	159 (30%)	369	0.00147 (0.00375)	0.0165 (0.0306)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	2e-05 (8e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	0.00129 (0.00339)	0.0126 (0.0247)
del 3p22 2	465 (88%)	63	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	2e-05 (8e-05)	0.0707 (0.11)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	0.00616 (0.0133)	0.0305 (0.0535)
del 9p23	152 (29%)	376	0.00363 (0.00838)	0.0361 (0.0619)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	0.00291 (0.00694)	0.124 (0.179)
amp 8q24 22	79 (15%)	449	0.227 (0.292)	0.105 (0.154)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	2e-05 (8e-05)	0.0242 (0.0435)
del 1p36 23	103 (20%)	425	0.00015 (0.000466)	0.00094 (0.00258)	1e-05 (4.5e-05)	0.0787 (0.122)	2e-05 (8e-05)	3e-05 (0.000112)	8e-05 (0.000264)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	0.00437 (0.01)	0.0209 (0.0378)	0.314 (0.383)
del 1p31 1	77 (15%)	451	0.00182 (0.00452)	0.00624 (0.0134)	1e-05 (4.5e-05)	0.0947 (0.143)	0.00024 (0.000726)	0.00144 (0.0037)	0.0147 (0.028)	2e-05 (8e-05)	1e-05 (4.5e-05)	0.00267 (0.00645)	0.00518 (0.0117)	0.618 (0.684)
del 6q26	151 (29%)	377	0.0153 (0.0286)	0.0985 (0.147)	1e-05 (4.5e-05)	0.0123 (0.0244)	4e-05 (0.000144)	2e-05 (8e-05)	0.00107 (0.0029)	0.00032 (0.000937)	1e-05 (4.5e-05)	0.00015 (0.000466)	0.0293 (0.0522)	0.133 (0.188)
del 6q26	151 (29%)	377	0.0149 (0.0283)	0.0969 (0.145)	1e-05 (4.5e-05)	0.0126 (0.0247)	2e-05 (8e-05)	3e-05 (0.000112)	0.00029 (0.000856)	0.00021 (0.000646)	1e-05 (4.5e-05)	0.00015 (0.000466)	0.0294 (0.0522)	0.133 (0.188)
del 14q31 1	228 (43%)	300	6e-05 (2e-04)	0.0004 (0.00115)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	4e-05 (0.000144)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	0.092 (0.14)	0.952 (0.957)
amp 3q26 32	87 (16%)	441	0.0575 (0.092)	0.119 (0.172)	1e-05 (4.5e-05)	3e-05 (0.000112)	0.00324 (0.00762)	2e-05 (8e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	0.00126 (0.00334)	0.00467 (0.0106)	0.128 (0.183)
del 13q14 2	82 (16%)	446	0.014 (0.0272)	0.0845 (0.129)	1e-05 (4.5e-05)	0.0001 (0.000324)	1e-05 (4.5e-05)	5e-05 (0.000173)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	0.096 (0.144)	0.151 (0.208)
amp 7q36 3	176 (33%)	352	0.452 (0.524)	0.86 (0.887)	1e-05 (4.5e-05)	0.00581 (0.0128)	0.00049 (0.0014)	0.00312 (0.00739)	1e-05 (4.5e-05)	0.00615 (0.0133)	0.00671 (0.0142)	0.0145 (0.0278)	0.148 (0.204)	0.787 (0.829)
del 4q34 3	78 (15%)	450	0.238 (0.302)	0.493 (0.563)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	0.0399 (0.0671)	0.00547 (0.0122)	0.00014 (0.000446)	1e-05 (4.5e-05)	0.154 (0.211)	0.00855 (0.0177)	0.18 (0.239)	0.0168 (0.0311)
del 8p23 2	154 (29%)	374	0.504 (0.572)	0.245 (0.308)	1e-05 (4.5e-05)	0.0405 (0.0676)	0.0055 (0.0122)	0.0108 (0.0218)	0.00143 (0.0037)	6e-05 (2e-04)	0.00111 (0.00298)	0.00094 (0.00258)	0.14 (0.195)	0.339 (0.407)
del 1q43	42 (8%)	486	0.0105 (0.0213)	0.0114 (0.0227)	5e-05 (0.000173)	0.356 (0.424)	0.0198 (0.0361)	0.064 (0.101)	0.0056 (0.0124)	4e-05 (0.000144)	0.0998 (0.148)	0.016 (0.0299)	0.293 (0.36)	0.824 (0.857)
del 3p14 1	373 (71%)	155	0.00334 (0.00781)	0.0104 (0.0211)	1e-05 (4.5e-05)	0.00613 (0.0133)	0.0911 (0.139)	0.0556 (0.0893)	1e-05 (4.5e-05)	1e-05 (4.5e-05)	0.0927 (0.14)	0.00702 (0.0148)	0.335 (0.403)	0.88 (0.898)
del 10q23 31	96 (18%)	432	0.44 (0.511)	0.543 (0.607)	1e-05 (4.5e-05)	0.00132 (0.00344)	0.915 (0.928)	0.00665 (0.0142)	0.0473 (0.0777)	0.00028 (0.00084)	0.0143 (0.0276)	2e-05 (8e-05)	0.802 (0.837)	0.436 (0.508)
amp 1q32 1	62 (12%)	466	0.408 (0.478)	0.901 (0.916)	1e-05 (4.5e-05)	0.0403 (0.0675)	0.0648 (0.102)	0.0503 (0.0816)	1e-05 (4.5e-05)	0.00173 (0.00432)	1e-05 (4.5e-05)	0.00064 (0.00181)	0.278 (0.342)	0.749 (0.805)
amp 5q35 1	332 (63%)	196	0.0635 (0.101)	0.0484 (0.0791)	0.00035 (0.00102)	0.335 (0.403)	0.0398 (0.0671)	0.00945 (0.0194)	0.00105 (0.00286)	5e-05 (0.000173)	0.129 (0.184)	0.407 (0.478)	0.62 (0.684)	0.741 (0.799)
amp xp11 4	33 (6%)	495	0.845 (0.877)	0.8 (0.837)	0.00207 (0.0051)	0.116 (0.168)	0.00069 (0.00194)	0.00211 (0.00517)	0.0301 (0.0532)	0.00029 (0.000856)	0.0487 (0.0793)	0.246 (0.308)	0.792 (0.831)	1 (1.00)
del 3p12 2	305 (58%)	223	0.0399 (0.0671)	0.0654 (0.102)	1e-05 (4.5e-05)	0.0192 (0.0354)	0.349 (0.416)	0.562 (0.626)	0.00085 (0.00237)	2e-05 (8e-05)	0.258 (0.32)	0.0455 (0.0752)	0.524 (0.59)	0.737 (0.796)
amp 1q24 1	62 (12%)	466	0.26 (0.321)	0.787 (0.829)	1e-05 (4.5e-05)	0.147 (0.203)	0.166 (0.223)	0.135 (0.189)	1e-05 (4.5e-05)	0.00339 (0.00787)	3e-05 (0.000112)	0.00714 (0.0149)	0.584 (0.649)	0.925 (0.935)
amp 10p14	20 (4%)	508	0.19 (0.248)	0.775 (0.821)	3e-05 (0.000112)	0.18 (0.238)	0.328 (0.397)	0.203 (0.262)	0.00221 (0.00538)	4e-05 (0.000144)	0.0321 (0.0561)	0.0349 (0.0601)	0.863 (0.887)	0.37 (0.438)
amp xp22 2	31 (6%)	497	1 (1.00)	0.522 (0.589)	0.00836 (0.0174)	0.236 (0.302)	0.00114 (0.00304)	0.0152 (0.0286)	0.0553 (0.0893)	0.00457 (0.0104)	0.0371 (0.0633)	0.348 (0.416)	0.943 (0.951)	0.879 (0.898)
del 2q37 3	50 (9%)	478	0.00168 (0.00423)	0.00023 (0.000702)	0.767 (0.817)	0.621 (0.684)	0.241 (0.305)	0.114 (0.166)	9e-05 (0.000295)	6e-05 (2e-04)	0.0123 (0.0244)	0.0675 (0.105)	0.253 (0.316)	0.134 (0.188)
amp 4q32 1	16 (3%)	512	0.19 (0.248)	0.775 (0.821)	0.238 (0.302)	0.707 (0.769)	0.632 (0.693)	0.219 (0.282)	0.0201 (0.0366)	0.0127 (0.0247)	0.00154 (0.0039)	0.102 (0.15)	0.235 (0.302)	0.495 (0.564)
del 3q11 2	161 (30%)	367	0.186 (0.244)	0.165 (0.223)	1e-05 (4.5e-05)	0.0408 (0.0677)	0.866 (0.888)	0.471 (0.544)	0.517 (0.586)	6e-05 (2e-04)	0.539 (0.605)	0.0615 (0.0979)	0.752 (0.805)	0.76 (0.812)
amp xq11 2	29 (5%)	499	0.172 (0.229)	0.163 (0.222)	0.164 (0.222)	0.255 (0.318)	0.171 (0.229)	0.0282 (0.0506)	0.195 (0.253)	0.309 (0.378)	0.145 (0.202)	0.424 (0.496)	0.393 (0.464)	0.853 (0.883)
amp xq28	37 (7%)	491	0.489 (0.561)	0.7 (0.763)	0.164 (0.222)	0.636 (0.696)	0.184 (0.242)	0.107 (0.156)	0.0792 (0.122)	0.0341 (0.0591)	0.105 (0.154)	0.326 (0.397)	0.73 (0.791)	0.487 (0.561)

