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

Thyroid Adenocarcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1QZ29G0

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 36 focal events and 10 molecular subtypes across 499 patients, 163 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q31.2 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q31.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_5q21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5q33.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_22q11.21 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xp11.22 cnv correlated to 'METHLYATION_CNMF'.
del_1q42.13 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2p23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p22 cnv correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p12 cnv correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8q24.22 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q22.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p12.31 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q21.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q14.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q25.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
del_18q21.33 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
del_19p13.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.12 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q21.1 cnv correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 36 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 163 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 5q33 1	21 (4%)	478	0.00019 (0.00175)	0.00031 (0.00266)	0.247 (0.36)	0.0716 (0.14)	0.00107 (0.0067)	4e-05 (0.000533)	0.00236 (0.0118)	1e-05 (0.000225)	0.00182 (0.00993)	0.00037 (0.00303)
del 2p23 1	12 (2%)	487	0.00357 (0.0162)	0.00111 (0.00677)	0.635 (0.734)	0.0932 (0.168)	1e-05 (0.000225)	2e-05 (0.000343)	0.0033 (0.0154)	1e-05 (0.000225)	0.00739 (0.0269)	1e-05 (0.000225)
del 2q22 1	10 (2%)	489	0.00221 (0.0114)	0.00207 (0.011)	0.58 (0.687)	0.093 (0.168)	0.00018 (0.00171)	3e-05 (0.00047)	0.0135 (0.045)	1e-05 (0.000225)	0.00142 (0.00811)	2e-05 (0.000343)
del 2q37 3	13 (3%)	486	0.00017 (0.00165)	0.00045 (0.00352)	0.701 (0.786)	0.102 (0.18)	0.00016 (0.0016)	3e-05 (0.00047)	0.00857 (0.0302)	1e-05 (0.000225)	0.0006 (0.00424)	2e-05 (0.000343)
del 9p21 3	20 (4%)	479	0.0125 (0.043)	0.0159 (0.0507)	0.941 (0.99)	0.647 (0.744)	0.047 (0.105)	0.0255 (0.0706)	0.0264 (0.0726)	0.00044 (0.00352)	0.0023 (0.0117)	0.00218 (0.0114)
del 22q13 1	89 (18%)	410	1e-05 (0.000225)	1e-05 (0.000225)	0.409 (0.515)	0.509 (0.618)	1e-05 (0.000225)	1e-05 (0.000225)	0.00503 (0.0199)	6e-05 (0.000745)	1e-05 (0.000225)	5e-05 (0.000643)
del 22q13 32	90 (18%)	409	1e-05 (0.000225)	1e-05 (0.000225)	0.409 (0.515)	0.51 (0.618)	1e-05 (0.000225)	1e-05 (0.000225)	0.00296 (0.0144)	4e-05 (0.000533)	1e-05 (0.000225)	4e-05 (0.000533)
amp 1q31 2	29 (6%)	470	0.34 (0.45)	4e-05 (0.000533)	0.0163 (0.0507)	0.0218 (0.0627)	0.00016 (0.0016)	2e-05 (0.000343)	0.0129 (0.0435)	0.0816 (0.155)	0.0582 (0.125)	0.0295 (0.0793)
amp 5q21 1	23 (5%)	476	0.00671 (0.0246)	0.0173 (0.052)	0.269 (0.384)	0.0876 (0.163)	0.0166 (0.0507)	0.0127 (0.043)	0.041 (0.0978)	0.00595 (0.0225)	0.0544 (0.119)	0.0269 (0.0733)
del 8q24 22	7 (1%)	492	0.0965 (0.172)	0.0306 (0.08)	0.773 (0.85)	0.175 (0.275)	0.00377 (0.0166)	0.00108 (0.0067)	0.00826 (0.0294)	7e-05 (0.000787)	0.0005 (0.00367)	0.00029 (0.00255)
del 10q23 31	12 (2%)	487	0.139 (0.233)	0.1 (0.178)	0.0161 (0.0507)	0.16 (0.261)	0.002 (0.0107)	0.00428 (0.0177)	0.0241 (0.0679)	0.0007 (0.00475)	0.0103 (0.0361)	0.00053 (0.00382)
del 13q12 3	16 (3%)	483	0.00326 (0.0154)	0.00558 (0.0216)	0.103 (0.18)	0.0881 (0.163)	0.00135 (0.00784)	0.019 (0.0556)	0.346 (0.453)	0.00647 (0.024)	0.0228 (0.0647)	0.00537 (0.021)
del 13q14 3	20 (4%)	479	0.0027 (0.0133)	0.0556 (0.121)	0.037 (0.0906)	0.177 (0.278)	0.00151 (0.00849)	0.00371 (0.0165)	0.219 (0.324)	0.00155 (0.00858)	0.00329 (0.0154)	0.00047 (0.00352)
del 15q25 3	8 (2%)	491	0.173 (0.274)	0.0119 (0.0413)	0.151 (0.251)	0.0963 (0.172)	0.00123 (0.00726)	0.00028 (0.00252)	0.0146 (0.0483)	2e-05 (0.000343)	0.00411 (0.0175)	0.0001 (0.00109)
del 19p13 2	7 (1%)	492	0.795 (0.86)	0.00487 (0.0195)	0.483 (0.591)	0.325 (0.432)	0.00361 (0.0162)	0.00098 (0.0063)	0.00459 (0.0186)	7e-05 (0.000787)	0.00011 (0.00116)	7e-05 (0.000787)
del 19p13 12	8 (2%)	491	0.818 (0.877)	0.0317 (0.0809)	0.0839 (0.158)	0.106 (0.185)	0.0189 (0.0556)	0.00595 (0.0225)	0.0217 (0.0627)	0.00037 (0.00303)	0.0008 (0.00524)	0.00065 (0.0045)
del 9q22 33	27 (5%)	472	0.00046 (0.00352)	0.0523 (0.115)	0.573 (0.682)	0.116 (0.202)	0.246 (0.36)	0.0289 (0.0783)	0.0348 (0.0864)	0.00344 (0.0159)	0.00433 (0.0177)	0.00769 (0.0277)
amp 22q11 21	7 (1%)	492	0.0319 (0.0809)	0.0625 (0.129)			0.0152 (0.0496)	0.0394 (0.0959)	0.0772 (0.149)	0.0312 (0.0802)	0.0587 (0.125)	0.00611 (0.0229)
del 8p23 2	4 (1%)	495	0.201 (0.305)	0.302 (0.413)			0.0695 (0.137)	0.0472 (0.105)	0.0431 (0.0982)	0.00429 (0.0177)	0.0408 (0.0978)	0.0155 (0.0504)
del 8p22	4 (1%)	495	0.2 (0.305)	0.299 (0.413)			0.0692 (0.137)	0.0478 (0.106)	0.0424 (0.0981)	0.00413 (0.0175)	0.0413 (0.0979)	0.0164 (0.0507)
del 8p12	4 (1%)	495	0.2 (0.305)	0.302 (0.413)			0.0698 (0.137)	0.0469 (0.105)	0.0431 (0.0982)	0.00412 (0.0175)	0.0417 (0.098)	0.0166 (0.0507)
del 10p12 31	7 (1%)	492	0.0792 (0.152)	0.277 (0.388)	0.785 (0.857)	0.267 (0.384)	0.0311 (0.0802)	0.0169 (0.051)	0.315 (0.422)	0.00075 (0.005)	0.0409 (0.0978)	0.00118 (0.00708)
del 10q21 2	12 (2%)	487	0.0425 (0.0981)	0.378 (0.489)	0.274 (0.388)	0.689 (0.777)	0.0346 (0.0864)	0.0658 (0.133)	0.379 (0.49)	0.174 (0.275)	0.048 (0.106)	0.0164 (0.0507)
amp 4q31 21	9 (2%)	490	0.0298 (0.0793)	0.0307 (0.08)	0.786 (0.857)	0.63 (0.734)	0.305 (0.414)	0.0839 (0.158)	0.711 (0.795)	0.355 (0.461)	0.404 (0.514)	0.152 (0.251)
del 16q23 3	6 (1%)	493	0.0187 (0.0556)	0.276 (0.388)	0.121 (0.209)	0.408 (0.515)	0.0867 (0.163)	0.143 (0.239)	0.0361 (0.0889)	0.205 (0.31)	0.063 (0.13)	0.06 (0.126)
del 21q21 1	9 (2%)	490	0.434 (0.542)	0.793 (0.86)	0.312 (0.419)	0.351 (0.458)	0.551 (0.659)	0.802 (0.865)	0.0607 (0.126)	0.0245 (0.0685)	0.161 (0.261)	0.0343 (0.0863)
amp xp11 22	8 (2%)	491	0.0575 (0.124)	0.03 (0.0793)	1 (1.00)	0.301 (0.413)	0.165 (0.263)	0.06 (0.126)	0.28 (0.39)	0.0744 (0.144)	0.0588 (0.125)	0.156 (0.257)
del 1q42 13	5 (1%)	494	0.389 (0.498)	0.686 (0.777)	0.123 (0.211)	0.934 (0.987)	0.0694 (0.137)	0.156 (0.257)	0.475 (0.584)	0.311 (0.419)	0.345 (0.453)	0.0423 (0.0981)
del 18q21 33	5 (1%)	494	0.456 (0.564)	0.066 (0.133)	0.775 (0.85)	0.514 (0.622)	0.171 (0.272)	0.125 (0.213)	0.132 (0.223)	0.0227 (0.0647)	0.119 (0.206)	0.0916 (0.168)
amp 13q14 2	6 (1%)	493	0.18 (0.281)	0.422 (0.529)	0.634 (0.734)	0.219 (0.324)	0.212 (0.316)	0.267 (0.384)	1 (1.00)	0.341 (0.45)	0.385 (0.494)	0.634 (0.734)
amp xq22 3	15 (3%)	484	0.306 (0.414)	0.662 (0.759)	0.774 (0.85)	0.519 (0.623)	0.72 (0.802)	0.901 (0.959)	0.935 (0.987)	0.637 (0.734)	0.324 (0.431)	0.943 (0.99)
del 4q34 3	5 (1%)	494	0.0883 (0.163)	0.691 (0.777)	0.774 (0.85)	0.517 (0.622)	0.439 (0.545)	0.574 (0.682)	0.474 (0.584)	0.0737 (0.143)	0.206 (0.31)	0.0695 (0.137)
del 5p15 2	4 (1%)	495	1 (1.00)	0.193 (0.3)			0.273 (0.388)	0.275 (0.388)	0.439 (0.545)	0.683 (0.775)	0.263 (0.38)	0.681 (0.775)
del 7q34	4 (1%)	495	0.811 (0.872)	0.505 (0.617)			0.852 (0.91)	0.677 (0.774)	0.908 (0.964)	1 (1.00)	0.634 (0.734)	1 (1.00)
del 17p13 1	8 (2%)	491	0.212 (0.316)	0.796 (0.86)	0.628 (0.734)	0.393 (0.502)	0.762 (0.847)	0.6 (0.708)	0.305 (0.414)	0.162 (0.261)	0.263 (0.38)	0.16 (0.261)
del xq28	4 (1%)	495	0.2 (0.305)	0.302 (0.413)	0.0644 (0.132)	0.199 (0.305)	0.164 (0.263)	0.245 (0.359)	0.212 (0.316)	0.092 (0.168)	0.136 (0.229)	0.0927 (0.168)

