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

Liver Hepatocellular Carcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

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 (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C11Z4351

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 53 focal events and 8 molecular subtypes across 208 patients, 53 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p22.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_1q22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_1q42.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_3q26.31 cnv correlated to 'CN_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF'.
amp_5q35.3 cnv correlated to 'CN_CNMF'.
amp_6p25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_6p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_6q12 cnv correlated to 'CN_CNMF'.
amp_6q12 cnv correlated to 'CN_CNMF'.
amp_8q11.1 cnv correlated to 'CN_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF'.
amp_13q32.3 cnv correlated to 'CN_CNMF'.
amp_19q13.11 cnv correlated to 'MRNASEQ_CNMF'.
amp_20q13.13 cnv correlated to 'CN_CNMF'.
amp_20q13.33 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_1p36.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_3p13 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_4q24 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_4q34.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF'.
del_10q23.31 cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_10q25.2 cnv correlated to 'MRNASEQ_CNMF'.
del_13q14.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_13q22.2 cnv correlated to 'CN_CNMF'.
del_14q32.33 cnv correlated to 'CN_CNMF'.
del_16q23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_17p11.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 53 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 53 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	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
del 16q23 2	88 (42%)	120	2e-05 (0.00812)	0.00042 (0.159)	2e-05 (0.00812)	0.00045 (0.17)	0.589 (1.00)	0.0388 (1.00)	0.0546 (1.00)	0.0014 (0.504)
amp 1q22	153 (74%)	55	1e-05 (0.00424)	1e-05 (0.00424)	5e-05 (0.0199)	0.148 (1.00)	0.0638 (1.00)	0.1 (1.00)	0.0777 (1.00)	0.00473 (1.00)
amp 6p25 2	94 (45%)	114	1e-05 (0.00424)	0.00013 (0.0507)	0.00047 (0.177)	0.0988 (1.00)	0.701 (1.00)	0.424 (1.00)	0.183 (1.00)	0.7 (1.00)
amp 6p21 1	93 (45%)	115	1e-05 (0.00424)	1e-05 (0.00424)	0.00027 (0.103)	0.692 (1.00)	0.75 (1.00)	0.0982 (1.00)	0.21 (1.00)	0.422 (1.00)
del 1p36 23	96 (46%)	112	2e-05 (0.00812)	1e-05 (0.00424)	3e-05 (0.0121)	0.00743 (1.00)	0.349 (1.00)	0.0127 (1.00)	0.0674 (1.00)	0.0552 (1.00)
del 4q34 1	89 (43%)	119	1e-05 (0.00424)	1e-05 (0.00424)	0.00017 (0.0656)	0.0377 (1.00)	0.858 (1.00)	0.0369 (1.00)	0.287 (1.00)	0.00936 (1.00)
del 4q34 3	90 (43%)	118	1e-05 (0.00424)	8e-05 (0.0315)	7e-05 (0.0277)	0.275 (1.00)	1 (1.00)	0.0498 (1.00)	0.309 (1.00)	0.0249 (1.00)
amp 1p22 3	51 (25%)	157	0.0004 (0.152)	0.0268 (1.00)	0.00016 (0.0619)	0.00418 (1.00)	0.0775 (1.00)	0.362 (1.00)	0.0537 (1.00)	0.0479 (1.00)
