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

Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

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/C1F18XZ6

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 31 focal events and 10 molecular subtypes across 288 patients, 192 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_2p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
amp_2q32.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_3q27.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5q35.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2p12 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_3p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5p15.33 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q35.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_6q22.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_6q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q24.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.42 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_22q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp11.4 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq28 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_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 31 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, 192 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 7q31 2	177 (61%)	111	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.0199 (0.037)	3e-05 (0.000137)	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.0408 (0.068)	0.00061 (0.00195)	5e-05 (0.000209)	1e-05 (5.54e-05)
del 5q35 2	11 (4%)	277	0.0272 (0.0482)	0.00021 (0.000748)	0.033 (0.0565)	0.00023 (0.000792)	0.00049 (0.00162)	2e-05 (9.84e-05)	0.00364 (0.00848)	0.00077 (0.00239)	0.00164 (0.00454)	1e-05 (5.54e-05)
amp 17q25 2	201 (70%)	87	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.0034 (0.00798)	8e-05 (0.000322)	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.0711 (0.111)	0.0113 (0.0225)	0.00192 (0.00513)	5e-05 (0.000209)
del 9p21 3	40 (14%)	248	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.368 (0.449)	0.00104 (0.00307)	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.00023 (0.000792)	0.0125 (0.0245)	0.00013 (0.000491)	3e-05 (0.000137)
del 3p22 1	25 (9%)	263	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.385 (0.461)	0.0294 (0.0518)	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.126 (0.181)	0.0446 (0.0727)	0.0249 (0.0443)	9e-05 (0.000353)
del 14q24 2	50 (17%)	238	1e-05 (5.54e-05)	0.00021 (0.000748)	0.0232 (0.0418)	0.0026 (0.0065)	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.491 (0.566)	1 (1.00)	0.00684 (0.0145)	0.00442 (0.0102)
amp 3q27 1	100 (35%)	188	1e-05 (5.54e-05)	0.0332 (0.0566)	0.302 (0.388)	0.00108 (0.00316)	2e-05 (9.84e-05)	0.0175 (0.0329)	0.0586 (0.0936)	0.00179 (0.00487)	0.703 (0.772)	0.00589 (0.0129)
amp 19p13 2	31 (11%)	257	1e-05 (5.54e-05)	0.00529 (0.0119)	0.00691 (0.0146)	0.00152 (0.00425)	0.00047 (0.00157)	0.00131 (0.0038)	0.147 (0.208)	0.348 (0.431)	0.0594 (0.094)	0.0145 (0.0277)
del 4q34 3	32 (11%)	256	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.275 (0.358)	0.0139 (0.0268)	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.259 (0.342)	0.469 (0.545)	0.00924 (0.0187)	2e-05 (9.84e-05)
del 10q21 1	19 (7%)	269	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.761 (0.822)	0.0433 (0.0711)	7e-05 (0.000289)	0.00071 (0.00222)	0.796 (0.851)	0.792 (0.851)	0.032 (0.0552)	0.0202 (0.0373)
del 11q23 3	29 (10%)	259	1e-05 (5.54e-05)	0.00011 (0.000421)	0.338 (0.423)	0.0414 (0.0686)	3e-05 (0.000137)	0.00137 (0.0039)	0.33 (0.418)	0.373 (0.453)	0.00587 (0.0129)	0.0113 (0.0225)
del 14q11 2	51 (18%)	237	1e-05 (5.54e-05)	0.00198 (0.00525)	0.0638 (0.1)	0.00478 (0.0109)	2e-05 (9.84e-05)	1e-05 (5.54e-05)	0.493 (0.566)	0.96 (0.986)	0.0227 (0.0412)	0.0168 (0.0317)
del 15q13 3	35 (12%)	253	1e-05 (5.54e-05)	0.00024 (0.000818)	0.119 (0.172)	0.03 (0.0525)	3e-05 (0.000137)	1e-05 (5.54e-05)	0.078 (0.121)	0.109 (0.16)	0.0418 (0.069)	0.00276 (0.00676)
del 22q12 2	63 (22%)	225	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.44 (0.514)	0.00641 (0.0138)	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.967 (0.99)	0.746 (0.811)	0.038 (0.064)	0.00215 (0.00565)
del xp11 4	34 (12%)	254	1e-05 (5.54e-05)	2e-05 (9.84e-05)	0.351 (0.432)	0.00103 (0.00307)	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.463 (0.54)	0.38 (0.458)	0.0017 (0.00466)	3e-05 (0.000137)
del 1p36 31	55 (19%)	233	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.552 (0.627)	0.13 (0.185)	1e-05 (5.54e-05)	1e-05 (5.54e-05)	0.877 (0.923)	0.878 (0.923)	0.0236 (0.0423)	0.0022 (0.00573)
del 6q22 31	29 (10%)	259	1e-05 (5.54e-05)	0.00053 (0.00173)	0.889 (0.93)	0.00457 (0.0105)	0.00016 (0.000598)	2e-05 (9.84e-05)	0.376 (0.455)	0.705 (0.772)	0.013 (0.0253)	0.0729 (0.114)
del 6q25 3	32 (11%)	256	1e-05 (5.54e-05)	4e-05 (0.000175)	0.699 (0.771)	0.0197 (0.0369)	1e-05 (5.54e-05)	2e-05 (9.84e-05)	0.329 (0.418)	1 (1.00)	0.0406 (0.068)	0.108 (0.159)
del 11q22 3	31 (11%)	257	1e-05 (5.54e-05)	0.00022 (0.000775)	0.637 (0.716)	0.101 (0.151)	8e-05 (0.000322)	0.00272 (0.00675)	0.238 (0.318)	0.431 (0.51)	0.00238 (0.0061)	0.00548 (0.0122)
del 16q24 1	12 (4%)	276	0.00029 (0.000977)	0.00011 (0.000421)	0.222 (0.303)	0.0927 (0.14)	0.00295 (0.00714)	0.00183 (0.00493)	1 (1.00)	0.313 (0.399)	0.0101 (0.0204)	0.0366 (0.0621)
del xq28	28 (10%)	260	1e-05 (5.54e-05)	5e-05 (0.000209)	0.952 (0.98)	0.106 (0.158)	1e-05 (5.54e-05)	0.00018 (0.000664)	0.596 (0.672)	0.937 (0.972)	0.00718 (0.015)	0.00091 (0.00279)
amp 5q35 2	37 (13%)	251	1e-05 (5.54e-05)	0.00021 (0.000748)	0.254 (0.338)	0.873 (0.923)	0.00277 (0.00676)	1e-05 (5.54e-05)	0.0532 (0.0855)	0.021 (0.0385)	0.434 (0.51)	0.0594 (0.094)
del 2q22 1	10 (3%)	278	0.00337 (0.00797)	0.00596 (0.0129)	0.00645 (0.0138)	0.717 (0.783)	9e-05 (0.000353)	0.00731 (0.0152)	0.67 (0.747)	1 (1.00)	0.197 (0.273)	0.524 (0.597)
del 2q37 3	12 (4%)	276	0.0964 (0.145)	0.00254 (0.00645)	0.0007 (0.00221)	0.213 (0.293)	0.0151 (0.0287)	0.00257 (0.00648)	0.132 (0.187)	0.294 (0.379)	0.0498 (0.0804)	0.231 (0.312)
del 19p13 3	23 (8%)	265	4e-05 (0.000175)	0.0122 (0.024)	0.891 (0.93)	0.81 (0.863)	0.00877 (0.0179)	0.00488 (0.011)	0.354 (0.434)	0.195 (0.273)	0.0878 (0.133)	0.0136 (0.0264)
del 5p15 33	13 (5%)	275	0.26 (0.342)	0.00232 (0.00599)	0.681 (0.756)	0.0786 (0.121)	0.0309 (0.0538)	0.00097 (0.00292)	0.433 (0.51)	0.226 (0.307)	0.333 (0.42)	0.00569 (0.0126)
del 6p12 3	26 (9%)	262	1e-05 (5.54e-05)	0.00057 (0.00184)	1 (1.00)	0.236 (0.317)	0.00133 (0.00382)	0.00097 (0.00292)	0.123 (0.178)	0.59 (0.668)	0.259 (0.342)	0.201 (0.278)
del 19q13 42	19 (7%)	269	4e-05 (0.000175)	0.0219 (0.04)	0.795 (0.851)	0.412 (0.489)	0.00151 (0.00425)	0.00329 (0.00785)	0.505 (0.577)	0.472 (0.546)	0.227 (0.307)	0.305 (0.391)
amp 2p23 2	45 (16%)	243	1e-05 (5.54e-05)	0.00816 (0.0168)	0.76 (0.822)	0.0488 (0.0791)	0.0988 (0.148)	0.951 (0.98)	0.289 (0.374)	0.18 (0.252)	0.391 (0.466)	0.0797 (0.122)
amp 2q32 1	53 (18%)	235	1e-05 (5.54e-05)	0.0319 (0.0552)	0.838 (0.89)	0.116 (0.168)	0.349 (0.431)	0.938 (0.972)	0.381 (0.458)	0.349 (0.431)	0.976 (0.995)	0.337 (0.422)
del 2p12	8 (3%)	280	0.0869 (0.133)	0.00796 (0.0165)	0.168 (0.237)	0.668 (0.747)	0.00322 (0.00774)	0.108 (0.159)	0.222 (0.303)	0.268 (0.351)	0.694 (0.769)	1 (1.00)