'amp_1q31.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00053

Table S1. Gene #1: 'amp_1q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
AMP PEAK 1(1Q31.2) MUTATED	11	3	7	1	7
AMP PEAK 1(1Q31.2) WILD-TYPE	35	144	77	41	173

Figure S1. Get High-res Image Gene #1: 'amp_1q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q31.2' versus 'RPPA_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.051

Table S2. Gene #1: 'amp_1q31.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	64	42	49
AMP PEAK 1(1Q31.2) MUTATED	0	6	1	5
AMP PEAK 1(1Q31.2) WILD-TYPE	64	58	41	44

Figure S2. Get High-res Image Gene #1: 'amp_1q31.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_1q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.063

Table S3. Gene #1: 'amp_1q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	28	33	29	47	27	9
AMP PEAK 1(1Q31.2) MUTATED	0	1	3	0	3	5	0
AMP PEAK 1(1Q31.2) WILD-TYPE	46	27	30	29	44	22	9

Figure S3. Get High-res Image Gene #1: 'amp_1q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q31.2' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0016

Table S4. Gene #1: 'amp_1q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
AMP PEAK 1(1Q31.2) MUTATED	19	3	5	2
AMP PEAK 1(1Q31.2) WILD-TYPE	139	164	53	112

Figure S4. Get High-res Image Gene #1: 'amp_1q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00034

Table S5. Gene #1: 'amp_1q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
AMP PEAK 1(1Q31.2) MUTATED	18	3	1	2	5
AMP PEAK 1(1Q31.2) WILD-TYPE	86	131	85	93	73

Figure S5. Get High-res Image Gene #1: 'amp_1q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q31.2' versus 'MIRSEQ_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.044

Table S6. Gene #1: 'amp_1q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
AMP PEAK 1(1Q31.2) MUTATED	16	4	3	6
AMP PEAK 1(1Q31.2) WILD-TYPE	149	141	116	63

Figure S6. Get High-res Image Gene #1: 'amp_1q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.079

Table S7. Gene #1: 'amp_1q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
AMP PEAK 1(1Q31.2) MUTATED	15	3	7
AMP PEAK 1(1Q31.2) WILD-TYPE	148	117	178

Figure S7. Get High-res Image Gene #1: 'amp_1q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q31.21' versus 'CN_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.079

Table S8. Gene #2: 'amp_4q31.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
AMP PEAK 3(4Q31.21) MUTATED	0	1	8
AMP PEAK 3(4Q31.21) WILD-TYPE	132	137	221

Figure S8. Get High-res Image Gene #2: 'amp_4q31.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q31.21' versus 'METHLYATION_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.08

Table S9. Gene #2: 'amp_4q31.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
AMP PEAK 3(4Q31.21) MUTATED	0	6	2	1	0
AMP PEAK 3(4Q31.21) WILD-TYPE	46	141	82	41	180

Figure S9. Get High-res Image Gene #2: 'amp_4q31.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q21.1' versus 'CN_CNMF'