amp 1q42 3	146 (70%)	62	0.00018 (0.0693)	0.00018 (0.0693)	0.00109 (0.396)	0.0564 (1.00)	0.551 (1.00)	0.753 (1.00)	0.361 (1.00)	0.0384 (1.00)
amp 20q13 33	74 (36%)	134	1e-05 (0.00424)	0.0345 (1.00)	0.00077 (0.283)	0.00063 (0.234)	0.155 (1.00)	0.018 (1.00)	0.00092 (0.336)	0.0184 (1.00)
del 4q24	98 (47%)	110	1e-05 (0.00424)	0.00077 (0.283)	0.00011 (0.043)	0.0295 (1.00)	0.679 (1.00)	0.0205 (1.00)	0.1 (1.00)	0.00196 (0.69)
del 10q23 31	62 (30%)	146	0.176 (1.00)	0.284 (1.00)	7e-05 (0.0277)	0.0795 (1.00)	0.219 (1.00)	0.00013 (0.0507)	0.234 (1.00)	0.00195 (0.688)
del 13q14 2	100 (48%)	108	1e-05 (0.00424)	0.121 (1.00)	0.0322 (1.00)	0.00051 (0.191)	0.952 (1.00)	0.0875 (1.00)	0.012 (1.00)	0.0721 (1.00)
del 17p11 2	116 (56%)	92	0.00041 (0.155)	0.09 (1.00)	0.0762 (1.00)	0.039 (1.00)	0.00202 (0.709)	0.00192 (0.68)	8e-05 (0.0315)	0.00443 (1.00)
amp 3q26 31	44 (21%)	164	0.00013 (0.0507)	0.0563 (1.00)	0.659 (1.00)	0.585 (1.00)	0.0226 (1.00)	0.0173 (1.00)	0.163 (1.00)	0.0319 (1.00)
amp 5p15 33	95 (46%)	113	1e-05 (0.00424)	0.0296 (1.00)	0.515 (1.00)	0.184 (1.00)	0.326 (1.00)	0.261 (1.00)	0.404 (1.00)	0.343 (1.00)
amp 5q35 3	68 (33%)	140	5e-05 (0.0199)	0.0831 (1.00)	0.7 (1.00)	0.98 (1.00)	0.828 (1.00)	0.941 (1.00)	0.955 (1.00)	0.859 (1.00)
amp 6q12	67 (32%)	141	0.00034 (0.13)	0.0189 (1.00)	0.00953 (1.00)	0.243 (1.00)	0.505 (1.00)	0.828 (1.00)	0.246 (1.00)	0.871 (1.00)
amp 6q12	51 (25%)	157	6e-05 (0.0238)	0.00792 (1.00)	0.0019 (0.674)	0.114 (1.00)	0.604 (1.00)	0.399 (1.00)	0.0109 (1.00)	0.317 (1.00)
amp 8q11 1	85 (41%)	123	1e-05 (0.00424)	0.93 (1.00)	0.135 (1.00)	0.189 (1.00)	0.446 (1.00)	0.459 (1.00)	0.33 (1.00)	0.13 (1.00)
amp 8q24 21	123 (59%)	85	1e-05 (0.00424)	0.088 (1.00)	0.0626 (1.00)	0.0247 (1.00)	0.265 (1.00)	0.183 (1.00)	0.298 (1.00)	0.0957 (1.00)
amp 13q32 3	40 (19%)	168	1e-05 (0.00424)	0.0203 (1.00)	0.00085 (0.311)	0.0463 (1.00)	0.642 (1.00)	0.211 (1.00)	0.281 (1.00)	0.293 (1.00)
amp 19q13 11	58 (28%)	150	0.00185 (0.659)	0.00104 (0.379)	0.00053 (0.198)	0.00183 (0.653)	0.133 (1.00)	0.0657 (1.00)	0.0012 (0.434)	0.0104 (1.00)
amp 20q13 13	72 (35%)	136	4e-05 (0.016)	0.202 (1.00)	0.00677 (1.00)	0.00215 (0.752)	0.128 (1.00)	0.0191 (1.00)	0.00523 (1.00)	0.0234 (1.00)
del 3p13	43 (21%)	165	0.214 (1.00)	0.0659 (1.00)	0.00073 (0.27)	3e-05 (0.0121)	0.0877 (1.00)	0.0403 (1.00)	0.00073 (0.27)	0.00579 (1.00)
del 8p23 2	134 (64%)	74	1e-05 (0.00424)	0.0162 (1.00)	0.0525 (1.00)	0.86 (1.00)	0.897 (1.00)	0.327 (1.00)	0.43 (1.00)	0.387 (1.00)
del 9p21 3	83 (40%)	125	8e-05 (0.0315)	0.0339 (1.00)	0.772 (1.00)	0.304 (1.00)	0.872 (1.00)	0.0708 (1.00)	0.394 (1.00)	0.135 (1.00)
del 10q25 2	64 (31%)	144	0.0878 (1.00)	0.565 (1.00)	0.00021 (0.0804)	0.0876 (1.00)	0.412 (1.00)	0.0035 (1.00)	0.445 (1.00)	0.0791 (1.00)
del 13q22 2	80 (38%)	128	1e-05 (0.00424)	0.149 (1.00)	0.143 (1.00)	0.00305 (1.00)	0.645 (1.00)	0.318 (1.00)	0.0189 (1.00)	0.235 (1.00)
del 14q32 33	74 (36%)	134	0.00052 (0.194)	0.133 (1.00)	0.0687 (1.00)	0.0147 (1.00)	0.191 (1.00)	0.239 (1.00)	0.0451 (1.00)	0.144 (1.00)