'amp_2p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S1. Gene #1: 'amp_2p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 1(2P23.2) MUTATED	2	3	14	26
AMP PEAK 1(2P23.2) WILD-TYPE	112	73	32	26

Figure S1. Get High-res Image Gene #1: 'amp_2p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p23.2' versus 'METHLYATION_CNMF'

P value = 0.00816 (Fisher's exact test), Q value = 0.017

Table S2. Gene #1: 'amp_2p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
AMP PEAK 1(2P23.2) MUTATED	5	16	21
AMP PEAK 1(2P23.2) WILD-TYPE	77	55	98

Figure S2. Get High-res Image Gene #1: 'amp_2p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0488 (Fisher's exact test), Q value = 0.079

Table S3. Gene #1: 'amp_2p23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
AMP PEAK 1(2P23.2) MUTATED	7	8	15	2
AMP PEAK 1(2P23.2) WILD-TYPE	32	58	50	41

Figure S3. Get High-res Image Gene #1: 'amp_2p23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_2q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S4. Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 2(2Q32.1) MUTATED	4	4	15	30
AMP PEAK 2(2Q32.1) WILD-TYPE	110	72	31	22

Figure S4. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q32.1' versus 'METHLYATION_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.055

Table S5. Gene #2: 'amp_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
AMP PEAK 2(2Q32.1) MUTATED	8	18	24
AMP PEAK 2(2Q32.1) WILD-TYPE	74	53	95

Figure S5. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q27.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S6. Gene #3: 'amp_3q27.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 3(3Q27.1) MUTATED	20	17	45	18
AMP PEAK 3(3Q27.1) WILD-TYPE	94	59	1	34

Figure S6. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q27.1' versus 'METHLYATION_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.057

Table S7. Gene #3: 'amp_3q27.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
AMP PEAK 3(3Q27.1) MUTATED	25	18	51
AMP PEAK 3(3Q27.1) WILD-TYPE	57	53	68

Figure S7. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q27.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0032

Table S8. Gene #3: 'amp_3q27.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
AMP PEAK 3(3Q27.1) MUTATED	23	23	15	10
AMP PEAK 3(3Q27.1) WILD-TYPE	16	43	50	33

Figure S8. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3q27.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S9. Gene #3: 'amp_3q27.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
AMP PEAK 3(3Q27.1) MUTATED	18	38	31	13
AMP PEAK 3(3Q27.1) WILD-TYPE	16	58	35	79

Figure S9. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q27.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.033

Table S10. Gene #3: 'amp_3q27.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
AMP PEAK 3(3Q27.1) MUTATED	37	53	10
AMP PEAK 3(3Q27.1) WILD-TYPE	81	70	37

Figure S10. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q27.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.0049

Table S11. Gene #3: 'amp_3q27.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
AMP PEAK 3(3Q27.1) MUTATED	41	39	20
AMP PEAK 3(3Q27.1) WILD-TYPE	79	41	68

Figure S11. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q27.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00589 (Fisher's exact test), Q value = 0.013

Table S12. Gene #3: 'amp_3q27.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
AMP PEAK 3(3Q27.1) MUTATED	45	18	3	5
AMP PEAK 3(3Q27.1) WILD-TYPE	58	57	12	24

Figure S12. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S13. Gene #4: 'amp_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 4(5Q35.2) MUTATED	19	2	0	16
AMP PEAK 4(5Q35.2) WILD-TYPE	95	74	46	36

Figure S13. Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.2' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00075

Table S14. Gene #4: 'amp_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
AMP PEAK 4(5Q35.2) MUTATED	12	17	5
AMP PEAK 4(5Q35.2) WILD-TYPE	70	54	114

Figure S14. Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.2' versus 'MRNASEQ_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.0068