P value = 0.00671 (Fisher's exact test), Q value = 0.025

Table S10. Gene #3: 'amp_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
AMP PEAK 4(5Q21.1) MUTATED	5	1	17
AMP PEAK 4(5Q21.1) WILD-TYPE	127	137	212

Figure S10. Get High-res Image Gene #3: 'amp_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q21.1' versus 'METHLYATION_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.052

Table S11. Gene #3: 'amp_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
AMP PEAK 4(5Q21.1) MUTATED	1	14	4	0	4
AMP PEAK 4(5Q21.1) WILD-TYPE	45	133	80	42	176

Figure S11. Get High-res Image Gene #3: 'amp_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q21.1' versus 'MRNASEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.051

Table S12. Gene #3: 'amp_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
AMP PEAK 4(5Q21.1) MUTATED	3	15	2	3
AMP PEAK 4(5Q21.1) WILD-TYPE	155	152	56	111

Figure S12. Get High-res Image Gene #3: 'amp_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.043

Table S13. Gene #3: 'amp_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
AMP PEAK 4(5Q21.1) MUTATED	2	14	3	3	1
AMP PEAK 4(5Q21.1) WILD-TYPE	102	120	83	92	77

Figure S13. Get High-res Image Gene #3: 'amp_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q21.1' versus 'MIRSEQ_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.098

Table S14. Gene #3: 'amp_5q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
AMP PEAK 4(5Q21.1) MUTATED	6	13	3	1
AMP PEAK 4(5Q21.1) WILD-TYPE	159	132	116	68

Figure S14. Get High-res Image Gene #3: 'amp_5q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00595 (Fisher's exact test), Q value = 0.023

Table S15. Gene #3: 'amp_5q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
AMP PEAK 4(5Q21.1) MUTATED	5	13	5
AMP PEAK 4(5Q21.1) WILD-TYPE	173	115	187

Figure S15. Get High-res Image Gene #3: 'amp_5q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.073

Table S16. Gene #3: 'amp_5q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
AMP PEAK 4(5Q21.1) MUTATED	5	10	4
AMP PEAK 4(5Q21.1) WILD-TYPE	158	110	181

Figure S16. Get High-res Image Gene #3: 'amp_5q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q33.1' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0018

Table S17. Gene #4: 'amp_5q33.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
AMP PEAK 5(5Q33.1) MUTATED	3	0	18
AMP PEAK 5(5Q33.1) WILD-TYPE	129	138	211

Figure S17. Get High-res Image Gene #4: 'amp_5q33.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q33.1' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0027

Table S18. Gene #4: 'amp_5q33.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
AMP PEAK 5(5Q33.1) MUTATED	1	16	1	0	3
AMP PEAK 5(5Q33.1) WILD-TYPE	45	131	83	42	177

Figure S18. Get High-res Image Gene #4: 'amp_5q33.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q33.1' versus 'MRNASEQ_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0067

Table S19. Gene #4: 'amp_5q33.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
AMP PEAK 5(5Q33.1) MUTATED	2	16	1	2
AMP PEAK 5(5Q33.1) WILD-TYPE	156	151	57	112

Figure S19. Get High-res Image Gene #4: 'amp_5q33.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00053

Table S20. Gene #4: 'amp_5q33.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
AMP PEAK 5(5Q33.1) MUTATED	2	16	1	2	0
AMP PEAK 5(5Q33.1) WILD-TYPE	102	118	85	93	78

Figure S20. Get High-res Image Gene #4: 'amp_5q33.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q33.1' versus 'MIRSEQ_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.012

Table S21. Gene #4: 'amp_5q33.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
AMP PEAK 5(5Q33.1) MUTATED	5	14	1	1
AMP PEAK 5(5Q33.1) WILD-TYPE	160	131	118	68

Figure S21. Get High-res Image Gene #4: 'amp_5q33.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q33.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S22. Gene #4: 'amp_5q33.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
AMP PEAK 5(5Q33.1) MUTATED	4	15	2
AMP PEAK 5(5Q33.1) WILD-TYPE	174	113	190

Figure S22. Get High-res Image Gene #4: 'amp_5q33.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q33.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.0099

Table S23. Gene #4: 'amp_5q33.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
AMP PEAK 5(5Q33.1) MUTATED	4	12	1	1
AMP PEAK 5(5Q33.1) WILD-TYPE	127	113	107	103

Figure S23. Get High-res Image Gene #4: 'amp_5q33.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5q33.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.003

Table S24. Gene #4: 'amp_5q33.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
AMP PEAK 5(5Q33.1) MUTATED	4	12	2
AMP PEAK 5(5Q33.1) WILD-TYPE	159	108	183

Figure S24. Get High-res Image Gene #4: 'amp_5q33.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q11.21' versus 'CN_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.081

Table S25. Gene #6: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
AMP PEAK 7(22Q11.21) MUTATED	5	1	1
AMP PEAK 7(22Q11.21) WILD-TYPE	127	137	228

Figure S25. Get High-res Image Gene #6: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.05

Table S26. Gene #6: 'amp_22q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
AMP PEAK 7(22Q11.21) MUTATED	0	5	2	0
AMP PEAK 7(22Q11.21) WILD-TYPE	158	162	56	114

Figure S26. Get High-res Image Gene #6: 'amp_22q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0394 (Fisher's exact test), Q value = 0.096

Table S27. Gene #6: 'amp_22q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
AMP PEAK 7(22Q11.21) MUTATED	0	5	2	0	0
AMP PEAK 7(22Q11.21) WILD-TYPE	104	129	84	95	78

Figure S27. Get High-res Image Gene #6: 'amp_22q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_22q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.08

Table S28. Gene #6: 'amp_22q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
AMP PEAK 7(22Q11.21) MUTATED	1	5	1
AMP PEAK 7(22Q11.21) WILD-TYPE	177	123	191

Figure S28. Get High-res Image Gene #6: 'amp_22q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_22q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00611 (Fisher's exact test), Q value = 0.023

Table S29. Gene #6: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
AMP PEAK 7(22Q11.21) MUTATED	2	5	0
AMP PEAK 7(22Q11.21) WILD-TYPE	161	115	185

Figure S29. Get High-res Image Gene #6: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.22' versus 'METHLYATION_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.079

Table S30. Gene #7: 'amp_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
AMP PEAK 8(XP11.22) MUTATED	0	6	2	0	0
AMP PEAK 8(XP11.22) WILD-TYPE	46	141	82	42	180

Figure S30. Get High-res Image Gene #7: 'amp_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q42.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.098

Table S31. Gene #9: 'del_1q42.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 1(1Q42.13) MUTATED	1	3	0
DEL PEAK 1(1Q42.13) WILD-TYPE	162	117	185

Figure S31. Get High-res Image Gene #9: 'del_1q42.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2p23.1' versus 'CN_CNMF'

P value = 0.00357 (Fisher's exact test), Q value = 0.016

Table S32. Gene #10: 'del_2p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
DEL PEAK 2(2P23.1) MUTATED	1	0	11
DEL PEAK 2(2P23.1) WILD-TYPE	131	138	218