'amp_1q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S1. Gene #1: 'amp_1q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
AMP PEAK 1(1Q24.1) MUTATED	12	3	47
AMP PEAK 1(1Q24.1) WILD-TYPE	226	132	108

Figure S1. Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q24.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S2. Gene #1: 'amp_1q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
AMP PEAK 1(1Q24.1) MUTATED	3	19	38
AMP PEAK 1(1Q24.1) WILD-TYPE	108	202	155

Figure S2. Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00339 (Fisher's exact test), Q value = 0.0079

Table S3. Gene #1: 'amp_1q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 1(1Q24.1) MUTATED	7	3	18	25	7	0
AMP PEAK 1(1Q24.1) WILD-TYPE	110	30	165	107	28	25

Figure S3. Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q24.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S4. Gene #1: 'amp_1q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
AMP PEAK 1(1Q24.1) MUTATED	4	19	37
AMP PEAK 1(1Q24.1) WILD-TYPE	120	185	145

Figure S4. Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00714 (Fisher's exact test), Q value = 0.015

Table S5. Gene #1: 'amp_1q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
AMP PEAK 1(1Q24.1) MUTATED	15	20	15	10
AMP PEAK 1(1Q24.1) WILD-TYPE	129	114	180	27

Figure S5. Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S6. Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
AMP PEAK 2(1Q32.1) MUTATED	9	3	50
AMP PEAK 2(1Q32.1) WILD-TYPE	229	132	105

Figure S6. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'METHLYATION_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.067

Table S7. Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
AMP PEAK 2(1Q32.1) MUTATED	6	11	12
AMP PEAK 2(1Q32.1) WILD-TYPE	122	65	98

Figure S7. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S8. Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
AMP PEAK 2(1Q32.1) MUTATED	2	19	39
AMP PEAK 2(1Q32.1) WILD-TYPE	109	202	154

Figure S8. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00173 (Fisher's exact test), Q value = 0.0043

Table S9. Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 2(1Q32.1) MUTATED	7	2	18	26	7	0
AMP PEAK 2(1Q32.1) WILD-TYPE	110	31	165	106	28	25

Figure S9. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S10. Gene #2: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
AMP PEAK 2(1Q32.1) MUTATED	4	18	38
AMP PEAK 2(1Q32.1) WILD-TYPE	120	186	144

Figure S10. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0018

Table S11. Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
AMP PEAK 2(1Q32.1) MUTATED	12	20	16	12
AMP PEAK 2(1Q32.1) WILD-TYPE	132	114	179	25

Figure S11. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S12. Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
AMP PEAK 3(3Q26.32) MUTATED	14	19	54
AMP PEAK 3(3Q26.32) WILD-TYPE	224	116	101

Figure S12. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.32' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S13. Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
AMP PEAK 3(3Q26.32) MUTATED	7	14	30
AMP PEAK 3(3Q26.32) WILD-TYPE	121	62	80

Figure S13. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.32' versus 'RPPA_CNMF'

P value = 0.00324 (Fisher's exact test), Q value = 0.0076

Table S14. Gene #3: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
AMP PEAK 3(3Q26.32) MUTATED	11	18	15	21	9	4
AMP PEAK 3(3Q26.32) WILD-TYPE	97	44	60	59	70	39

Figure S14. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.32' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S15. Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
AMP PEAK 3(3Q26.32) MUTATED	14	22	42
AMP PEAK 3(3Q26.32) WILD-TYPE	107	174	88

Figure S15. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S16. Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
AMP PEAK 3(3Q26.32) MUTATED	14	18	55
AMP PEAK 3(3Q26.32) WILD-TYPE	97	203	138

Figure S16. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S17. Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 3(3Q26.32) MUTATED	14	4	14	43	8	4
AMP PEAK 3(3Q26.32) WILD-TYPE	103	29	169	89	27	21

Figure S17. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S18. Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
AMP PEAK 3(3Q26.32) MUTATED	13	16	55
AMP PEAK 3(3Q26.32) WILD-TYPE	111	188	127

Figure S18. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0033

Table S19. Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
AMP PEAK 3(3Q26.32) MUTATED	29	32	17	6
AMP PEAK 3(3Q26.32) WILD-TYPE	115	102	178	31

Figure S19. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00467 (Fisher's exact test), Q value = 0.011

Table S20. Gene #3: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	21	48	35
AMP PEAK 3(3Q26.32) MUTATED	3	1	3	11
AMP PEAK 3(3Q26.32) WILD-TYPE	35	20	45	24

Figure S20. Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4q32.1' versus 'MRNASEQ_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.037

Table S21. Gene #4: 'amp_4q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
AMP PEAK 4(4Q32.1) MUTATED	7	2	6
AMP PEAK 4(4Q32.1) WILD-TYPE	104	219	187

Figure S21. Get High-res Image Gene #4: 'amp_4q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.025

Table S22. Gene #4: 'amp_4q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 4(4Q32.1) MUTATED	4	0	2	5	0	4
AMP PEAK 4(4Q32.1) WILD-TYPE	113	33	181	127	35	21

Figure S22. Get High-res Image Gene #4: 'amp_4q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q32.1' versus 'MIRSEQ_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0039

Table S23. Gene #4: 'amp_4q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
AMP PEAK 4(4Q32.1) MUTATED	3	1	12
AMP PEAK 4(4Q32.1) WILD-TYPE	121	203	170