Table S15. Gene #4: 'amp_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
AMP PEAK 4(5Q35.2) MUTATED	4	4	9	20
AMP PEAK 4(5Q35.2) WILD-TYPE	30	92	57	72

Figure S15. Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S16. Gene #4: 'amp_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
AMP PEAK 4(5Q35.2) MUTATED	29	4	4
AMP PEAK 4(5Q35.2) WILD-TYPE	89	119	43

Figure S16. Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.038

Table S17. Gene #4: 'amp_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
AMP PEAK 4(5Q35.2) MUTATED	23	5	9
AMP PEAK 4(5Q35.2) WILD-TYPE	97	75	79

Figure S17. Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S18. Gene #5: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 5(7Q31.2) MUTATED	32	75	43	27
AMP PEAK 5(7Q31.2) WILD-TYPE	82	1	3	25

Figure S18. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S19. Gene #5: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
AMP PEAK 5(7Q31.2) MUTATED	39	25	102
AMP PEAK 5(7Q31.2) WILD-TYPE	43	46	17

Figure S19. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.037

Table S20. Gene #5: 'amp_7q31.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
AMP PEAK 5(7Q31.2) MUTATED	46	60	28
AMP PEAK 5(7Q31.2) WILD-TYPE	29	22	28

Figure S20. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S21. Gene #5: 'amp_7q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
AMP PEAK 5(7Q31.2) MUTATED	31	53	30	20
AMP PEAK 5(7Q31.2) WILD-TYPE	8	13	35	23

Figure S21. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S22. Gene #5: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
AMP PEAK 5(7Q31.2) MUTATED	29	84	39	25
AMP PEAK 5(7Q31.2) WILD-TYPE	5	12	27	67

Figure S22. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S23. Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
AMP PEAK 5(7Q31.2) MUTATED	54	105	18
AMP PEAK 5(7Q31.2) WILD-TYPE	64	18	29

Figure S23. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

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

Table S24. Gene #5: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
AMP PEAK 5(7Q31.2) MUTATED	47	77	53
AMP PEAK 5(7Q31.2) WILD-TYPE	42	33	36

Figure S24. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0019

Table S25. Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
AMP PEAK 5(7Q31.2) MUTATED	67	63	47
AMP PEAK 5(7Q31.2) WILD-TYPE	53	17	41

Figure S25. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00021

Table S26. Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
AMP PEAK 5(7Q31.2) MUTATED	34	64	35
AMP PEAK 5(7Q31.2) WILD-TYPE	36	17	36

Figure S26. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S27. Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
AMP PEAK 5(7Q31.2) MUTATED	72	32	4	25
AMP PEAK 5(7Q31.2) WILD-TYPE	31	43	11	4

Figure S27. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S28. Gene #6: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 6(17Q25.2) MUTATED	43	76	45	37
AMP PEAK 6(17Q25.2) WILD-TYPE	71	0	1	15

Figure S28. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S29. Gene #6: 'amp_17q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
AMP PEAK 6(17Q25.2) MUTATED	44	39	106
AMP PEAK 6(17Q25.2) WILD-TYPE	38	32	13

Figure S29. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.2' versus 'RPPA_CNMF'

P value = 0.0034 (Fisher's exact test), Q value = 0.008

Table S30. Gene #6: 'amp_17q25.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
AMP PEAK 6(17Q25.2) MUTATED	56	64	29
AMP PEAK 6(17Q25.2) WILD-TYPE	19	18	27

Figure S30. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_17q25.2' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00032

Table S31. Gene #6: 'amp_17q25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
AMP PEAK 6(17Q25.2) MUTATED	35	53	37	24
AMP PEAK 6(17Q25.2) WILD-TYPE	4	13	28	19

Figure S31. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q25.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S32. Gene #6: 'amp_17q25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
AMP PEAK 6(17Q25.2) MUTATED	24	88	46	43
AMP PEAK 6(17Q25.2) WILD-TYPE	10	8	20	49

Figure S32. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S33. Gene #6: 'amp_17q25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
AMP PEAK 6(17Q25.2) MUTATED	73	109	19
AMP PEAK 6(17Q25.2) WILD-TYPE	45	14	28

Figure S33. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.023

Table S34. Gene #6: 'amp_17q25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
AMP PEAK 6(17Q25.2) MUTATED	77	66	58
AMP PEAK 6(17Q25.2) WILD-TYPE	43	14	30

Figure S34. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00192 (Fisher's exact test), Q value = 0.0051

Table S35. Gene #6: 'amp_17q25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
AMP PEAK 6(17Q25.2) MUTATED	43	67	42
AMP PEAK 6(17Q25.2) WILD-TYPE	27	14	29

Figure S35. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00021

Table S36. Gene #6: 'amp_17q25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
AMP PEAK 6(17Q25.2) MUTATED	79	40	7	26
AMP PEAK 6(17Q25.2) WILD-TYPE	24	35	8	3

Figure S36. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S37. Gene #7: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 7(19P13.2) MUTATED	1	22	0	8
AMP PEAK 7(19P13.2) WILD-TYPE	113	54	46	44

Figure S37. Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 0.00529 (Fisher's exact test), Q value = 0.012

Table S38. Gene #7: 'amp_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
AMP PEAK 7(19P13.2) MUTATED	4	3	20
AMP PEAK 7(19P13.2) WILD-TYPE	78	68	99

Figure S38. Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'RPPA_CNMF'

P value = 0.00691 (Fisher's exact test), Q value = 0.015

Table S39. Gene #7: 'amp_19p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
AMP PEAK 7(19P13.2) MUTATED	4	15	2
AMP PEAK 7(19P13.2) WILD-TYPE	71	67	54

Figure S39. Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_19p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00152 (Fisher's exact test), Q value = 0.0042

Table S40. Gene #7: 'amp_19p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
AMP PEAK 7(19P13.2) MUTATED	1	13	7	0
AMP PEAK 7(19P13.2) WILD-TYPE	38	53	58	43

Figure S40. Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0016

Table S41. Gene #7: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
AMP PEAK 7(19P13.2) MUTATED	1	21	2	7
AMP PEAK 7(19P13.2) WILD-TYPE	33	75	64	85

Figure S41. Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.0038

Table S42. Gene #7: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
AMP PEAK 7(19P13.2) MUTATED	4	20	7
AMP PEAK 7(19P13.2) WILD-TYPE	114	103	40

Figure S42. Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S43. Gene #7: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
AMP PEAK 7(19P13.2) MUTATED	7	5	1	8
AMP PEAK 7(19P13.2) WILD-TYPE	96	70	14	21

Figure S43. Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S44. Gene #8: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 1(1P36.31) MUTATED	21	0	2	32
DEL PEAK 1(1P36.31) WILD-TYPE	93	76	44	20