Figure S32. Get High-res Image Gene #10: 'del_2p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p23.1' versus 'METHLYATION_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0068

Table S33. Gene #10: 'del_2p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
DEL PEAK 2(2P23.1) MUTATED	0	10	2	0	0
DEL PEAK 2(2P23.1) WILD-TYPE	46	137	82	42	180

Figure S33. Get High-res Image Gene #10: 'del_2p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S34. Gene #10: 'del_2p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 2(2P23.1) MUTATED	0	12	0	0
DEL PEAK 2(2P23.1) WILD-TYPE	158	155	58	114

Figure S34. Get High-res Image Gene #10: 'del_2p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2p23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00034

Table S35. Gene #10: 'del_2p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 2(2P23.1) MUTATED	0	11	1	0	0
DEL PEAK 2(2P23.1) WILD-TYPE	104	123	85	95	78

Figure S35. Get High-res Image Gene #10: 'del_2p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2p23.1' versus 'MIRSEQ_CNMF'

P value = 0.0033 (Fisher's exact test), Q value = 0.015

Table S36. Gene #10: 'del_2p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 2(2P23.1) MUTATED	1	8	0	3
DEL PEAK 2(2P23.1) WILD-TYPE	164	137	119	66

Figure S36. Get High-res Image Gene #10: 'del_2p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2p23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S37. Gene #10: 'del_2p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 2(2P23.1) MUTATED	0	11	1
DEL PEAK 2(2P23.1) WILD-TYPE	178	117	191

Figure S37. Get High-res Image Gene #10: 'del_2p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2p23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00739 (Fisher's exact test), Q value = 0.027

Table S38. Gene #10: 'del_2p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 2(2P23.1) MUTATED	1	7	0	1
DEL PEAK 2(2P23.1) WILD-TYPE	130	118	108	103

Figure S38. Get High-res Image Gene #10: 'del_2p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2p23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S39. Gene #10: 'del_2p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 2(2P23.1) MUTATED	0	9	0
DEL PEAK 2(2P23.1) WILD-TYPE	163	111	185

Figure S39. Get High-res Image Gene #10: 'del_2p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.011

Table S40. Gene #11: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
DEL PEAK 3(2Q22.1) MUTATED	0	0	10
DEL PEAK 3(2Q22.1) WILD-TYPE	132	138	219

Figure S40. Get High-res Image Gene #11: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.011

Table S41. Gene #11: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
DEL PEAK 3(2Q22.1) MUTATED	0	9	1	0	0
DEL PEAK 3(2Q22.1) WILD-TYPE	46	138	83	42	180

Figure S41. Get High-res Image Gene #11: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0017

Table S42. Gene #11: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 3(2Q22.1) MUTATED	0	10	0	0
DEL PEAK 3(2Q22.1) WILD-TYPE	158	157	58	114

Figure S42. Get High-res Image Gene #11: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00047

Table S43. Gene #11: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 3(2Q22.1) MUTATED	0	10	0	0	0
DEL PEAK 3(2Q22.1) WILD-TYPE	104	124	86	95	78

Figure S43. Get High-res Image Gene #11: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.045

Table S44. Gene #11: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 3(2Q22.1) MUTATED	1	6	0	3
DEL PEAK 3(2Q22.1) WILD-TYPE	164	139	119	66

Figure S44. Get High-res Image Gene #11: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S45. Gene #11: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 3(2Q22.1) MUTATED	0	10	0
DEL PEAK 3(2Q22.1) WILD-TYPE	178	118	192

Figure S45. Get High-res Image Gene #11: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0081

Table S46. Gene #11: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 3(2Q22.1) MUTATED	1	7	0	0
DEL PEAK 3(2Q22.1) WILD-TYPE	130	118	108	104

Figure S46. Get High-res Image Gene #11: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00034

Table S47. Gene #11: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 3(2Q22.1) MUTATED	0	8	0
DEL PEAK 3(2Q22.1) WILD-TYPE	163	112	185

Figure S47. Get High-res Image Gene #11: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0017

Table S48. Gene #12: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
DEL PEAK 4(2Q37.3) MUTATED	0	0	13
DEL PEAK 4(2Q37.3) WILD-TYPE	132	138	216

Figure S48. Get High-res Image Gene #12: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0035

Table S49. Gene #12: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
DEL PEAK 4(2Q37.3) MUTATED	0	11	2	0	0
DEL PEAK 4(2Q37.3) WILD-TYPE	46	136	82	42	180

Figure S49. Get High-res Image Gene #12: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0016

Table S50. Gene #12: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 4(2Q37.3) MUTATED	0	12	0	1
DEL PEAK 4(2Q37.3) WILD-TYPE	158	155	58	113

Figure S50. Get High-res Image Gene #12: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00047

Table S51. Gene #12: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 4(2Q37.3) MUTATED	0	12	1	0	0
DEL PEAK 4(2Q37.3) WILD-TYPE	104	122	85	95	78

Figure S51. Get High-res Image Gene #12: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.00857 (Fisher's exact test), Q value = 0.03

Table S52. Gene #12: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 4(2Q37.3) MUTATED	2	7	0	4
DEL PEAK 4(2Q37.3) WILD-TYPE	163	138	119	65

Figure S52. Get High-res Image Gene #12: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S53. Gene #12: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 4(2Q37.3) MUTATED	0	12	1
DEL PEAK 4(2Q37.3) WILD-TYPE	178	116	191

Figure S53. Get High-res Image Gene #12: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0042

Table S54. Gene #12: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 4(2Q37.3) MUTATED	1	9	0	1
DEL PEAK 4(2Q37.3) WILD-TYPE	130	116	108	103

Figure S54. Get High-res Image Gene #12: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00034

Table S55. Gene #12: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 4(2Q37.3) MUTATED	0	10	1
DEL PEAK 4(2Q37.3) WILD-TYPE	163	110	184

Figure S55. Get High-res Image Gene #12: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.11

Table S56. Gene #16: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 11(8P23.2) MUTATED	0	4	0	0	0
DEL PEAK 11(8P23.2) WILD-TYPE	104	130	86	95	78

Figure S56. Get High-res Image Gene #16: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 0.098

Table S57. Gene #16: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 11(8P23.2) MUTATED	0	2	0	2
DEL PEAK 11(8P23.2) WILD-TYPE	165	143	119	67

Figure S57. Get High-res Image Gene #16: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00429 (Fisher's exact test), Q value = 0.018

Table S58. Gene #16: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 11(8P23.2) MUTATED	0	4	0
DEL PEAK 11(8P23.2) WILD-TYPE	178	124	192

Figure S58. Get High-res Image Gene #16: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.098

Table S59. Gene #16: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 11(8P23.2) MUTATED	0	3	0	0
DEL PEAK 11(8P23.2) WILD-TYPE	131	122	108	104

Figure S59. Get High-res Image Gene #16: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.05

Table S60. Gene #16: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 11(8P23.2) MUTATED	0	3	0
DEL PEAK 11(8P23.2) WILD-TYPE	163	117	185

Figure S60. Get High-res Image Gene #16: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.11

Table S61. Gene #17: 'del_8p22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 12(8P22) MUTATED	0	4	0	0	0
DEL PEAK 12(8P22) WILD-TYPE	104	130	86	95	78