Figure S23. Get High-res Image Gene #4: 'amp_4q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0484 (Fisher's exact test), Q value = 0.079

Table S24. Gene #5: 'amp_5q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
AMP PEAK 5(5Q35.1) MUTATED	8	5	0	9	7	5	3
AMP PEAK 5(5Q35.1) WILD-TYPE	3	7	4	2	6	4	7

Figure S24. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5q35.1' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.001

Table S25. Gene #5: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
AMP PEAK 5(5Q35.1) MUTATED	162	65	105
AMP PEAK 5(5Q35.1) WILD-TYPE	76	70	50

Figure S25. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5q35.1' versus 'RPPA_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.067

Table S26. Gene #5: 'amp_5q35.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
AMP PEAK 5(5Q35.1) MUTATED	73	35	58	48	44	30
AMP PEAK 5(5Q35.1) WILD-TYPE	35	27	17	32	35	13

Figure S26. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00945 (Fisher's exact test), Q value = 0.019

Table S27. Gene #5: 'amp_5q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
AMP PEAK 5(5Q35.1) MUTATED	88	129	71
AMP PEAK 5(5Q35.1) WILD-TYPE	33	67	59

Figure S27. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_5q35.1' versus 'MRNASEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0029

Table S28. Gene #5: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
AMP PEAK 5(5Q35.1) MUTATED	53	149	128
AMP PEAK 5(5Q35.1) WILD-TYPE	58	72	65

Figure S28. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S29. Gene #5: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 5(5Q35.1) MUTATED	79	15	121	84	26	5
AMP PEAK 5(5Q35.1) WILD-TYPE	38	18	62	48	9	20

Figure S29. Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q36.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S30. Gene #6: 'amp_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
AMP PEAK 6(7Q36.3) MUTATED	39	48	89
AMP PEAK 6(7Q36.3) WILD-TYPE	199	87	66

Figure S30. Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q36.3' versus 'METHLYATION_CNMF'

P value = 0.00581 (Fisher's exact test), Q value = 0.013

Table S31. Gene #6: 'amp_7q36.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
AMP PEAK 6(7Q36.3) MUTATED	32	16	45
AMP PEAK 6(7Q36.3) WILD-TYPE	96	60	65

Figure S31. Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q36.3' versus 'RPPA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0014

Table S32. Gene #6: 'amp_7q36.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
AMP PEAK 6(7Q36.3) MUTATED	23	30	31	35	23	10
AMP PEAK 6(7Q36.3) WILD-TYPE	85	32	44	45	56	33

Figure S32. Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7q36.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00312 (Fisher's exact test), Q value = 0.0074

Table S33. Gene #6: 'amp_7q36.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
AMP PEAK 6(7Q36.3) MUTATED	40	53	59
AMP PEAK 6(7Q36.3) WILD-TYPE	81	143	71

Figure S33. Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7q36.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S34. Gene #6: 'amp_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
AMP PEAK 6(7Q36.3) MUTATED	33	53	88
AMP PEAK 6(7Q36.3) WILD-TYPE	78	168	105

Figure S34. Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00615 (Fisher's exact test), Q value = 0.013

Table S35. Gene #6: 'amp_7q36.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 6(7Q36.3) MUTATED	39	11	45	60	13	6
AMP PEAK 6(7Q36.3) WILD-TYPE	78	22	138	72	22	19

Figure S35. Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q36.3' versus 'MIRSEQ_CNMF'

P value = 0.00671 (Fisher's exact test), Q value = 0.014

Table S36. Gene #6: 'amp_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
AMP PEAK 6(7Q36.3) MUTATED	37	58	78
AMP PEAK 6(7Q36.3) WILD-TYPE	87	146	104

Figure S36. Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.028

Table S37. Gene #6: 'amp_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
AMP PEAK 6(7Q36.3) MUTATED	48	57	52	16
AMP PEAK 6(7Q36.3) WILD-TYPE	96	77	143	21

Figure S37. Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S38. Gene #7: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
AMP PEAK 7(8Q24.22) MUTATED	6	17	56
AMP PEAK 7(8Q24.22) WILD-TYPE	232	118	99

Figure S38. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S39. Gene #7: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
AMP PEAK 7(8Q24.22) MUTATED	6	14	33
AMP PEAK 7(8Q24.22) WILD-TYPE	122	62	77

Figure S39. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.22' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S40. Gene #7: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
AMP PEAK 7(8Q24.22) MUTATED	5	24	15	15	10	2
AMP PEAK 7(8Q24.22) WILD-TYPE	103	38	60	65	69	41

Figure S40. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.22' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S41. Gene #7: 'amp_8q24.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
AMP PEAK 7(8Q24.22) MUTATED	15	18	38
AMP PEAK 7(8Q24.22) WILD-TYPE	106	178	92

Figure S41. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S42. Gene #7: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
AMP PEAK 7(8Q24.22) MUTATED	8	9	61
AMP PEAK 7(8Q24.22) WILD-TYPE	103	212	132

Figure S42. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S43. Gene #7: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 7(8Q24.22) MUTATED	9	2	8	54	4	1
AMP PEAK 7(8Q24.22) WILD-TYPE	108	31	175	78	31	24

Figure S43. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S44. Gene #7: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
AMP PEAK 7(8Q24.22) MUTATED	13	11	53
AMP PEAK 7(8Q24.22) WILD-TYPE	111	193	129

Figure S44. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S45. Gene #7: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
AMP PEAK 7(8Q24.22) MUTATED	29	24	11	13
AMP PEAK 7(8Q24.22) WILD-TYPE	115	110	184	24

Figure S45. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S46. Gene #7: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	21	48	35
AMP PEAK 7(8Q24.22) MUTATED	3	1	1	14
AMP PEAK 7(8Q24.22) WILD-TYPE	35	20	47	21

Figure S46. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.043

Table S47. Gene #7: 'amp_8q24.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	56	47
AMP PEAK 7(8Q24.22) MUTATED	3	13	3
AMP PEAK 7(8Q24.22) WILD-TYPE	36	43	44

Figure S47. Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p14' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S48. Gene #8: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
AMP PEAK 8(10P14) MUTATED	1	5	14
AMP PEAK 8(10P14) WILD-TYPE	237	130	141

Figure S48. Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p14' versus 'MRNASEQ_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.0054

Table S49. Gene #8: 'amp_10p14' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
AMP PEAK 8(10P14) MUTATED	4	2	14
AMP PEAK 8(10P14) WILD-TYPE	107	219	179

Figure S49. Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S50. Gene #8: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 8(10P14) MUTATED	2	2	0	14	2	0
AMP PEAK 8(10P14) WILD-TYPE	115	31	183	118	33	25

Figure S50. Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p14' versus 'MIRSEQ_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.056

Table S51. Gene #8: 'amp_10p14' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
AMP PEAK 8(10P14) MUTATED	5	3	12
AMP PEAK 8(10P14) WILD-TYPE	119	201	170

Figure S51. Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10p14' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0349 (Fisher's exact test), Q value = 0.06

Table S52. Gene #8: 'amp_10p14' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
AMP PEAK 8(10P14) MUTATED	7	6	3	4
AMP PEAK 8(10P14) WILD-TYPE	137	128	192	33

Figure S52. Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xp22.2' versus 'CN_CNMF'

P value = 0.00836 (Fisher's exact test), Q value = 0.017

Table S53. Gene #9: 'amp_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
AMP PEAK 9(XP22.2) MUTATED	8	6	17
AMP PEAK 9(XP22.2) WILD-TYPE	230	129	138