Figure S44. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S45. Gene #8: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 1(1P36.31) MUTATED	15	28	9
DEL PEAK 1(1P36.31) WILD-TYPE	67	43	110

Figure S45. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S46. Gene #8: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 1(1P36.31) MUTATED	0	5	10	40
DEL PEAK 1(1P36.31) WILD-TYPE	34	91	56	52

Figure S46. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S47. Gene #8: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 1(1P36.31) MUTATED	28	8	19
DEL PEAK 1(1P36.31) WILD-TYPE	90	115	28

Figure S47. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.042

Table S48. Gene #8: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 1(1P36.31) MUTATED	13	8	19
DEL PEAK 1(1P36.31) WILD-TYPE	57	73	52

Figure S48. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0022 (Fisher's exact test), Q value = 0.0057

Table S49. Gene #8: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 1(1P36.31) MUTATED	16	19	5	0
DEL PEAK 1(1P36.31) WILD-TYPE	87	56	10	29

Figure S49. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2p12' versus 'METHLYATION_CNMF'

P value = 0.00796 (Fisher's exact test), Q value = 0.016

Table S50. Gene #9: 'del_2p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 2(2P12) MUTATED	3	5	0
DEL PEAK 2(2P12) WILD-TYPE	79	66	119

Figure S50. Get High-res Image Gene #9: 'del_2p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p12' versus 'MRNASEQ_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.0077

Table S51. Gene #9: 'del_2p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 2(2P12) MUTATED	1	0	0	7
DEL PEAK 2(2P12) WILD-TYPE	33	96	66	85

Figure S51. Get High-res Image Gene #9: 'del_2p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.008

Table S52. Gene #10: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 3(2Q22.1) MUTATED	4	0	0	6
DEL PEAK 3(2Q22.1) WILD-TYPE	110	76	46	46

Figure S52. Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.00596 (Fisher's exact test), Q value = 0.013

Table S53. Gene #10: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 3(2Q22.1) MUTATED	4	5	0
DEL PEAK 3(2Q22.1) WILD-TYPE	78	66	119

Figure S53. Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CNMF'

P value = 0.00645 (Fisher's exact test), Q value = 0.014

Table S54. Gene #10: 'del_2q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
DEL PEAK 3(2Q22.1) MUTATED	2	0	5
DEL PEAK 3(2Q22.1) WILD-TYPE	73	82	51

Figure S54. Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00035

Table S55. Gene #10: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 3(2Q22.1) MUTATED	0	0	0	10
DEL PEAK 3(2Q22.1) WILD-TYPE	34	96	66	82

Figure S55. Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00731 (Fisher's exact test), Q value = 0.015

Table S56. Gene #10: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 3(2Q22.1) MUTATED	7	0	3
DEL PEAK 3(2Q22.1) WILD-TYPE	111	123	44

Figure S56. Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.0065

Table S57. Gene #11: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 4(2Q37.3) MUTATED	4	6	0
DEL PEAK 4(2Q37.3) WILD-TYPE	78	65	119

Figure S57. Get High-res Image Gene #11: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0022

Table S58. Gene #11: 'del_2q37.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
DEL PEAK 4(2Q37.3) MUTATED	0	1	7
DEL PEAK 4(2Q37.3) WILD-TYPE	75	81	49

Figure S58. Get High-res Image Gene #11: 'del_2q37.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.029

Table S59. Gene #11: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 4(2Q37.3) MUTATED	0	1	2	9
DEL PEAK 4(2Q37.3) WILD-TYPE	34	95	64	83

Figure S59. Get High-res Image Gene #11: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00257 (Fisher's exact test), Q value = 0.0065

Table S60. Gene #11: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 4(2Q37.3) MUTATED	9	0	3
DEL PEAK 4(2Q37.3) WILD-TYPE	109	123	44

Figure S60. Get High-res Image Gene #11: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.08

Table S61. Gene #11: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 4(2Q37.3) MUTATED	7	1	3
DEL PEAK 4(2Q37.3) WILD-TYPE	63	80	68

Figure S61. Get High-res Image Gene #11: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S62. Gene #12: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 5(3P22.1) MUTATED	6	0	0	19
DEL PEAK 5(3P22.1) WILD-TYPE	108	76	46	33

Figure S62. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S63. Gene #12: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 5(3P22.1) MUTATED	5	18	1
DEL PEAK 5(3P22.1) WILD-TYPE	77	53	118

Figure S63. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p22.1' versus 'RPPA_CHIERARCHICAL'

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

Table S64. Gene #12: 'del_3p22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 5(3P22.1) MUTATED	3	4	12	1
DEL PEAK 5(3P22.1) WILD-TYPE	36	62	53	42

Figure S64. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3p22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S65. Gene #12: 'del_3p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 5(3P22.1) MUTATED	0	0	4	21
DEL PEAK 5(3P22.1) WILD-TYPE	34	96	62	71

Figure S65. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S66. Gene #12: 'del_3p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 5(3P22.1) MUTATED	21	0	4
DEL PEAK 5(3P22.1) WILD-TYPE	97	123	43

Figure S66. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.073

Table S67. Gene #12: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
DEL PEAK 5(3P22.1) MUTATED	13	2	10
DEL PEAK 5(3P22.1) WILD-TYPE	107	78	78

Figure S67. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.044

Table S68. Gene #12: 'del_3p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 5(3P22.1) MUTATED	10	3	11
DEL PEAK 5(3P22.1) WILD-TYPE	60	78	60

Figure S68. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00035

Table S69. Gene #12: 'del_3p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 5(3P22.1) MUTATED	5	18	1	0
DEL PEAK 5(3P22.1) WILD-TYPE	98	57	14	29

Figure S69. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S70. Gene #13: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 6(4Q34.3) MUTATED	8	1	1	22
DEL PEAK 6(4Q34.3) WILD-TYPE	106	75	45	30

Figure S70. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S71. Gene #13: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 6(4Q34.3) MUTATED	6	22	2
DEL PEAK 6(4Q34.3) WILD-TYPE	76	49	117

Figure S71. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.027

Table S72. Gene #13: 'del_4q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 6(4Q34.3) MUTATED	2	4	15	4
DEL PEAK 6(4Q34.3) WILD-TYPE	37	62	50	39

Figure S72. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S73. Gene #13: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 6(4Q34.3) MUTATED	0	1	3	28
DEL PEAK 6(4Q34.3) WILD-TYPE	34	95	63	64

Figure S73. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S74. Gene #13: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 6(4Q34.3) MUTATED	18	2	12
DEL PEAK 6(4Q34.3) WILD-TYPE	100	121	35