del 19p13 3	47 (23%)	161	4e-05 (0.016)	0.0432 (1.00)	0.0284 (1.00)	0.0373 (1.00)	0.954 (1.00)	0.0121 (1.00)	0.822 (1.00)	0.0597 (1.00)
amp 2p24 1	44 (21%)	164	0.00515 (1.00)	0.774 (1.00)	0.821 (1.00)	0.336 (1.00)	0.975 (1.00)	0.533 (1.00)	0.0927 (1.00)	0.829 (1.00)
amp 2q31 2	41 (20%)	167	0.042 (1.00)	0.761 (1.00)	0.756 (1.00)	0.796 (1.00)	0.299 (1.00)	0.173 (1.00)	0.169 (1.00)	0.639 (1.00)
amp 4q13 3	17 (8%)	191	0.36 (1.00)	0.142 (1.00)	0.748 (1.00)	0.538 (1.00)	1 (1.00)	0.647 (1.00)	0.542 (1.00)	0.848 (1.00)
amp 7q21 2	75 (36%)	133	0.967 (1.00)	0.106 (1.00)	0.882 (1.00)	0.553 (1.00)	0.342 (1.00)	0.0719 (1.00)	0.163 (1.00)	0.719 (1.00)
amp 7q31 2	73 (35%)	135	0.808 (1.00)	0.145 (1.00)	0.7 (1.00)	0.654 (1.00)	0.122 (1.00)	0.0211 (1.00)	0.0369 (1.00)	0.336 (1.00)
amp 9q34 2	31 (15%)	177	0.0438 (1.00)	0.486 (1.00)	0.00756 (1.00)	0.0392 (1.00)	0.478 (1.00)	0.12 (1.00)	0.0623 (1.00)	0.17 (1.00)
amp 10p15 1	46 (22%)	162	0.47 (1.00)	0.0373 (1.00)	0.0792 (1.00)	0.00159 (0.571)	0.318 (1.00)	0.845 (1.00)	0.0226 (1.00)	0.329 (1.00)
amp 11q13 3	39 (19%)	169	0.145 (1.00)	0.676 (1.00)	0.0838 (1.00)	0.403 (1.00)	0.282 (1.00)	0.301 (1.00)	0.675 (1.00)	0.583 (1.00)
amp 15q26 3	33 (16%)	175	0.159 (1.00)	0.194 (1.00)	0.102 (1.00)	0.137 (1.00)	0.473 (1.00)	0.174 (1.00)	0.632 (1.00)	0.387 (1.00)
amp 17p11 2	30 (14%)	178	0.537 (1.00)	0.124 (1.00)	0.257 (1.00)	0.294 (1.00)	0.437 (1.00)	0.715 (1.00)	0.316 (1.00)	0.835 (1.00)
amp 17q25 3	88 (42%)	120	0.00313 (1.00)	0.00324 (1.00)	0.336 (1.00)	0.949 (1.00)	0.165 (1.00)	0.554 (1.00)	0.289 (1.00)	0.348 (1.00)
amp xq28	49 (24%)	159	0.0134 (1.00)	0.041 (1.00)	0.282 (1.00)	0.0738 (1.00)	0.0751 (1.00)	0.205 (1.00)	0.179 (1.00)	0.0673 (1.00)
del 2q22 1	25 (12%)	183	0.0306 (1.00)	1 (1.00)	0.577 (1.00)	0.924 (1.00)	0.0112 (1.00)	0.655 (1.00)	0.897 (1.00)	0.411 (1.00)
del 2q37 3	42 (20%)	166	0.00775 (1.00)	0.772 (1.00)	0.0203 (1.00)	0.0707 (1.00)	0.00131 (0.473)	0.103 (1.00)	0.179 (1.00)	0.0565 (1.00)
del 4p16 3	46 (22%)	162	0.0017 (0.609)	0.0369 (1.00)	0.2 (1.00)	0.317 (1.00)	0.0456 (1.00)	0.00379 (1.00)	0.156 (1.00)	0.0279 (1.00)
del 6q27	75 (36%)	133	0.119 (1.00)	0.298 (1.00)	0.45 (1.00)	0.724 (1.00)	0.946 (1.00)	0.0519 (1.00)	0.876 (1.00)	0.135 (1.00)
del 11q14 1	46 (22%)	162	0.21 (1.00)	0.5 (1.00)	0.273 (1.00)	0.275 (1.00)	0.254 (1.00)	0.608 (1.00)	0.303 (1.00)	0.684 (1.00)
del 11q23 3	54 (26%)	154	0.0275 (1.00)	0.0707 (1.00)	0.0906 (1.00)	0.167 (1.00)	0.0795 (1.00)	0.467 (1.00)	0.117 (1.00)	0.406 (1.00)
del 12p12 1	49 (24%)	159	0.205 (1.00)	0.115 (1.00)	0.00273 (0.953)	0.347 (1.00)	0.09 (1.00)	0.142 (1.00)	0.00469 (1.00)	0.12 (1.00)
del 12q24 33	37 (18%)	171	0.0628 (1.00)	0.199 (1.00)	0.834 (1.00)	0.586 (1.00)	0.733 (1.00)	0.751 (1.00)	0.621 (1.00)	0.851 (1.00)
del 14q23 3	75 (36%)	133	0.00069 (0.256)	0.351 (1.00)	0.0347 (1.00)	0.0079 (1.00)	0.506 (1.00)	0.0477 (1.00)	0.139 (1.00)	0.0328 (1.00)
del 22q13 32	61 (29%)	147	0.854 (1.00)	1 (1.00)	0.297 (1.00)	0.571 (1.00)	0.57 (1.00)	0.365 (1.00)	0.791 (1.00)	0.43 (1.00)