Figure S53. Get High-res Image Gene #9: 'amp_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp22.2' versus 'RPPA_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.003

Table S54. Gene #9: 'amp_xp22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
AMP PEAK 9(XP22.2) MUTATED	0	4	7	10	3	1
AMP PEAK 9(XP22.2) WILD-TYPE	108	58	68	70	76	42

Figure S54. Get High-res Image Gene #9: 'amp_xp22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_xp22.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.029

Table S55. Gene #9: 'amp_xp22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
AMP PEAK 9(XP22.2) MUTATED	4	7	14
AMP PEAK 9(XP22.2) WILD-TYPE	117	189	116

Figure S55. Get High-res Image Gene #9: 'amp_xp22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00457 (Fisher's exact test), Q value = 0.01

Table S56. Gene #9: 'amp_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 9(XP22.2) MUTATED	3	4	6	16	2	0
AMP PEAK 9(XP22.2) WILD-TYPE	114	29	177	116	33	25

Figure S56. Get High-res Image Gene #9: 'amp_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp22.2' versus 'MIRSEQ_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.063

Table S57. Gene #9: 'amp_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
AMP PEAK 9(XP22.2) MUTATED	5	8	18
AMP PEAK 9(XP22.2) WILD-TYPE	119	196	164

Figure S57. Get High-res Image Gene #9: 'amp_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xp11.4' versus 'CN_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.0051

Table S58. Gene #10: 'amp_xp11.4' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
AMP PEAK 10(XP11.4) MUTATED	8	6	19
AMP PEAK 10(XP11.4) WILD-TYPE	230	129	136

Figure S58. Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.4' versus 'RPPA_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0019

Table S59. Gene #10: 'amp_xp11.4' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
AMP PEAK 10(XP11.4) MUTATED	0	5	5	10	5	0
AMP PEAK 10(XP11.4) WILD-TYPE	108	57	70	70	74	43

Figure S59. Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_xp11.4' versus 'RPPA_CHIERARCHICAL'

P value = 0.00211 (Fisher's exact test), Q value = 0.0052

Table S60. Gene #10: 'amp_xp11.4' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
AMP PEAK 10(XP11.4) MUTATED	2	8	15
AMP PEAK 10(XP11.4) WILD-TYPE	119	188	115

Figure S60. Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_xp11.4' versus 'MRNASEQ_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.053

Table S61. Gene #10: 'amp_xp11.4' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
AMP PEAK 10(XP11.4) MUTATED	9	7	17
AMP PEAK 10(XP11.4) WILD-TYPE	102	214	176

Figure S61. Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00086

Table S62. Gene #10: 'amp_xp11.4' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 10(XP11.4) MUTATED	2	4	7	19	1	0
AMP PEAK 10(XP11.4) WILD-TYPE	115	29	176	113	34	25

Figure S62. Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.4' versus 'MIRSEQ_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.079

Table S63. Gene #10: 'amp_xp11.4' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
AMP PEAK 10(XP11.4) MUTATED	6	8	18
AMP PEAK 10(XP11.4) WILD-TYPE	118	196	164

Figure S63. Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xq11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.051

Table S64. Gene #11: 'amp_xq11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
AMP PEAK 11(XQ11.2) MUTATED	2	9	12
AMP PEAK 11(XQ11.2) WILD-TYPE	119	187	118

Figure S64. Get High-res Image Gene #11: 'amp_xq11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.059

Table S65. Gene #12: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
AMP PEAK 12(XQ28) MUTATED	5	2	9	14	6	0
AMP PEAK 12(XQ28) WILD-TYPE	112	31	174	118	29	25

Figure S65. Get High-res Image Gene #12: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00047

Table S66. Gene #13: 'del_1p36.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 1(1P36.23) MUTATED	2	8	8
DEL PEAK 1(1P36.23) WILD-TYPE	31	16	5

Figure S66. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.23' versus 'MRNA_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0026

Table S67. Gene #13: 'del_1p36.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 1(1P36.23) MUTATED	0	2	2	5	1	1	7
DEL PEAK 1(1P36.23) WILD-TYPE	11	10	2	6	12	8	3

Figure S67. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S68. Gene #13: 'del_1p36.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 1(1P36.23) MUTATED	13	37	53
DEL PEAK 1(1P36.23) WILD-TYPE	225	98	102

Figure S68. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.23' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S69. Gene #13: 'del_1p36.23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
DEL PEAK 1(1P36.23) MUTATED	10	20	20	26	7	6
DEL PEAK 1(1P36.23) WILD-TYPE	98	42	55	54	72	37

Figure S69. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.23' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S70. Gene #13: 'del_1p36.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
DEL PEAK 1(1P36.23) MUTATED	26	22	41
DEL PEAK 1(1P36.23) WILD-TYPE	95	174	89

Figure S70. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.23' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00026

Table S71. Gene #13: 'del_1p36.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 1(1P36.23) MUTATED	21	26	56
DEL PEAK 1(1P36.23) WILD-TYPE	90	195	137

Figure S71. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S72. Gene #13: 'del_1p36.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 1(1P36.23) MUTATED	11	6	23	41	10	12
DEL PEAK 1(1P36.23) WILD-TYPE	106	27	160	91	25	13

Figure S72. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S73. Gene #13: 'del_1p36.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
DEL PEAK 1(1P36.23) MUTATED	19	23	61
DEL PEAK 1(1P36.23) WILD-TYPE	105	181	121

Figure S73. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00437 (Fisher's exact test), Q value = 0.01

Table S74. Gene #13: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 1(1P36.23) MUTATED	32	34	25	12
DEL PEAK 1(1P36.23) WILD-TYPE	112	100	170	25

Figure S74. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.038

Table S75. Gene #13: 'del_1p36.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	21	48	35
DEL PEAK 1(1P36.23) MUTATED	8	3	3	11
DEL PEAK 1(1P36.23) WILD-TYPE	30	18	45	24

Figure S75. Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p31.1' versus 'MRNA_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.0045

Table S76. Gene #14: 'del_1p31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 2(1P31.1) MUTATED	2	5	7
DEL PEAK 2(1P31.1) WILD-TYPE	31	19	6

Figure S76. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00624 (Fisher's exact test), Q value = 0.013

Table S77. Gene #14: 'del_1p31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 2(1P31.1) MUTATED	0	3	2	1	1	1	6
DEL PEAK 2(1P31.1) WILD-TYPE	11	9	2	10	12	8	4

Figure S77. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S78. Gene #14: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 2(1P31.1) MUTATED	8	29	40
DEL PEAK 2(1P31.1) WILD-TYPE	230	106	115

Figure S78. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p31.1' versus 'RPPA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00073

Table S79. Gene #14: 'del_1p31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
DEL PEAK 2(1P31.1) MUTATED	9	16	12	21	4	5
DEL PEAK 2(1P31.1) WILD-TYPE	99	46	63	59	75	38

Figure S79. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p31.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.0037

Table S80. Gene #14: 'del_1p31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
DEL PEAK 2(1P31.1) MUTATED	20	17	30
DEL PEAK 2(1P31.1) WILD-TYPE	101	179	100

Figure S80. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p31.1' versus 'MRNASEQ_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.028

Table S81. Gene #14: 'del_1p31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 2(1P31.1) MUTATED	20	21	36
DEL PEAK 2(1P31.1) WILD-TYPE	91	200	157