Figure S74. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00924 (Fisher's exact test), Q value = 0.019

Table S75. Gene #13: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 6(4Q34.3) MUTATED	10	3	13
DEL PEAK 6(4Q34.3) WILD-TYPE	60	78	58

Figure S75. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S76. Gene #13: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 6(4Q34.3) MUTATED	7	11	8	0
DEL PEAK 6(4Q34.3) WILD-TYPE	96	64	7	29

Figure S76. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.006

Table S77. Gene #14: 'del_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 7(5P15.33) MUTATED	2	9	2
DEL PEAK 7(5P15.33) WILD-TYPE	80	62	117

Figure S77. Get High-res Image Gene #14: 'del_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.054

Table S78. Gene #14: 'del_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 7(5P15.33) MUTATED	0	1	4	8
DEL PEAK 7(5P15.33) WILD-TYPE	34	95	62	84

Figure S78. Get High-res Image Gene #14: 'del_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0029

Table S79. Gene #14: 'del_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 7(5P15.33) MUTATED	5	1	7
DEL PEAK 7(5P15.33) WILD-TYPE	113	122	40

Figure S79. Get High-res Image Gene #14: 'del_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00569 (Fisher's exact test), Q value = 0.013

Table S80. Gene #14: 'del_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 7(5P15.33) MUTATED	2	4	4	1
DEL PEAK 7(5P15.33) WILD-TYPE	101	71	11	28

Figure S80. Get High-res Image Gene #14: 'del_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q35.2' versus 'CN_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.048

Table S81. Gene #15: 'del_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 8(5Q35.2) MUTATED	3	1	1	6
DEL PEAK 8(5Q35.2) WILD-TYPE	111	75	45	46

Figure S81. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.2' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00075

Table S82. Gene #15: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 8(5Q35.2) MUTATED	2	8	0
DEL PEAK 8(5Q35.2) WILD-TYPE	80	63	119

Figure S82. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q35.2' versus 'RPPA_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.057

Table S83. Gene #15: 'del_5q35.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
DEL PEAK 8(5Q35.2) MUTATED	5	0	3
DEL PEAK 8(5Q35.2) WILD-TYPE	70	82	53

Figure S83. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q35.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00079

Table S84. Gene #15: 'del_5q35.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 8(5Q35.2) MUTATED	0	0	8	0
DEL PEAK 8(5Q35.2) WILD-TYPE	39	66	57	43

Figure S84. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_5q35.2' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0016

Table S85. Gene #15: 'del_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 8(5Q35.2) MUTATED	0	0	1	10
DEL PEAK 8(5Q35.2) WILD-TYPE	34	96	65	82

Figure S85. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S86. Gene #15: 'del_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 8(5Q35.2) MUTATED	3	0	8
DEL PEAK 8(5Q35.2) WILD-TYPE	115	123	39

Figure S86. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q35.2' versus 'MIRSEQ_CNMF'

P value = 0.00364 (Fisher's exact test), Q value = 0.0085

Table S87. Gene #15: 'del_5q35.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
DEL PEAK 8(5Q35.2) MUTATED	0	3	8
DEL PEAK 8(5Q35.2) WILD-TYPE	89	107	81

Figure S87. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0024

Table S88. Gene #15: 'del_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
DEL PEAK 8(5Q35.2) MUTATED	2	0	9
DEL PEAK 8(5Q35.2) WILD-TYPE	118	80	79

Figure S88. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q35.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0045

Table S89. Gene #15: 'del_5q35.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 8(5Q35.2) MUTATED	2	0	8
DEL PEAK 8(5Q35.2) WILD-TYPE	68	81	63

Figure S89. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S90. Gene #15: 'del_5q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 8(5Q35.2) MUTATED	0	2	8	0
DEL PEAK 8(5Q35.2) WILD-TYPE	103	73	7	29

Figure S90. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S91. Gene #16: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 9(6P12.3) MUTATED	8	0	1	17
DEL PEAK 9(6P12.3) WILD-TYPE	106	76	45	35

Figure S91. Get High-res Image Gene #16: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p12.3' versus 'METHLYATION_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0018

Table S92. Gene #16: 'del_6p12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 9(6P12.3) MUTATED	5	15	5
DEL PEAK 9(6P12.3) WILD-TYPE	77	56	114

Figure S92. Get High-res Image Gene #16: 'del_6p12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p12.3' versus 'MRNASEQ_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0038

Table S93. Gene #16: 'del_6p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 9(6P12.3) MUTATED	0	4	5	17
DEL PEAK 9(6P12.3) WILD-TYPE	34	92	61	75

Figure S93. Get High-res Image Gene #16: 'del_6p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0029

Table S94. Gene #16: 'del_6p12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 9(6P12.3) MUTATED	12	4	10
DEL PEAK 9(6P12.3) WILD-TYPE	106	119	37

Figure S94. Get High-res Image Gene #16: 'del_6p12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S95. Gene #17: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 10(6Q22.31) MUTATED	8	0	1	20
DEL PEAK 10(6Q22.31) WILD-TYPE	106	76	45	32

Figure S95. Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0017

Table S96. Gene #17: 'del_6q22.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 10(6Q22.31) MUTATED	9	15	4
DEL PEAK 10(6Q22.31) WILD-TYPE	73	56	115

Figure S96. Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q22.31' versus 'RPPA_CHIERARCHICAL'

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

Table S97. Gene #17: 'del_6q22.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 10(6Q22.31) MUTATED	3	5	15	1
DEL PEAK 10(6Q22.31) WILD-TYPE	36	61	50	42

Figure S97. Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 6e-04

Table S98. Gene #17: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 10(6Q22.31) MUTATED	1	3	5	20
DEL PEAK 10(6Q22.31) WILD-TYPE	33	93	61	72

Figure S98. Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S99. Gene #17: 'del_6q22.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 10(6Q22.31) MUTATED	13	3	13
DEL PEAK 10(6Q22.31) WILD-TYPE	105	120	34

Figure S99. Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.025

Table S100. Gene #17: 'del_6q22.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 10(6Q22.31) MUTATED	3	5	13
DEL PEAK 10(6Q22.31) WILD-TYPE	67	76	58

Figure S100. Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S101. Gene #18: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 11(6Q25.3) MUTATED	7	0	1	24
DEL PEAK 11(6Q25.3) WILD-TYPE	107	76	45	28

Figure S101. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q25.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S102. Gene #18: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 11(6Q25.3) MUTATED	8	19	4
DEL PEAK 11(6Q25.3) WILD-TYPE	74	52	115