'amp_1p22.3' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.15

Table S1. Gene #1: 'amp_1p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 1(1P22.3) MUTATED	11	10	30
AMP PEAK 1(1P22.3) WILD-TYPE	40	72	45

Figure S1. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p22.3' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.062

Table S2. Gene #1: 'amp_1p22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	31	57	38	40
AMP PEAK 1(1P22.3) MUTATED	4	13	9	18	6
AMP PEAK 1(1P22.3) WILD-TYPE	35	18	48	20	34

Figure S2. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_1q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S3. Gene #2: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 2(1Q22) MUTATED	44	42	67
AMP PEAK 2(1Q22) WILD-TYPE	7	40	8

Figure S3. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S4. Gene #2: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	59	50
AMP PEAK 2(1Q22) MUTATED	75	51	19
AMP PEAK 2(1Q22) WILD-TYPE	15	8	31

Figure S4. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.02

Table S5. Gene #2: 'amp_1q22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	31	57	38	40
AMP PEAK 2(1Q22) MUTATED	19	24	37	36	34
AMP PEAK 2(1Q22) WILD-TYPE	20	7	20	2	6

Figure S5. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_1q42.3' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.069

Table S6. Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 3(1Q42.3) MUTATED	41	44	61
AMP PEAK 3(1Q42.3) WILD-TYPE	10	38	14

Figure S6. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.3' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.069

Table S7. Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	59	50
AMP PEAK 3(1Q42.3) MUTATED	72	44	23
AMP PEAK 3(1Q42.3) WILD-TYPE	18	15	27

Figure S7. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.31' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.051

Table S8. Gene #6: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 6(3Q26.31) MUTATED	5	11	28
AMP PEAK 6(3Q26.31) WILD-TYPE	46	71	47

Figure S8. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S9. Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 8(5P15.33) MUTATED	34	21	40
AMP PEAK 8(5P15.33) WILD-TYPE	17	61	35

Figure S9. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.02

Table S10. Gene #9: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 9(5Q35.3) MUTATED	27	14	27
AMP PEAK 9(5Q35.3) WILD-TYPE	24	68	48