Figure S81. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S82. Gene #14: 'del_1p31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 2(1P31.1) MUTATED	11	6	16	28	4	12
DEL PEAK 2(1P31.1) WILD-TYPE	106	27	167	104	31	13

Figure S82. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S83. Gene #14: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
DEL PEAK 2(1P31.1) MUTATED	10	20	47
DEL PEAK 2(1P31.1) WILD-TYPE	114	184	135

Figure S83. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.0065

Table S84. Gene #14: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 2(1P31.1) MUTATED	17	33	20	7
DEL PEAK 2(1P31.1) WILD-TYPE	127	101	175	30

Figure S84. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00518 (Fisher's exact test), Q value = 0.012

Table S85. Gene #14: 'del_1p31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	21	48	35
DEL PEAK 2(1P31.1) MUTATED	6	0	2	9
DEL PEAK 2(1P31.1) WILD-TYPE	32	21	46	26

Figure S85. Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1q43' versus 'MRNA_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.021

Table S86. Gene #15: 'del_1q43' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 3(1Q43) MUTATED	2	1	5
DEL PEAK 3(1Q43) WILD-TYPE	31	23	8

Figure S86. Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1q43' versus 'MRNA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.023

Table S87. Gene #15: 'del_1q43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 3(1Q43) MUTATED	0	1	0	0	1	1	5
DEL PEAK 3(1Q43) WILD-TYPE	11	11	4	11	12	8	5

Figure S87. Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1q43' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S88. Gene #15: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 3(1Q43) MUTATED	7	22	13
DEL PEAK 3(1Q43) WILD-TYPE	231	113	142

Figure S88. Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q43' versus 'RPPA_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.036

Table S89. Gene #15: 'del_1q43' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
DEL PEAK 3(1Q43) MUTATED	9	5	4	13	1	3
DEL PEAK 3(1Q43) WILD-TYPE	99	57	71	67	78	40

Figure S89. Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1q43' versus 'MRNASEQ_CNMF'

P value = 0.0056 (Fisher's exact test), Q value = 0.012

Table S90. Gene #15: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 3(1Q43) MUTATED	17	16	9
DEL PEAK 3(1Q43) WILD-TYPE	94	205	184

Figure S90. Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S91. Gene #15: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 3(1Q43) MUTATED	6	1	13	9	2	11
DEL PEAK 3(1Q43) WILD-TYPE	111	32	170	123	33	14

Figure S91. Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1q43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.03

Table S92. Gene #15: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 3(1Q43) MUTATED	10	19	13	0
DEL PEAK 3(1Q43) WILD-TYPE	134	115	182	37

Figure S92. Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.0042

Table S93. Gene #16: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 4(2Q37.3) MUTATED	1	4	6
DEL PEAK 4(2Q37.3) WILD-TYPE	32	20	7

Figure S93. Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 7e-04

Table S94. Gene #16: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 4(2Q37.3) MUTATED	0	4	0	0	1	0	6
DEL PEAK 4(2Q37.3) WILD-TYPE	11	8	4	11	12	9	4

Figure S94. Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00029

Table S95. Gene #16: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 4(2Q37.3) MUTATED	21	9	19
DEL PEAK 4(2Q37.3) WILD-TYPE	90	212	174

Figure S95. Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S96. Gene #16: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 4(2Q37.3) MUTATED	13	1	7	18	1	9
DEL PEAK 4(2Q37.3) WILD-TYPE	104	32	176	114	34	16

Figure S96. Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.024

Table S97. Gene #16: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
DEL PEAK 4(2Q37.3) MUTATED	11	11	26
DEL PEAK 4(2Q37.3) WILD-TYPE	113	193	156

Figure S97. Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S98. Gene #17: 'del_3p26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 5(3P26.3) MUTATED	32	22	3
DEL PEAK 5(3P26.3) WILD-TYPE	1	2	10

Figure S98. Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p26.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S99. Gene #17: 'del_3p26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 5(3P26.3) MUTATED	11	11	1	11	12	9	2
DEL PEAK 5(3P26.3) WILD-TYPE	0	1	3	0	1	0	8

Figure S99. Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S100. Gene #17: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 5(3P26.3) MUTATED	236	69	150
DEL PEAK 5(3P26.3) WILD-TYPE	2	66	5

Figure S100. Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S101. Gene #17: 'del_3p26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 5(3P26.3) MUTATED	118	50	103
DEL PEAK 5(3P26.3) WILD-TYPE	10	26	7

Figure S101. Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p26.3' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S102. Gene #17: 'del_3p26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
DEL PEAK 5(3P26.3) MUTATED	106	54	67	60	64	39
DEL PEAK 5(3P26.3) WILD-TYPE	2	8	8	20	15	4

Figure S102. Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 0.058

Table S103. Gene #17: 'del_3p26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
DEL PEAK 5(3P26.3) MUTATED	112	172	106
DEL PEAK 5(3P26.3) WILD-TYPE	9	24	24

Figure S103. Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S104. Gene #17: 'del_3p26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 5(3P26.3) MUTATED	70	211	171
DEL PEAK 5(3P26.3) WILD-TYPE	41	10	22

Figure S104. Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S105. Gene #17: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 5(3P26.3) MUTATED	108	20	175	114	33	2
DEL PEAK 5(3P26.3) WILD-TYPE	9	13	8	18	2	23

Figure S105. Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.3' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00035

Table S106. Gene #17: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
DEL PEAK 5(3P26.3) MUTATED	103	191	144
DEL PEAK 5(3P26.3) WILD-TYPE	21	13	38

Figure S106. Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S107. Gene #17: 'del_3p26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 5(3P26.3) MUTATED	112	108	184	34
DEL PEAK 5(3P26.3) WILD-TYPE	32	26	11	3

Figure S107. Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.0069

Table S108. Gene #17: 'del_3p26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	21	48	35
DEL PEAK 5(3P26.3) MUTATED	27	14	46	28
DEL PEAK 5(3P26.3) WILD-TYPE	11	7	2	7

Figure S108. Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00971 (Fisher's exact test), Q value = 0.02

Table S109. Gene #17: 'del_3p26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	56	47
DEL PEAK 5(3P26.3) MUTATED	27	44	44
DEL PEAK 5(3P26.3) WILD-TYPE	12	12	3

Figure S109. Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p22.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S110. Gene #18: 'del_3p22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 6(3P22.2) MUTATED	32	22	3
DEL PEAK 6(3P22.2) WILD-TYPE	1	2	10

Figure S110. Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p22.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S111. Gene #18: 'del_3p22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 6(3P22.2) MUTATED	11	11	1	11	12	9	2
DEL PEAK 6(3P22.2) WILD-TYPE	0	1	3	0	1	0	8

Figure S111. Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S112. Gene #18: 'del_3p22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 6(3P22.2) MUTATED	238	75	152
DEL PEAK 6(3P22.2) WILD-TYPE	0	60	3

Figure S112. Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S113. Gene #18: 'del_3p22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 6(3P22.2) MUTATED	119	52	106
DEL PEAK 6(3P22.2) WILD-TYPE	9	24	4

Figure S113. Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p22.2' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S114. Gene #18: 'del_3p22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
DEL PEAK 6(3P22.2) MUTATED	107	59	66	63	65	40
DEL PEAK 6(3P22.2) WILD-TYPE	1	3	9	17	14	3

Figure S114. Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S115. Gene #18: 'del_3p22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 6(3P22.2) MUTATED	70	216	176
DEL PEAK 6(3P22.2) WILD-TYPE	41	5	17