Figure S61. Get High-res Image Gene #17: 'del_8p22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_CNMF'

P value = 0.0424 (Fisher's exact test), Q value = 0.098

Table S62. Gene #17: 'del_8p22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 12(8P22) MUTATED	0	2	0	2
DEL PEAK 12(8P22) WILD-TYPE	165	143	119	67

Figure S62. Get High-res Image Gene #17: 'del_8p22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00413 (Fisher's exact test), Q value = 0.017

Table S63. Gene #17: 'del_8p22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 12(8P22) MUTATED	0	4	0
DEL PEAK 12(8P22) WILD-TYPE	178	124	192

Figure S63. Get High-res Image Gene #17: 'del_8p22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.098

Table S64. Gene #17: 'del_8p22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 12(8P22) MUTATED	0	3	0	0
DEL PEAK 12(8P22) WILD-TYPE	131	122	108	104

Figure S64. Get High-res Image Gene #17: 'del_8p22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.051

Table S65. Gene #17: 'del_8p22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 12(8P22) MUTATED	0	3	0
DEL PEAK 12(8P22) WILD-TYPE	163	117	185

Figure S65. Get High-res Image Gene #17: 'del_8p22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.11

Table S66. Gene #18: 'del_8p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 13(8P12) MUTATED	0	4	0	0	0
DEL PEAK 13(8P12) WILD-TYPE	104	130	86	95	78

Figure S66. Get High-res Image Gene #18: 'del_8p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p12' versus 'MIRSEQ_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 0.098

Table S67. Gene #18: 'del_8p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 13(8P12) MUTATED	0	2	0	2
DEL PEAK 13(8P12) WILD-TYPE	165	143	119	67

Figure S67. Get High-res Image Gene #18: 'del_8p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00412 (Fisher's exact test), Q value = 0.017

Table S68. Gene #18: 'del_8p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 13(8P12) MUTATED	0	4	0
DEL PEAK 13(8P12) WILD-TYPE	178	124	192

Figure S68. Get High-res Image Gene #18: 'del_8p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.098

Table S69. Gene #18: 'del_8p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 13(8P12) MUTATED	0	3	0	0
DEL PEAK 13(8P12) WILD-TYPE	131	122	108	104

Figure S69. Get High-res Image Gene #18: 'del_8p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.051

Table S70. Gene #18: 'del_8p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 13(8P12) MUTATED	0	3	0
DEL PEAK 13(8P12) WILD-TYPE	163	117	185

Figure S70. Get High-res Image Gene #18: 'del_8p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8q24.22' versus 'METHLYATION_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.08

Table S71. Gene #19: 'del_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
DEL PEAK 14(8Q24.22) MUTATED	0	6	1	0	0
DEL PEAK 14(8Q24.22) WILD-TYPE	46	141	83	42	180

Figure S71. Get High-res Image Gene #19: 'del_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8q24.22' versus 'MRNASEQ_CNMF'

P value = 0.00377 (Fisher's exact test), Q value = 0.017

Table S72. Gene #19: 'del_8q24.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 14(8Q24.22) MUTATED	0	7	0	0
DEL PEAK 14(8Q24.22) WILD-TYPE	158	160	58	114

Figure S72. Get High-res Image Gene #19: 'del_8q24.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0067

Table S73. Gene #19: 'del_8q24.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 14(8Q24.22) MUTATED	0	7	0	0	0
DEL PEAK 14(8Q24.22) WILD-TYPE	104	127	86	95	78

Figure S73. Get High-res Image Gene #19: 'del_8q24.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8q24.22' versus 'MIRSEQ_CNMF'

P value = 0.00826 (Fisher's exact test), Q value = 0.029

Table S74. Gene #19: 'del_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 14(8Q24.22) MUTATED	0	5	0	2
DEL PEAK 14(8Q24.22) WILD-TYPE	165	140	119	67

Figure S74. Get High-res Image Gene #19: 'del_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00079

Table S75. Gene #19: 'del_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 14(8Q24.22) MUTATED	0	7	0
DEL PEAK 14(8Q24.22) WILD-TYPE	178	121	192

Figure S75. Get High-res Image Gene #19: 'del_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0037

Table S76. Gene #19: 'del_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 14(8Q24.22) MUTATED	0	6	0	0
DEL PEAK 14(8Q24.22) WILD-TYPE	131	119	108	104

Figure S76. Get High-res Image Gene #19: 'del_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8q24.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0025

Table S77. Gene #19: 'del_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 14(8Q24.22) MUTATED	0	6	0
DEL PEAK 14(8Q24.22) WILD-TYPE	163	114	185

Figure S77. Get High-res Image Gene #19: 'del_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.043

Table S78. Gene #20: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
DEL PEAK 15(9P21.3) MUTATED	10	1	9
DEL PEAK 15(9P21.3) WILD-TYPE	122	137	220

Figure S78. Get High-res Image Gene #20: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.051

Table S79. Gene #20: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
DEL PEAK 15(9P21.3) MUTATED	2	11	5	0	2
DEL PEAK 15(9P21.3) WILD-TYPE	44	136	79	42	178

Figure S79. Get High-res Image Gene #20: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.11

Table S80. Gene #20: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 15(9P21.3) MUTATED	3	12	3	2
DEL PEAK 15(9P21.3) WILD-TYPE	155	155	55	112

Figure S80. Get High-res Image Gene #20: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0255 (Fisher's exact test), Q value = 0.071

Table S81. Gene #20: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 15(9P21.3) MUTATED	4	12	1	2	1
DEL PEAK 15(9P21.3) WILD-TYPE	100	122	85	93	77

Figure S81. Get High-res Image Gene #20: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.073

Table S82. Gene #20: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 15(9P21.3) MUTATED	9	8	0	3
DEL PEAK 15(9P21.3) WILD-TYPE	156	137	119	66

Figure S82. Get High-res Image Gene #20: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0035

Table S83. Gene #20: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 15(9P21.3) MUTATED	8	11	1
DEL PEAK 15(9P21.3) WILD-TYPE	170	117	191

Figure S83. Get High-res Image Gene #20: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0023 (Fisher's exact test), Q value = 0.012

Table S84. Gene #20: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 15(9P21.3) MUTATED	8	9	0	1
DEL PEAK 15(9P21.3) WILD-TYPE	123	116	108	103

Figure S84. Get High-res Image Gene #20: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00218 (Fisher's exact test), Q value = 0.011

Table S85. Gene #20: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 15(9P21.3) MUTATED	8	9	1
DEL PEAK 15(9P21.3) WILD-TYPE	155	111	184

Figure S85. Get High-res Image Gene #20: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q22.33' versus 'CN_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0035

Table S86. Gene #21: 'del_9q22.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
DEL PEAK 16(9Q22.33) MUTATED	15	1	11
DEL PEAK 16(9Q22.33) WILD-TYPE	117	137	218

Figure S86. Get High-res Image Gene #21: 'del_9q22.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q22.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.078

Table S87. Gene #21: 'del_9q22.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 16(9Q22.33) MUTATED	8	13	1	3	2
DEL PEAK 16(9Q22.33) WILD-TYPE	96	121	85	92	76