Figure S102. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.037

Table S103. Gene #18: 'del_6q25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 11(6Q25.3) MUTATED	4	5	15	2
DEL PEAK 11(6Q25.3) WILD-TYPE	35	61	50	41

Figure S103. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6q25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S104. Gene #18: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 11(6Q25.3) MUTATED	0	3	6	23
DEL PEAK 11(6Q25.3) WILD-TYPE	34	93	60	69

Figure S104. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S105. Gene #18: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 11(6Q25.3) MUTATED	17	3	12
DEL PEAK 11(6Q25.3) WILD-TYPE	101	120	35

Figure S105. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.068

Table S106. Gene #18: 'del_6q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 11(6Q25.3) MUTATED	4	6	13
DEL PEAK 11(6Q25.3) WILD-TYPE	66	75	58

Figure S106. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S107. Gene #19: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 12(9P21.3) MUTATED	11	2	1	26
DEL PEAK 12(9P21.3) WILD-TYPE	103	74	45	26

Figure S107. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S108. Gene #19: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 12(9P21.3) MUTATED	12	22	3
DEL PEAK 12(9P21.3) WILD-TYPE	70	49	116

Figure S108. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.0031

Table S109. Gene #19: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 12(9P21.3) MUTATED	3	5	19	3
DEL PEAK 12(9P21.3) WILD-TYPE	36	61	46	40

Figure S109. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S110. Gene #19: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 12(9P21.3) MUTATED	1	2	4	33
DEL PEAK 12(9P21.3) WILD-TYPE	33	94	62	59

Figure S110. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S111. Gene #19: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 12(9P21.3) MUTATED	20	0	20
DEL PEAK 12(9P21.3) WILD-TYPE	98	123	27

Figure S111. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00079

Table S112. Gene #19: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
DEL PEAK 12(9P21.3) MUTATED	3	16	21
DEL PEAK 12(9P21.3) WILD-TYPE	86	94	68

Figure S112. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.024

Table S113. Gene #19: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
DEL PEAK 12(9P21.3) MUTATED	10	10	20
DEL PEAK 12(9P21.3) WILD-TYPE	110	70	68

Figure S113. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00049

Table S114. Gene #19: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 12(9P21.3) MUTATED	8	4	21
DEL PEAK 12(9P21.3) WILD-TYPE	62	77	50

Figure S114. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S115. Gene #19: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 12(9P21.3) MUTATED	8	19	6	0
DEL PEAK 12(9P21.3) WILD-TYPE	95	56	9	29

Figure S115. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S116. Gene #20: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 13(10Q21.1) MUTATED	5	0	0	14
DEL PEAK 13(10Q21.1) WILD-TYPE	109	76	46	38

Figure S116. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S117. Gene #20: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 13(10Q21.1) MUTATED	2	15	2
DEL PEAK 13(10Q21.1) WILD-TYPE	80	56	117

Figure S117. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.071

Table S118. Gene #20: 'del_10q21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 13(10Q21.1) MUTATED	1	4	10	1
DEL PEAK 13(10Q21.1) WILD-TYPE	38	62	55	42

Figure S118. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00029

Table S119. Gene #20: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 13(10Q21.1) MUTATED	0	1	3	15
DEL PEAK 13(10Q21.1) WILD-TYPE	34	95	63	77

Figure S119. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0022

Table S120. Gene #20: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 13(10Q21.1) MUTATED	13	1	5
DEL PEAK 13(10Q21.1) WILD-TYPE	105	122	42

Figure S120. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.055

Table S121. Gene #20: 'del_10q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 13(10Q21.1) MUTATED	3	2	9
DEL PEAK 13(10Q21.1) WILD-TYPE	67	79	62

Figure S121. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0202 (Fisher's exact test), Q value = 0.037

Table S122. Gene #20: 'del_10q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 13(10Q21.1) MUTATED	3	9	2	0
DEL PEAK 13(10Q21.1) WILD-TYPE	100	66	13	29

Figure S122. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S123. Gene #21: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 14(11Q22.3) MUTATED	8	4	1	18
DEL PEAK 14(11Q22.3) WILD-TYPE	106	72	45	34

Figure S123. Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.3' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00077

Table S124. Gene #21: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 14(11Q22.3) MUTATED	8	17	5
DEL PEAK 14(11Q22.3) WILD-TYPE	74	54	114

Figure S124. Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q22.3' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00032

Table S125. Gene #21: 'del_11q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 14(11Q22.3) MUTATED	1	5	3	22
DEL PEAK 14(11Q22.3) WILD-TYPE	33	91	63	70

Figure S125. Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.0067

Table S126. Gene #21: 'del_11q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 14(11Q22.3) MUTATED	17	5	9
DEL PEAK 14(11Q22.3) WILD-TYPE	101	118	38

Figure S126. Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.0061

Table S127. Gene #21: 'del_11q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 14(11Q22.3) MUTATED	6	3	15
DEL PEAK 14(11Q22.3) WILD-TYPE	64	78	56

Figure S127. Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00548 (Fisher's exact test), Q value = 0.012

Table S128. Gene #21: 'del_11q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 14(11Q22.3) MUTATED	7	15	2	0
DEL PEAK 14(11Q22.3) WILD-TYPE	96	60	13	29

Figure S128. Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S129. Gene #22: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 15(11Q23.3) MUTATED	6	4	0	19
DEL PEAK 15(11Q23.3) WILD-TYPE	108	72	46	33

Figure S129. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00042

Table S130. Gene #22: 'del_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 15(11Q23.3) MUTATED	7	17	4
DEL PEAK 15(11Q23.3) WILD-TYPE	75	54	115

Figure S130. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0414 (Fisher's exact test), Q value = 0.069

Table S131. Gene #22: 'del_11q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 15(11Q23.3) MUTATED	3	3	13	4
DEL PEAK 15(11Q23.3) WILD-TYPE	36	63	52	39

Figure S131. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q23.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S132. Gene #22: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 15(11Q23.3) MUTATED	1	4	3	21
DEL PEAK 15(11Q23.3) WILD-TYPE	33	92	63	71

Figure S132. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.0039

Table S133. Gene #22: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 15(11Q23.3) MUTATED	17	4	8
DEL PEAK 15(11Q23.3) WILD-TYPE	101	119	39

Figure S133. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00587 (Fisher's exact test), Q value = 0.013

Table S134. Gene #22: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 15(11Q23.3) MUTATED	6	3	14
DEL PEAK 15(11Q23.3) WILD-TYPE	64	78	57

Figure S134. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.023

Table S135. Gene #22: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 15(11Q23.3) MUTATED	7	14	2	0
DEL PEAK 15(11Q23.3) WILD-TYPE	96	61	13	29