Figure S115. Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S116. Gene #18: 'del_3p22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 6(3P22.2) MUTATED	110	19	179	116	35	3
DEL PEAK 6(3P22.2) WILD-TYPE	7	14	4	16	0	22

Figure S116. Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S117. Gene #18: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
DEL PEAK 6(3P22.2) MUTATED	103	197	148
DEL PEAK 6(3P22.2) WILD-TYPE	21	7	34

Figure S117. Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S118. Gene #18: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 6(3P22.2) MUTATED	114	111	187	36
DEL PEAK 6(3P22.2) WILD-TYPE	30	23	8	1

Figure S118. Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00616 (Fisher's exact test), Q value = 0.013

Table S119. Gene #18: 'del_3p22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	21	48	35
DEL PEAK 6(3P22.2) MUTATED	29	14	46	28
DEL PEAK 6(3P22.2) WILD-TYPE	9	7	2	7

Figure S119. Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.053

Table S120. Gene #18: 'del_3p22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	56	47
DEL PEAK 6(3P22.2) MUTATED	29	44	44
DEL PEAK 6(3P22.2) WILD-TYPE	10	12	3

Figure S120. Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.1' versus 'MRNA_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.0078

Table S121. Gene #19: 'del_3p14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 7(3P14.1) MUTATED	22	19	3
DEL PEAK 7(3P14.1) WILD-TYPE	11	5	10

Figure S121. Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p14.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.021

Table S122. Gene #19: 'del_3p14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 7(3P14.1) MUTATED	8	9	1	10	7	7	2
DEL PEAK 7(3P14.1) WILD-TYPE	3	3	3	1	6	2	8

Figure S122. Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S123. Gene #19: 'del_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 7(3P14.1) MUTATED	199	32	142
DEL PEAK 7(3P14.1) WILD-TYPE	39	103	13

Figure S123. Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p14.1' versus 'METHLYATION_CNMF'

P value = 0.00613 (Fisher's exact test), Q value = 0.013

Table S124. Gene #19: 'del_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 7(3P14.1) MUTATED	98	44	86
DEL PEAK 7(3P14.1) WILD-TYPE	30	32	24

Figure S124. Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S125. Gene #19: 'del_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 7(3P14.1) MUTATED	49	175	147
DEL PEAK 7(3P14.1) WILD-TYPE	62	46	46

Figure S125. Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S126. Gene #19: 'del_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 7(3P14.1) MUTATED	90	14	140	100	25	2
DEL PEAK 7(3P14.1) WILD-TYPE	27	19	43	32	10	23

Figure S126. Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00702 (Fisher's exact test), Q value = 0.015

Table S127. Gene #19: 'del_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 7(3P14.1) MUTATED	89	91	149	31
DEL PEAK 7(3P14.1) WILD-TYPE	55	43	46	6

Figure S127. Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.2' versus 'MRNA_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.067

Table S128. Gene #20: 'del_3p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 8(3P12.2) MUTATED	18	13	2
DEL PEAK 8(3P12.2) WILD-TYPE	15	11	11

Figure S128. Get High-res Image Gene #20: 'del_3p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S129. Gene #20: 'del_3p12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 8(3P12.2) MUTATED	160	22	123
DEL PEAK 8(3P12.2) WILD-TYPE	78	113	32

Figure S129. Get High-res Image Gene #20: 'del_3p12.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.2' versus 'METHLYATION_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.035

Table S130. Gene #20: 'del_3p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 8(3P12.2) MUTATED	82	35	71
DEL PEAK 8(3P12.2) WILD-TYPE	46	41	39

Figure S130. Get High-res Image Gene #20: 'del_3p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.2' versus 'MRNASEQ_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0024

Table S131. Gene #20: 'del_3p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 8(3P12.2) MUTATED	47	134	123
DEL PEAK 8(3P12.2) WILD-TYPE	64	87	70

Figure S131. Get High-res Image Gene #20: 'del_3p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S132. Gene #20: 'del_3p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 8(3P12.2) MUTATED	75	13	109	84	21	2
DEL PEAK 8(3P12.2) WILD-TYPE	42	20	74	48	14	23

Figure S132. Get High-res Image Gene #20: 'del_3p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.075

Table S133. Gene #20: 'del_3p12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 8(3P12.2) MUTATED	70	80	118	26
DEL PEAK 8(3P12.2) WILD-TYPE	74	54	77	11

Figure S133. Get High-res Image Gene #20: 'del_3p12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S134. Gene #21: 'del_3q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 9(3Q11.2) MUTATED	83	13	65
DEL PEAK 9(3Q11.2) WILD-TYPE	155	122	90

Figure S134. Get High-res Image Gene #21: 'del_3q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q11.2' versus 'METHLYATION_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.068

Table S135. Gene #21: 'del_3q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 9(3Q11.2) MUTATED	45	15	38
DEL PEAK 9(3Q11.2) WILD-TYPE	83	61	72

Figure S135. Get High-res Image Gene #21: 'del_3q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S136. Gene #21: 'del_3q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 9(3Q11.2) MUTATED	49	6	50	50	5	1
DEL PEAK 9(3Q11.2) WILD-TYPE	68	27	133	82	30	24

Figure S136. Get High-res Image Gene #21: 'del_3q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S137. Gene #22: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 10(4Q34.3) MUTATED	10	17	51
DEL PEAK 10(4Q34.3) WILD-TYPE	228	118	104

Figure S137. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S138. Gene #22: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 10(4Q34.3) MUTATED	10	9	34
DEL PEAK 10(4Q34.3) WILD-TYPE	118	67	76

Figure S138. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.067

Table S139. Gene #22: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
DEL PEAK 10(4Q34.3) MUTATED	16	20	12	10	10	6
DEL PEAK 10(4Q34.3) WILD-TYPE	92	42	63	70	69	37

Figure S139. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00547 (Fisher's exact test), Q value = 0.012

Table S140. Gene #22: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
DEL PEAK 10(4Q34.3) MUTATED	22	21	31
DEL PEAK 10(4Q34.3) WILD-TYPE	99	175	99

Figure S140. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00045

Table S141. Gene #22: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 10(4Q34.3) MUTATED	8	25	45
DEL PEAK 10(4Q34.3) WILD-TYPE	103	196	148

Figure S141. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S142. Gene #22: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 10(4Q34.3) MUTATED	15	1	18	38	6	0
DEL PEAK 10(4Q34.3) WILD-TYPE	102	32	165	94	29	25

Figure S142. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00855 (Fisher's exact test), Q value = 0.018

Table S143. Gene #22: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 10(4Q34.3) MUTATED	23	15	26	13
DEL PEAK 10(4Q34.3) WILD-TYPE	121	119	169	24

Figure S143. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.031

Table S144. Gene #22: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	56	47
DEL PEAK 10(4Q34.3) MUTATED	3	15	4
DEL PEAK 10(4Q34.3) WILD-TYPE	36	41	43

Figure S144. Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.029

Table S145. Gene #23: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 11(6Q26) MUTATED	7	12	8
DEL PEAK 11(6Q26) WILD-TYPE	26	12	5

Figure S145. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S146. Gene #23: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 11(6Q26) MUTATED	37	26	88
DEL PEAK 11(6Q26) WILD-TYPE	201	109	67

Figure S146. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.024

Table S147. Gene #23: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 11(6Q26) MUTATED	27	14	39
DEL PEAK 11(6Q26) WILD-TYPE	101	62	71

Figure S147. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S148. Gene #23: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
DEL PEAK 11(6Q26) MUTATED	35	30	25	23	9	8
DEL PEAK 11(6Q26) WILD-TYPE	73	32	50	57	70	35