Figure S87. Get High-res Image Gene #21: 'del_9q22.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q22.33' versus 'MIRSEQ_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.086

Table S88. Gene #21: 'del_9q22.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 16(9Q22.33) MUTATED	13	9	1	4
DEL PEAK 16(9Q22.33) WILD-TYPE	152	136	118	65

Figure S88. Get High-res Image Gene #21: 'del_9q22.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q22.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00344 (Fisher's exact test), Q value = 0.016

Table S89. Gene #21: 'del_9q22.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 16(9Q22.33) MUTATED	12	12	3
DEL PEAK 16(9Q22.33) WILD-TYPE	166	116	189

Figure S89. Get High-res Image Gene #21: 'del_9q22.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q22.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00433 (Fisher's exact test), Q value = 0.018

Table S90. Gene #21: 'del_9q22.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 16(9Q22.33) MUTATED	12	10	1	2
DEL PEAK 16(9Q22.33) WILD-TYPE	119	115	107	102

Figure S90. Get High-res Image Gene #21: 'del_9q22.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9q22.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00769 (Fisher's exact test), Q value = 0.028

Table S91. Gene #21: 'del_9q22.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 16(9Q22.33) MUTATED	12	10	3
DEL PEAK 16(9Q22.33) WILD-TYPE	151	110	182

Figure S91. Get High-res Image Gene #21: 'del_9q22.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p12.31' versus 'MRNASEQ_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.08

Table S92. Gene #22: 'del_10p12.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 17(10P12.31) MUTATED	0	6	0	1
DEL PEAK 17(10P12.31) WILD-TYPE	158	161	58	113

Figure S92. Get High-res Image Gene #22: 'del_10p12.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p12.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.051

Table S93. Gene #22: 'del_10p12.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 17(10P12.31) MUTATED	0	6	0	1	0
DEL PEAK 17(10P12.31) WILD-TYPE	104	128	86	94	78

Figure S93. Get High-res Image Gene #22: 'del_10p12.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p12.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.005

Table S94. Gene #22: 'del_10p12.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 17(10P12.31) MUTATED	1	6	0
DEL PEAK 17(10P12.31) WILD-TYPE	177	122	192

Figure S94. Get High-res Image Gene #22: 'del_10p12.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p12.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.098

Table S95. Gene #22: 'del_10p12.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 17(10P12.31) MUTATED	2	5	0	0
DEL PEAK 17(10P12.31) WILD-TYPE	129	120	108	104

Figure S95. Get High-res Image Gene #22: 'del_10p12.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p12.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0071

Table S96. Gene #22: 'del_10p12.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 17(10P12.31) MUTATED	1	6	0
DEL PEAK 17(10P12.31) WILD-TYPE	162	114	185

Figure S96. Get High-res Image Gene #22: 'del_10p12.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.2' versus 'CN_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 0.098

Table S97. Gene #23: 'del_10q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
DEL PEAK 18(10Q21.2) MUTATED	1	1	10
DEL PEAK 18(10Q21.2) WILD-TYPE	131	137	219

Figure S97. Get High-res Image Gene #23: 'del_10q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.2' versus 'MRNASEQ_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.086

Table S98. Gene #23: 'del_10q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 18(10Q21.2) MUTATED	0	7	2	3
DEL PEAK 18(10Q21.2) WILD-TYPE	158	160	56	111

Figure S98. Get High-res Image Gene #23: 'del_10q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.11

Table S99. Gene #23: 'del_10q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 18(10Q21.2) MUTATED	5	6	1	0
DEL PEAK 18(10Q21.2) WILD-TYPE	126	119	107	104

Figure S99. Get High-res Image Gene #23: 'del_10q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.051

Table S100. Gene #23: 'del_10q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 18(10Q21.2) MUTATED	4	7	1
DEL PEAK 18(10Q21.2) WILD-TYPE	159	113	184

Figure S100. Get High-res Image Gene #23: 'del_10q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.051

Table S101. Gene #24: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	64	42	49
DEL PEAK 19(10Q23.31) MUTATED	5	0	1	0
DEL PEAK 19(10Q23.31) WILD-TYPE	59	64	41	49

Figure S101. Get High-res Image Gene #24: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.011

Table S102. Gene #24: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 19(10Q23.31) MUTATED	0	10	0	2
DEL PEAK 19(10Q23.31) WILD-TYPE	158	157	58	112

Figure S102. Get High-res Image Gene #24: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00428 (Fisher's exact test), Q value = 0.018

Table S103. Gene #24: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 19(10Q23.31) MUTATED	0	9	1	2	0
DEL PEAK 19(10Q23.31) WILD-TYPE	104	125	85	93	78

Figure S103. Get High-res Image Gene #24: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.068

Table S104. Gene #24: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 19(10Q23.31) MUTATED	3	8	0	1
DEL PEAK 19(10Q23.31) WILD-TYPE	162	137	119	68

Figure S104. Get High-res Image Gene #24: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0048

Table S105. Gene #24: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 19(10Q23.31) MUTATED	2	9	1
DEL PEAK 19(10Q23.31) WILD-TYPE	176	119	191

Figure S105. Get High-res Image Gene #24: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.036

Table S106. Gene #24: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 19(10Q23.31) MUTATED	3	8	1	0
DEL PEAK 19(10Q23.31) WILD-TYPE	128	117	107	104

Figure S106. Get High-res Image Gene #24: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0038

Table S107. Gene #24: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 19(10Q23.31) MUTATED	2	9	1
DEL PEAK 19(10Q23.31) WILD-TYPE	161	111	184

Figure S107. Get High-res Image Gene #24: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q12.3' versus 'CN_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.015

Table S108. Gene #25: 'del_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
DEL PEAK 20(13Q12.3) MUTATED	3	0	13
DEL PEAK 20(13Q12.3) WILD-TYPE	129	138	216

Figure S108. Get High-res Image Gene #25: 'del_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.3' versus 'METHLYATION_CNMF'

P value = 0.00558 (Fisher's exact test), Q value = 0.022

Table S109. Gene #25: 'del_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
DEL PEAK 20(13Q12.3) MUTATED	0	11	3	1	1
DEL PEAK 20(13Q12.3) WILD-TYPE	46	136	81	41	179

Figure S109. Get High-res Image Gene #25: 'del_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.3' versus 'MRNASEQ_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0078

Table S110. Gene #25: 'del_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 20(13Q12.3) MUTATED	0	11	3	2
DEL PEAK 20(13Q12.3) WILD-TYPE	158	156	55	112

Figure S110. Get High-res Image Gene #25: 'del_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.056

Table S111. Gene #25: 'del_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 20(13Q12.3) MUTATED	1	10	3	2	0
DEL PEAK 20(13Q12.3) WILD-TYPE	103	124	83	93	78

Figure S111. Get High-res Image Gene #25: 'del_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00647 (Fisher's exact test), Q value = 0.024

Table S112. Gene #25: 'del_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 20(13Q12.3) MUTATED	3	10	3
DEL PEAK 20(13Q12.3) WILD-TYPE	175	118	189

Figure S112. Get High-res Image Gene #25: 'del_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.065

Table S113. Gene #25: 'del_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 20(13Q12.3) MUTATED	3	10	2	1
DEL PEAK 20(13Q12.3) WILD-TYPE	128	115	106	103