Figure S135. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S136. Gene #23: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 16(14Q11.2) MUTATED	20	1	2	28
DEL PEAK 16(14Q11.2) WILD-TYPE	94	75	44	24

Figure S136. Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0052

Table S137. Gene #23: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 16(14Q11.2) MUTATED	17	19	10
DEL PEAK 16(14Q11.2) WILD-TYPE	65	52	109

Figure S137. Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00478 (Fisher's exact test), Q value = 0.011

Table S138. Gene #23: 'del_14q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 16(14Q11.2) MUTATED	6	7	20	3
DEL PEAK 16(14Q11.2) WILD-TYPE	33	59	45	40

Figure S138. Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S139. Gene #23: 'del_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 16(14Q11.2) MUTATED	4	5	13	29
DEL PEAK 16(14Q11.2) WILD-TYPE	30	91	53	63

Figure S139. Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S140. Gene #23: 'del_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 16(14Q11.2) MUTATED	24	8	19
DEL PEAK 16(14Q11.2) WILD-TYPE	94	115	28

Figure S140. Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.041

Table S141. Gene #23: 'del_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 16(14Q11.2) MUTATED	11	8	19
DEL PEAK 16(14Q11.2) WILD-TYPE	59	73	52

Figure S141. Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.032

Table S142. Gene #23: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 16(14Q11.2) MUTATED	12	20	4	2
DEL PEAK 16(14Q11.2) WILD-TYPE	91	55	11	27

Figure S142. Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S143. Gene #24: 'del_14q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 17(14Q24.2) MUTATED	21	0	1	28
DEL PEAK 17(14Q24.2) WILD-TYPE	93	76	45	24

Figure S143. Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.2' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00075

Table S144. Gene #24: 'del_14q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 17(14Q24.2) MUTATED	18	20	8
DEL PEAK 17(14Q24.2) WILD-TYPE	64	51	111

Figure S144. Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q24.2' versus 'RPPA_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.042

Table S145. Gene #24: 'del_14q24.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
DEL PEAK 17(14Q24.2) MUTATED	20	9	7
DEL PEAK 17(14Q24.2) WILD-TYPE	55	73	49

Figure S145. Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_14q24.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0026 (Fisher's exact test), Q value = 0.0065

Table S146. Gene #24: 'del_14q24.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 17(14Q24.2) MUTATED	7	6	20	3
DEL PEAK 17(14Q24.2) WILD-TYPE	32	60	45	40

Figure S146. Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_14q24.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S147. Gene #24: 'del_14q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 17(14Q24.2) MUTATED	4	4	11	31
DEL PEAK 17(14Q24.2) WILD-TYPE	30	92	55	61

Figure S147. Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S148. Gene #24: 'del_14q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 17(14Q24.2) MUTATED	24	7	19
DEL PEAK 17(14Q24.2) WILD-TYPE	94	116	28

Figure S148. Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00684 (Fisher's exact test), Q value = 0.015

Table S149. Gene #24: 'del_14q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 17(14Q24.2) MUTATED	12	7	20
DEL PEAK 17(14Q24.2) WILD-TYPE	58	74	51

Figure S149. Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00442 (Fisher's exact test), Q value = 0.01

Table S150. Gene #24: 'del_14q24.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 17(14Q24.2) MUTATED	13	21	4	1
DEL PEAK 17(14Q24.2) WILD-TYPE	90	54	11	28

Figure S150. Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S151. Gene #25: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 18(15Q13.3) MUTATED	12	0	3	20
DEL PEAK 18(15Q13.3) WILD-TYPE	102	76	43	32

Figure S151. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q13.3' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00082

Table S152. Gene #25: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 18(15Q13.3) MUTATED	11	17	5
DEL PEAK 18(15Q13.3) WILD-TYPE	71	54	114

Figure S152. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.053

Table S153. Gene #25: 'del_15q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 18(15Q13.3) MUTATED	4	5	16	4
DEL PEAK 18(15Q13.3) WILD-TYPE	35	61	49	39

Figure S153. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_15q13.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S154. Gene #25: 'del_15q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 18(15Q13.3) MUTATED	1	3	7	24
DEL PEAK 18(15Q13.3) WILD-TYPE	33	93	59	68

Figure S154. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S155. Gene #25: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 18(15Q13.3) MUTATED	16	4	15
DEL PEAK 18(15Q13.3) WILD-TYPE	102	119	32

Figure S155. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.069

Table S156. Gene #25: 'del_15q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 18(15Q13.3) MUTATED	8	6	15
DEL PEAK 18(15Q13.3) WILD-TYPE	62	75	56

Figure S156. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00276 (Fisher's exact test), Q value = 0.0068

Table S157. Gene #25: 'del_15q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 18(15Q13.3) MUTATED	12	11	6	0
DEL PEAK 18(15Q13.3) WILD-TYPE	91	64	9	29

Figure S157. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.1' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00098

Table S158. Gene #26: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 19(16Q24.1) MUTATED	4	0	0	8
DEL PEAK 19(16Q24.1) WILD-TYPE	110	76	46	44

Figure S158. Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q24.1' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00042

Table S159. Gene #26: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 19(16Q24.1) MUTATED	3	9	0
DEL PEAK 19(16Q24.1) WILD-TYPE	79	62	119

Figure S159. Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q24.1' versus 'MRNASEQ_CNMF'

P value = 0.00295 (Fisher's exact test), Q value = 0.0071

Table S160. Gene #26: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 19(16Q24.1) MUTATED	0	0	3	9
DEL PEAK 19(16Q24.1) WILD-TYPE	34	96	63	83

Figure S160. Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00183 (Fisher's exact test), Q value = 0.0049

Table S161. Gene #26: 'del_16q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 19(16Q24.1) MUTATED	8	0	4
DEL PEAK 19(16Q24.1) WILD-TYPE	110	123	43

Figure S161. Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.02

Table S162. Gene #26: 'del_16q24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 19(16Q24.1) MUTATED	5	0	6
DEL PEAK 19(16Q24.1) WILD-TYPE	65	81	65

Figure S162. Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0366 (Fisher's exact test), Q value = 0.062

Table S163. Gene #26: 'del_16q24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 19(16Q24.1) MUTATED	3	5	3	0
DEL PEAK 19(16Q24.1) WILD-TYPE	100	70	12	29

Figure S163. Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S164. Gene #27: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 20(19P13.3) MUTATED	4	4	1	14
DEL PEAK 20(19P13.3) WILD-TYPE	110	72	45	38

Figure S164. Get High-res Image Gene #27: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.024

Table S165. Gene #27: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 20(19P13.3) MUTATED	4	12	6
DEL PEAK 20(19P13.3) WILD-TYPE	78	59	113