Figure S148. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S149. Gene #23: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
DEL PEAK 11(6Q26) MUTATED	39	36	55
DEL PEAK 11(6Q26) WILD-TYPE	82	160	75

Figure S149. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0029

Table S150. Gene #23: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 11(6Q26) MUTATED	22	54	73
DEL PEAK 11(6Q26) WILD-TYPE	89	167	120

Figure S150. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.00094

Table S151. Gene #23: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 11(6Q26) MUTATED	26	6	40	58	10	9
DEL PEAK 11(6Q26) WILD-TYPE	91	27	143	74	25	16

Figure S151. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S152. Gene #23: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
DEL PEAK 11(6Q26) MUTATED	25	43	79
DEL PEAK 11(6Q26) WILD-TYPE	99	161	103

Figure S152. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00047

Table S153. Gene #23: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 11(6Q26) MUTATED	38	50	40	19
DEL PEAK 11(6Q26) WILD-TYPE	106	84	155	18

Figure S153. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.052

Table S154. Gene #23: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	21	48	35
DEL PEAK 11(6Q26) MUTATED	7	2	12	15
DEL PEAK 11(6Q26) WILD-TYPE	31	19	36	20

Figure S154. Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.028

Table S155. Gene #24: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 12(6Q26) MUTATED	7	12	8
DEL PEAK 12(6Q26) WILD-TYPE	26	12	5

Figure S155. Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S156. Gene #24: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 12(6Q26) MUTATED	37	26	88
DEL PEAK 12(6Q26) WILD-TYPE	201	109	67

Figure S156. Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.025

Table S157. Gene #24: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 12(6Q26) MUTATED	27	14	39
DEL PEAK 12(6Q26) WILD-TYPE	101	62	71

Figure S157. Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S158. Gene #24: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
DEL PEAK 12(6Q26) MUTATED	34	31	25	23	9	8
DEL PEAK 12(6Q26) WILD-TYPE	74	31	50	57	70	35

Figure S158. Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S159. Gene #24: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
DEL PEAK 12(6Q26) MUTATED	39	36	55
DEL PEAK 12(6Q26) WILD-TYPE	82	160	75

Figure S159. Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00086

Table S160. Gene #24: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 12(6Q26) MUTATED	21	54	74
DEL PEAK 12(6Q26) WILD-TYPE	90	167	119

Figure S160. Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00065

Table S161. Gene #24: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 12(6Q26) MUTATED	26	6	40	59	9	9
DEL PEAK 12(6Q26) WILD-TYPE	91	27	143	73	26	16

Figure S161. Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S162. Gene #24: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
DEL PEAK 12(6Q26) MUTATED	24	43	80
DEL PEAK 12(6Q26) WILD-TYPE	100	161	102

Figure S162. Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00047

Table S163. Gene #24: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 12(6Q26) MUTATED	38	50	40	19
DEL PEAK 12(6Q26) WILD-TYPE	106	84	155	18

Figure S163. Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.052

Table S164. Gene #24: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	21	48	35
DEL PEAK 12(6Q26) MUTATED	7	2	12	15
DEL PEAK 12(6Q26) WILD-TYPE	31	19	36	20

Figure S164. Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S165. Gene #25: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 13(8P23.2) MUTATED	43	37	74
DEL PEAK 13(8P23.2) WILD-TYPE	195	98	81

Figure S165. Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.068

Table S166. Gene #25: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 13(8P23.2) MUTATED	28	19	40
DEL PEAK 13(8P23.2) WILD-TYPE	100	57	70

Figure S166. Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CNMF'

P value = 0.0055 (Fisher's exact test), Q value = 0.012

Table S167. Gene #25: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
DEL PEAK 13(8P23.2) MUTATED	22	29	26	24	24	8
DEL PEAK 13(8P23.2) WILD-TYPE	86	33	49	56	55	35

Figure S167. Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.022

Table S168. Gene #25: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
DEL PEAK 13(8P23.2) MUTATED	32	49	52
DEL PEAK 13(8P23.2) WILD-TYPE	89	147	78

Figure S168. Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0037

Table S169. Gene #25: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 13(8P23.2) MUTATED	23	56	74
DEL PEAK 13(8P23.2) WILD-TYPE	88	165	119

Figure S169. Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S170. Gene #25: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 13(8P23.2) MUTATED	31	3	48	60	6	5
DEL PEAK 13(8P23.2) WILD-TYPE	86	30	135	72	29	20

Figure S170. Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.003

Table S171. Gene #25: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
DEL PEAK 13(8P23.2) MUTATED	36	44	71
DEL PEAK 13(8P23.2) WILD-TYPE	88	160	111

Figure S171. Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0026

Table S172. Gene #25: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 13(8P23.2) MUTATED	51	39	42	19
DEL PEAK 13(8P23.2) WILD-TYPE	93	95	153	18

Figure S172. Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 0.00363 (Fisher's exact test), Q value = 0.0084

Table S173. Gene #26: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 14(9P23) MUTATED	5	12	1
DEL PEAK 14(9P23) WILD-TYPE	28	12	12

Figure S173. Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.062

Table S174. Gene #26: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 14(9P23) MUTATED	2	7	0	5	1	2	1
DEL PEAK 14(9P23) WILD-TYPE	9	5	4	6	12	7	9

Figure S174. Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S175. Gene #26: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 14(9P23) MUTATED	9	34	109
DEL PEAK 14(9P23) WILD-TYPE	229	101	46

Figure S175. Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S176. Gene #26: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 14(9P23) MUTATED	6	21	68
DEL PEAK 14(9P23) WILD-TYPE	122	55	42

Figure S176. Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S177. Gene #26: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
DEL PEAK 14(9P23) MUTATED	17	38	31	21	19	10
DEL PEAK 14(9P23) WILD-TYPE	91	24	44	59	60	33

Figure S177. Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S178. Gene #26: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
DEL PEAK 14(9P23) MUTATED	34	42	60
DEL PEAK 14(9P23) WILD-TYPE	87	154	70

Figure S178. Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S179. Gene #26: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 14(9P23) MUTATED	16	25	110
DEL PEAK 14(9P23) WILD-TYPE	95	196	83

Figure S179. Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S180. Gene #26: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 14(9P23) MUTATED	32	3	15	84	13	4
DEL PEAK 14(9P23) WILD-TYPE	85	30	168	48	22	21

Figure S180. Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S181. Gene #26: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
DEL PEAK 14(9P23) MUTATED	26	25	96
DEL PEAK 14(9P23) WILD-TYPE	98	179	86

Figure S181. Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S182. Gene #26: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 14(9P23) MUTATED	44	56	23	24
DEL PEAK 14(9P23) WILD-TYPE	100	78	172	13

Figure S182. Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00291 (Fisher's exact test), Q value = 0.0069

Table S183. Gene #26: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	21	48	35
DEL PEAK 14(9P23) MUTATED	8	4	5	16
DEL PEAK 14(9P23) WILD-TYPE	30	17	43	19

Figure S183. Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0038

Table S184. Gene #27: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 15(9P21.3) MUTATED	5	13	1
DEL PEAK 15(9P21.3) WILD-TYPE	28	11	12

Figure S184. Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.031

Table S185. Gene #27: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 15(9P21.3) MUTATED	2	7	0	6	1	2	1
DEL PEAK 15(9P21.3) WILD-TYPE	9	5	4	5	12	7	9

Figure S185. Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S186. Gene #27: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 15(9P21.3) MUTATED	12	35	112
DEL PEAK 15(9P21.3) WILD-TYPE	226	100	43