Figure S113. Get High-res Image Gene #25: 'del_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00537 (Fisher's exact test), Q value = 0.021

Table S114. Gene #25: 'del_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 20(13Q12.3) MUTATED	2	10	4
DEL PEAK 20(13Q12.3) WILD-TYPE	161	110	181

Figure S114. Get High-res Image Gene #25: 'del_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.3' versus 'CN_CNMF'

P value = 0.0027 (Fisher's exact test), Q value = 0.013

Table S115. Gene #26: 'del_13q14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
DEL PEAK 21(13Q14.3) MUTATED	5	0	15
DEL PEAK 21(13Q14.3) WILD-TYPE	127	138	214

Figure S115. Get High-res Image Gene #26: 'del_13q14.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.3' versus 'RPPA_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.091

Table S116. Gene #26: 'del_13q14.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	64	42	49
DEL PEAK 21(13Q14.3) MUTATED	1	2	6	2
DEL PEAK 21(13Q14.3) WILD-TYPE	63	62	36	47

Figure S116. Get High-res Image Gene #26: 'del_13q14.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_13q14.3' versus 'MRNASEQ_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0085

Table S117. Gene #26: 'del_13q14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 21(13Q14.3) MUTATED	0	12	3	5
DEL PEAK 21(13Q14.3) WILD-TYPE	158	155	55	109

Figure S117. Get High-res Image Gene #26: 'del_13q14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00371 (Fisher's exact test), Q value = 0.016

Table S118. Gene #26: 'del_13q14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 21(13Q14.3) MUTATED	1	12	2	5	0
DEL PEAK 21(13Q14.3) WILD-TYPE	103	122	84	90	78

Figure S118. Get High-res Image Gene #26: 'del_13q14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00155 (Fisher's exact test), Q value = 0.0086

Table S119. Gene #26: 'del_13q14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 21(13Q14.3) MUTATED	2	12	6
DEL PEAK 21(13Q14.3) WILD-TYPE	176	116	186

Figure S119. Get High-res Image Gene #26: 'del_13q14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.015

Table S120. Gene #26: 'del_13q14.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 21(13Q14.3) MUTATED	2	12	4	1
DEL PEAK 21(13Q14.3) WILD-TYPE	129	113	104	103

Figure S120. Get High-res Image Gene #26: 'del_13q14.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q14.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0035

Table S121. Gene #26: 'del_13q14.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 21(13Q14.3) MUTATED	1	12	6
DEL PEAK 21(13Q14.3) WILD-TYPE	162	108	179

Figure S121. Get High-res Image Gene #26: 'del_13q14.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q25.3' versus 'METHLYATION_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.041

Table S122. Gene #27: 'del_15q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
DEL PEAK 23(15Q25.3) MUTATED	0	7	1	0	0
DEL PEAK 23(15Q25.3) WILD-TYPE	46	140	83	42	180

Figure S122. Get High-res Image Gene #27: 'del_15q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q25.3' versus 'MRNASEQ_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0073

Table S123. Gene #27: 'del_15q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 23(15Q25.3) MUTATED	0	8	0	0
DEL PEAK 23(15Q25.3) WILD-TYPE	158	159	58	114

Figure S123. Get High-res Image Gene #27: 'del_15q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.0025

Table S124. Gene #27: 'del_15q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 23(15Q25.3) MUTATED	0	8	0	0	0
DEL PEAK 23(15Q25.3) WILD-TYPE	104	126	86	95	78

Figure S124. Get High-res Image Gene #27: 'del_15q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q25.3' versus 'MIRSEQ_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.048

Table S125. Gene #27: 'del_15q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 23(15Q25.3) MUTATED	1	3	0	4
DEL PEAK 23(15Q25.3) WILD-TYPE	164	142	119	65

Figure S125. Get High-res Image Gene #27: 'del_15q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00034

Table S126. Gene #27: 'del_15q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 23(15Q25.3) MUTATED	0	8	0
DEL PEAK 23(15Q25.3) WILD-TYPE	178	120	192

Figure S126. Get High-res Image Gene #27: 'del_15q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00411 (Fisher's exact test), Q value = 0.017

Table S127. Gene #27: 'del_15q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 23(15Q25.3) MUTATED	1	6	0	0
DEL PEAK 23(15Q25.3) WILD-TYPE	130	119	108	104

Figure S127. Get High-res Image Gene #27: 'del_15q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0011

Table S128. Gene #27: 'del_15q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 23(15Q25.3) MUTATED	0	7	0
DEL PEAK 23(15Q25.3) WILD-TYPE	163	113	185

Figure S128. Get High-res Image Gene #27: 'del_15q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.3' versus 'CN_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.056

Table S129. Gene #28: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
DEL PEAK 24(16Q23.3) MUTATED	4	2	0
DEL PEAK 24(16Q23.3) WILD-TYPE	128	136	229

Figure S129. Get High-res Image Gene #28: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.3' versus 'MIRSEQ_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.089

Table S130. Gene #28: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 24(16Q23.3) MUTATED	4	0	0	2
DEL PEAK 24(16Q23.3) WILD-TYPE	161	145	119	67

Figure S130. Get High-res Image Gene #28: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0227 (Fisher's exact test), Q value = 0.065

Table S131. Gene #30: 'del_18q21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 26(18Q21.33) MUTATED	0	4	1
DEL PEAK 26(18Q21.33) WILD-TYPE	178	124	191

Figure S131. Get High-res Image Gene #30: 'del_18q21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 0.00487 (Fisher's exact test), Q value = 0.019

Table S132. Gene #31: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
DEL PEAK 27(19P13.2) MUTATED	0	7	0	0	0
DEL PEAK 27(19P13.2) WILD-TYPE	46	140	84	42	180

Figure S132. Get High-res Image Gene #31: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00361 (Fisher's exact test), Q value = 0.016

Table S133. Gene #31: 'del_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 27(19P13.2) MUTATED	0	7	0	0
DEL PEAK 27(19P13.2) WILD-TYPE	158	160	58	114

Figure S133. Get High-res Image Gene #31: 'del_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0063

Table S134. Gene #31: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 27(19P13.2) MUTATED	0	7	0	0	0
DEL PEAK 27(19P13.2) WILD-TYPE	104	127	86	95	78

Figure S134. Get High-res Image Gene #31: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00459 (Fisher's exact test), Q value = 0.019

Table S135. Gene #31: 'del_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 27(19P13.2) MUTATED	0	6	0	1
DEL PEAK 27(19P13.2) WILD-TYPE	165	139	119	68

Figure S135. Get High-res Image Gene #31: 'del_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00079

Table S136. Gene #31: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 27(19P13.2) MUTATED	0	7	0
DEL PEAK 27(19P13.2) WILD-TYPE	178	121	192

Figure S136. Get High-res Image Gene #31: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0012

Table S137. Gene #31: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 27(19P13.2) MUTATED	0	7	0	0
DEL PEAK 27(19P13.2) WILD-TYPE	131	118	108	104

Figure S137. Get High-res Image Gene #31: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00079

Table S138. Gene #31: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 27(19P13.2) MUTATED	0	7	0
DEL PEAK 27(19P13.2) WILD-TYPE	163	113	185