Figure S165. Get High-res Image Gene #27: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00877 (Fisher's exact test), Q value = 0.018

Table S166. Gene #27: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 20(19P13.3) MUTATED	0	3	8	12
DEL PEAK 20(19P13.3) WILD-TYPE	34	93	58	80

Figure S166. Get High-res Image Gene #27: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00488 (Fisher's exact test), Q value = 0.011

Table S167. Gene #27: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 20(19P13.3) MUTATED	17	4	2
DEL PEAK 20(19P13.3) WILD-TYPE	101	119	45

Figure S167. Get High-res Image Gene #27: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.026

Table S168. Gene #27: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 20(19P13.3) MUTATED	7	13	0	0
DEL PEAK 20(19P13.3) WILD-TYPE	96	62	15	29

Figure S168. Get High-res Image Gene #27: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.42' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S169. Gene #28: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 21(19Q13.42) MUTATED	2	3	2	12
DEL PEAK 21(19Q13.42) WILD-TYPE	112	73	44	40

Figure S169. Get High-res Image Gene #28: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.42' versus 'METHLYATION_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.04

Table S170. Gene #28: 'del_19q13.42' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 21(19Q13.42) MUTATED	5	10	4
DEL PEAK 21(19Q13.42) WILD-TYPE	77	61	115

Figure S170. Get High-res Image Gene #28: 'del_19q13.42' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.42' versus 'MRNASEQ_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0042

Table S171. Gene #28: 'del_19q13.42' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 21(19Q13.42) MUTATED	0	1	6	12
DEL PEAK 21(19Q13.42) WILD-TYPE	34	95	60	80

Figure S171. Get High-res Image Gene #28: 'del_19q13.42' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00329 (Fisher's exact test), Q value = 0.0078

Table S172. Gene #28: 'del_19q13.42' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 21(19Q13.42) MUTATED	14	2	3
DEL PEAK 21(19Q13.42) WILD-TYPE	104	121	44

Figure S172. Get High-res Image Gene #28: 'del_19q13.42' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S173. Gene #29: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 22(22Q12.2) MUTATED	23	6	2	32
DEL PEAK 22(22Q12.2) WILD-TYPE	91	70	44	20

Figure S173. Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S174. Gene #29: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 22(22Q12.2) MUTATED	13	36	11
DEL PEAK 22(22Q12.2) WILD-TYPE	69	35	108

Figure S174. Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q12.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00641 (Fisher's exact test), Q value = 0.014

Table S175. Gene #29: 'del_22q12.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 22(22Q12.2) MUTATED	4	12	25	10
DEL PEAK 22(22Q12.2) WILD-TYPE	35	54	40	33

Figure S175. Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_22q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S176. Gene #29: 'del_22q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 22(22Q12.2) MUTATED	0	7	13	43
DEL PEAK 22(22Q12.2) WILD-TYPE	34	89	53	49

Figure S176. Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S177. Gene #29: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 22(22Q12.2) MUTATED	36	9	18
DEL PEAK 22(22Q12.2) WILD-TYPE	82	114	29

Figure S177. Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.064

Table S178. Gene #29: 'del_22q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 22(22Q12.2) MUTATED	18	11	21
DEL PEAK 22(22Q12.2) WILD-TYPE	52	70	50

Figure S178. Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00215 (Fisher's exact test), Q value = 0.0056

Table S179. Gene #29: 'del_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 22(22Q12.2) MUTATED	20	22	7	1
DEL PEAK 22(22Q12.2) WILD-TYPE	83	53	8	28

Figure S179. Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp11.4' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S180. Gene #30: 'del_xp11.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 23(XP11.4) MUTATED	12	1	1	20
DEL PEAK 23(XP11.4) WILD-TYPE	102	75	45	32

Figure S180. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.4' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S181. Gene #30: 'del_xp11.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 23(XP11.4) MUTATED	8	21	3
DEL PEAK 23(XP11.4) WILD-TYPE	74	50	116

Figure S181. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp11.4' versus 'RPPA_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.0031

Table S182. Gene #30: 'del_xp11.4' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 23(XP11.4) MUTATED	1	5	15	1
DEL PEAK 23(XP11.4) WILD-TYPE	38	61	50	42

Figure S182. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_xp11.4' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S183. Gene #30: 'del_xp11.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 23(XP11.4) MUTATED	0	2	5	27
DEL PEAK 23(XP11.4) WILD-TYPE	34	94	61	65

Figure S183. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp11.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S184. Gene #30: 'del_xp11.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 23(XP11.4) MUTATED	19	3	12
DEL PEAK 23(XP11.4) WILD-TYPE	99	120	35

Figure S184. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.4' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.0047

Table S185. Gene #30: 'del_xp11.4' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 23(XP11.4) MUTATED	9	2	14
DEL PEAK 23(XP11.4) WILD-TYPE	61	79	57

Figure S185. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp11.4' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S186. Gene #30: 'del_xp11.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 23(XP11.4) MUTATED	4	17	4	0
DEL PEAK 23(XP11.4) WILD-TYPE	99	58	11	29

Figure S186. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S187. Gene #31: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 24(XQ28) MUTATED	10	0	1	17
DEL PEAK 24(XQ28) WILD-TYPE	104	76	45	35

Figure S187. Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq28' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00021

Table S188. Gene #31: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
DEL PEAK 24(XQ28) MUTATED	7	16	3
DEL PEAK 24(XQ28) WILD-TYPE	75	55	116

Figure S188. Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq28' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.5e-05

Table S189. Gene #31: 'del_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
DEL PEAK 24(XQ28) MUTATED	0	2	4	22
DEL PEAK 24(XQ28) WILD-TYPE	34	94	62	70

Figure S189. Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00066

Table S190. Gene #31: 'del_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 24(XQ28) MUTATED	15	3	10
DEL PEAK 24(XQ28) WILD-TYPE	103	120	37

Figure S190. Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00718 (Fisher's exact test), Q value = 0.015

Table S191. Gene #31: 'del_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
DEL PEAK 24(XQ28) MUTATED	6	2	12
DEL PEAK 24(XQ28) WILD-TYPE	64	79	59

Figure S191. Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.0028

Table S192. Gene #31: 'del_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
DEL PEAK 24(XQ28) MUTATED	4	12	4	0
DEL PEAK 24(XQ28) WILD-TYPE	99	63	11	29

Figure S192. Get High-res Image Gene #31: 'del_xq28' 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/KIRP-TP/19781624/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/20139337/KIRP-TP.transferedmergedcluster.txt
Number of patients = 288
Number of significantly focal cnvs = 31
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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