Figure S186. Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S187. Gene #27: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 15(9P21.3) MUTATED	6	24	68
DEL PEAK 15(9P21.3) WILD-TYPE	122	52	42

Figure S187. Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S188. Gene #27: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
DEL PEAK 15(9P21.3) MUTATED	18	40	31	22	22	10
DEL PEAK 15(9P21.3) WILD-TYPE	90	22	44	58	57	33

Figure S188. Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S189. Gene #27: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
DEL PEAK 15(9P21.3) MUTATED	34	45	64
DEL PEAK 15(9P21.3) WILD-TYPE	87	151	66

Figure S189. Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S190. Gene #27: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 15(9P21.3) MUTATED	18	27	113
DEL PEAK 15(9P21.3) WILD-TYPE	93	194	80

Figure S190. Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S191. Gene #27: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 15(9P21.3) MUTATED	32	2	16	90	14	4
DEL PEAK 15(9P21.3) WILD-TYPE	85	31	167	42	21	21

Figure S191. Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S192. Gene #27: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
DEL PEAK 15(9P21.3) MUTATED	29	26	98
DEL PEAK 15(9P21.3) WILD-TYPE	95	178	84

Figure S192. Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S193. Gene #27: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 15(9P21.3) MUTATED	48	55	24	26
DEL PEAK 15(9P21.3) WILD-TYPE	96	79	171	11

Figure S193. Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.0034

Table S194. Gene #27: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	21	48	35
DEL PEAK 15(9P21.3) MUTATED	8	5	5	17
DEL PEAK 15(9P21.3) WILD-TYPE	30	16	43	18

Figure S194. Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.025

Table S195. Gene #27: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	56	47
DEL PEAK 15(9P21.3) MUTATED	8	21	6
DEL PEAK 15(9P21.3) WILD-TYPE	31	35	41

Figure S195. Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S196. Gene #28: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 16(10Q23.31) MUTATED	17	29	50
DEL PEAK 16(10Q23.31) WILD-TYPE	221	106	105

Figure S196. Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.0034

Table S197. Gene #28: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 16(10Q23.31) MUTATED	17	9	33
DEL PEAK 16(10Q23.31) WILD-TYPE	111	67	77

Figure S197. Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00665 (Fisher's exact test), Q value = 0.014

Table S198. Gene #28: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
DEL PEAK 16(10Q23.31) MUTATED	20	27	36
DEL PEAK 16(10Q23.31) WILD-TYPE	101	169	94

Figure S198. Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.0473 (Fisher's exact test), Q value = 0.078

Table S199. Gene #28: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 16(10Q23.31) MUTATED	21	30	44
DEL PEAK 16(10Q23.31) WILD-TYPE	90	191	149

Figure S199. Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00084

Table S200. Gene #28: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 16(10Q23.31) MUTATED	22	3	21	37	3	9
DEL PEAK 16(10Q23.31) WILD-TYPE	95	30	162	95	32	16

Figure S200. Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.028

Table S201. Gene #28: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
DEL PEAK 16(10Q23.31) MUTATED	22	27	45
DEL PEAK 16(10Q23.31) WILD-TYPE	102	177	137

Figure S201. Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S202. Gene #28: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 16(10Q23.31) MUTATED	21	35	23	15
DEL PEAK 16(10Q23.31) WILD-TYPE	123	99	172	22

Figure S202. Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.027

Table S203. Gene #29: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 17(13Q14.2) MUTATED	1	7	3
DEL PEAK 17(13Q14.2) WILD-TYPE	32	17	10

Figure S203. Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S204. Gene #29: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 17(13Q14.2) MUTATED	11	23	48
DEL PEAK 17(13Q14.2) WILD-TYPE	227	112	107

Figure S204. Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00032

Table S205. Gene #29: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 17(13Q14.2) MUTATED	8	16	27
DEL PEAK 17(13Q14.2) WILD-TYPE	120	60	83

Figure S205. Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S206. Gene #29: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
DEL PEAK 17(13Q14.2) MUTATED	3	22	15	14	11	7
DEL PEAK 17(13Q14.2) WILD-TYPE	105	40	60	66	68	36

Figure S206. Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S207. Gene #29: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
DEL PEAK 17(13Q14.2) MUTATED	15	20	37
DEL PEAK 17(13Q14.2) WILD-TYPE	106	176	93

Figure S207. Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S208. Gene #29: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 17(13Q14.2) MUTATED	13	19	50
DEL PEAK 17(13Q14.2) WILD-TYPE	98	202	143

Figure S208. Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S209. Gene #29: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 17(13Q14.2) MUTATED	7	2	15	43	8	7
DEL PEAK 17(13Q14.2) WILD-TYPE	110	31	168	89	27	18

Figure S209. Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S210. Gene #29: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
DEL PEAK 17(13Q14.2) MUTATED	14	16	50
DEL PEAK 17(13Q14.2) WILD-TYPE	110	188	132

Figure S210. Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S211. Gene #29: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 17(13Q14.2) MUTATED	20	33	14	13
DEL PEAK 17(13Q14.2) WILD-TYPE	124	101	181	24

Figure S211. Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S212. Gene #30: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 18(14Q31.1) MUTATED	10	19	2
DEL PEAK 18(14Q31.1) WILD-TYPE	23	5	11

Figure S212. Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0012

Table S213. Gene #30: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	12	4	11	13	9	10
DEL PEAK 18(14Q31.1) MUTATED	4	7	1	11	5	1	2
DEL PEAK 18(14Q31.1) WILD-TYPE	7	5	3	0	8	8	8

Figure S213. Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S214. Gene #30: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	238	135	155
DEL PEAK 18(14Q31.1) MUTATED	70	47	111
DEL PEAK 18(14Q31.1) WILD-TYPE	168	88	44

Figure S214. Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S215. Gene #30: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	76	110
DEL PEAK 18(14Q31.1) MUTATED	32	36	65
DEL PEAK 18(14Q31.1) WILD-TYPE	96	40	45

Figure S215. Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S216. Gene #30: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	108	62	75	80	79	43
DEL PEAK 18(14Q31.1) MUTATED	37	41	56	27	26	13
DEL PEAK 18(14Q31.1) WILD-TYPE	71	21	19	53	53	30

Figure S216. Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S217. Gene #30: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	196	130
DEL PEAK 18(14Q31.1) MUTATED	69	64	67
DEL PEAK 18(14Q31.1) WILD-TYPE	52	132	63

Figure S217. Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S218. Gene #30: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	111	221	193
DEL PEAK 18(14Q31.1) MUTATED	21	73	131
DEL PEAK 18(14Q31.1) WILD-TYPE	90	148	62

Figure S218. Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S219. Gene #30: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	117	33	183	132	35	25
DEL PEAK 18(14Q31.1) MUTATED	45	7	57	81	33	2
DEL PEAK 18(14Q31.1) WILD-TYPE	72	26	126	51	2	23

Figure S219. Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S220. Gene #30: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	182
DEL PEAK 18(14Q31.1) MUTATED	38	66	118
DEL PEAK 18(14Q31.1) WILD-TYPE	86	138	64

Figure S220. Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S221. Gene #30: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	144	134	195	37
DEL PEAK 18(14Q31.1) MUTATED	52	84	62	24
DEL PEAK 18(14Q31.1) WILD-TYPE	92	50	133	13

Figure S221. Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/15087097/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/15107132/KIRC-TP.transferedmergedcluster.txt
Number of patients = 528
Number of significantly focal cnvs = 30
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

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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