Figure S138. Get High-res Image Gene #31: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.12' versus 'METHLYATION_CNMF'

P value = 0.0317 (Fisher's exact test), Q value = 0.081

Table S139. Gene #32: 'del_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
DEL PEAK 28(19P13.12) MUTATED	0	7	0	0	1
DEL PEAK 28(19P13.12) WILD-TYPE	46	140	84	42	179

Figure S139. Get High-res Image Gene #32: 'del_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.12' versus 'MRNASEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.056

Table S140. Gene #32: 'del_19p13.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 28(19P13.12) MUTATED	1	7	0	0
DEL PEAK 28(19P13.12) WILD-TYPE	157	160	58	114

Figure S140. Get High-res Image Gene #32: 'del_19p13.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00595 (Fisher's exact test), Q value = 0.023

Table S141. Gene #32: 'del_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 28(19P13.12) MUTATED	1	7	0	0	0
DEL PEAK 28(19P13.12) WILD-TYPE	103	127	86	95	78

Figure S141. Get High-res Image Gene #32: 'del_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.12' versus 'MIRSEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.063

Table S142. Gene #32: 'del_19p13.12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 28(19P13.12) MUTATED	0	6	1	1
DEL PEAK 28(19P13.12) WILD-TYPE	165	139	118	68

Figure S142. Get High-res Image Gene #32: 'del_19p13.12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.003

Table S143. Gene #32: 'del_19p13.12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 28(19P13.12) MUTATED	0	7	1
DEL PEAK 28(19P13.12) WILD-TYPE	178	121	191

Figure S143. Get High-res Image Gene #32: 'del_19p13.12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0052

Table S144. Gene #32: 'del_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 28(19P13.12) MUTATED	0	7	0	1
DEL PEAK 28(19P13.12) WILD-TYPE	131	118	108	103

Figure S144. Get High-res Image Gene #32: 'del_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0045

Table S145. Gene #32: 'del_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 28(19P13.12) MUTATED	0	7	1
DEL PEAK 28(19P13.12) WILD-TYPE	163	113	184

Figure S145. Get High-res Image Gene #32: 'del_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0245 (Fisher's exact test), Q value = 0.069

Table S146. Gene #33: 'del_21q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 30(21Q21.1) MUTATED	5	4	0
DEL PEAK 30(21Q21.1) WILD-TYPE	173	124	192

Figure S146. Get High-res Image Gene #33: 'del_21q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 0.086

Table S147. Gene #33: 'del_21q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 30(21Q21.1) MUTATED	5	3	0
DEL PEAK 30(21Q21.1) WILD-TYPE	158	117	185

Figure S147. Get High-res Image Gene #33: 'del_21q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S148. Gene #34: 'del_22q13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
DEL PEAK 31(22Q13.1) MUTATED	75	0	14
DEL PEAK 31(22Q13.1) WILD-TYPE	57	138	215

Figure S148. Get High-res Image Gene #34: 'del_22q13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S149. Gene #34: 'del_22q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
DEL PEAK 31(22Q13.1) MUTATED	3	46	9	2	29
DEL PEAK 31(22Q13.1) WILD-TYPE	43	101	75	40	151

Figure S149. Get High-res Image Gene #34: 'del_22q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S150. Gene #34: 'del_22q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 31(22Q13.1) MUTATED	8	47	8	26
DEL PEAK 31(22Q13.1) WILD-TYPE	150	120	50	88

Figure S150. Get High-res Image Gene #34: 'del_22q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S151. Gene #34: 'del_22q13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 31(22Q13.1) MUTATED	9	42	13	23	2
DEL PEAK 31(22Q13.1) WILD-TYPE	95	92	73	72	76

Figure S151. Get High-res Image Gene #34: 'del_22q13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.1' versus 'MIRSEQ_CNMF'

P value = 0.00503 (Fisher's exact test), Q value = 0.02

Table S152. Gene #34: 'del_22q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 31(22Q13.1) MUTATED	21	40	19	9
DEL PEAK 31(22Q13.1) WILD-TYPE	144	105	100	60

Figure S152. Get High-res Image Gene #34: 'del_22q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00074

Table S153. Gene #34: 'del_22q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 31(22Q13.1) MUTATED	21	40	28
DEL PEAK 31(22Q13.1) WILD-TYPE	157	88	164

Figure S153. Get High-res Image Gene #34: 'del_22q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S154. Gene #34: 'del_22q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 31(22Q13.1) MUTATED	17	39	8	17
DEL PEAK 31(22Q13.1) WILD-TYPE	114	86	100	87

Figure S154. Get High-res Image Gene #34: 'del_22q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00064

Table S155. Gene #34: 'del_22q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 31(22Q13.1) MUTATED	21	38	22
DEL PEAK 31(22Q13.1) WILD-TYPE	142	82	163

Figure S155. Get High-res Image Gene #34: 'del_22q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S156. Gene #35: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	138	229
DEL PEAK 32(22Q13.32) MUTATED	75	0	15
DEL PEAK 32(22Q13.32) WILD-TYPE	57	138	214

Figure S156. Get High-res Image Gene #35: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S157. Gene #35: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	147	84	42	180
DEL PEAK 32(22Q13.32) MUTATED	3	47	9	2	29
DEL PEAK 32(22Q13.32) WILD-TYPE	43	100	75	40	151

Figure S157. Get High-res Image Gene #35: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S158. Gene #35: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	158	167	58	114
DEL PEAK 32(22Q13.32) MUTATED	8	48	8	26
DEL PEAK 32(22Q13.32) WILD-TYPE	150	119	50	88

Figure S158. Get High-res Image Gene #35: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S159. Gene #35: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	134	86	95	78
DEL PEAK 32(22Q13.32) MUTATED	9	43	13	23	2
DEL PEAK 32(22Q13.32) WILD-TYPE	95	91	73	72	76

Figure S159. Get High-res Image Gene #35: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.00296 (Fisher's exact test), Q value = 0.014

Table S160. Gene #35: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	165	145	119	69
DEL PEAK 32(22Q13.32) MUTATED	21	41	19	9
DEL PEAK 32(22Q13.32) WILD-TYPE	144	104	100	60

Figure S160. Get High-res Image Gene #35: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00053

Table S161. Gene #35: 'del_22q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	128	192
DEL PEAK 32(22Q13.32) MUTATED	21	41	28
DEL PEAK 32(22Q13.32) WILD-TYPE	157	87	164

Figure S161. Get High-res Image Gene #35: 'del_22q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S162. Gene #35: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	131	125	108	104
DEL PEAK 32(22Q13.32) MUTATED	17	40	8	17
DEL PEAK 32(22Q13.32) WILD-TYPE	114	85	100	87

Figure S162. Get High-res Image Gene #35: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00053

Table S163. Gene #35: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	120	185
DEL PEAK 32(22Q13.32) MUTATED	21	39	22
DEL PEAK 32(22Q13.32) WILD-TYPE	142	81	163

Figure S163. Get High-res Image Gene #35: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/22511444/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THCA-TP/22542946/THCA-TP.transferedmergedcluster.txt
Number of patients = 499
Number of significantly focal cnvs = 36
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

Download Results

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

References

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

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

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