Figure S10. Get High-res Image Gene #9: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S11. Gene #10: 'amp_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 10(6P25.2) MUTATED	23	19	52
AMP PEAK 10(6P25.2) WILD-TYPE	28	63	23

Figure S11. Get High-res Image Gene #10: 'amp_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p25.2' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.051

Table S12. Gene #10: 'amp_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	59	50
AMP PEAK 10(6P25.2) MUTATED	46	32	9
AMP PEAK 10(6P25.2) WILD-TYPE	44	27	41

Figure S12. Get High-res Image Gene #10: 'amp_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p25.2' versus 'MRNASEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.18

Table S13. Gene #10: 'amp_6p25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	31	57	38	40
AMP PEAK 10(6P25.2) MUTATED	11	14	20	28	21
AMP PEAK 10(6P25.2) WILD-TYPE	28	17	37	10	19

Figure S13. Get High-res Image Gene #10: 'amp_6p25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S14. Gene #11: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 11(6P21.1) MUTATED	23	20	50
AMP PEAK 11(6P21.1) WILD-TYPE	28	62	25

Figure S14. Get High-res Image Gene #11: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S15. Gene #11: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	59	50
AMP PEAK 11(6P21.1) MUTATED	52	27	8
AMP PEAK 11(6P21.1) WILD-TYPE	38	32	42

Figure S15. Get High-res Image Gene #11: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.1

Table S16. Gene #11: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	31	57	38	40
AMP PEAK 11(6P21.1) MUTATED	8	13	24	27	21
AMP PEAK 11(6P21.1) WILD-TYPE	31	18	33	11	19

Figure S16. Get High-res Image Gene #11: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.13

Table S17. Gene #12: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 12(6Q12) MUTATED	16	15	36
AMP PEAK 12(6Q12) WILD-TYPE	35	67	39

Figure S17. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.024

Table S18. Gene #13: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 13(6Q12) MUTATED	13	8	30
AMP PEAK 13(6Q12) WILD-TYPE	38	74	45

Figure S18. Get High-res Image Gene #13: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S19. Gene #16: 'amp_8q11.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 16(8Q11.1) MUTATED	42	20	23
AMP PEAK 16(8Q11.1) WILD-TYPE	9	62	52

Figure S19. Get High-res Image Gene #16: 'amp_8q11.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S20. Gene #17: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 17(8Q24.21) MUTATED	51	31	41
AMP PEAK 17(8Q24.21) WILD-TYPE	0	51	34

Figure S20. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S21. Gene #21: 'amp_13q32.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 21(13Q32.3) MUTATED	12	3	25
AMP PEAK 21(13Q32.3) WILD-TYPE	39	79	50

Figure S21. Get High-res Image Gene #21: 'amp_13q32.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.2

Table S22. Gene #25: 'amp_19q13.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	31	57	38	40
AMP PEAK 25(19Q13.11) MUTATED	11	9	11	21	5
AMP PEAK 25(19Q13.11) WILD-TYPE	28	22	46	17	35

Figure S22. Get High-res Image Gene #25: 'amp_19q13.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_20q13.13' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.016

Table S23. Gene #26: 'amp_20q13.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 26(20Q13.13) MUTATED	21	14	37
AMP PEAK 26(20Q13.13) WILD-TYPE	30	68	38

Figure S23. Get High-res Image Gene #26: 'amp_20q13.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S24. Gene #27: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
AMP PEAK 27(20Q13.33) MUTATED	21	13	40
AMP PEAK 27(20Q13.33) WILD-TYPE	30	69	35

Figure S24. Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.23

Table S25. Gene #27: 'amp_20q13.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	84	39
AMP PEAK 27(20Q13.33) MUTATED	39	29	5
AMP PEAK 27(20Q13.33) WILD-TYPE	43	55	34

Figure S25. Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0081

Table S26. Gene #29: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
DEL PEAK 1(1P36.23) MUTATED	23	24	49
DEL PEAK 1(1P36.23) WILD-TYPE	28	58	26

Figure S26. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S27. Gene #29: 'del_1p36.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	59	50
DEL PEAK 1(1P36.23) MUTATED	38	43	12
DEL PEAK 1(1P36.23) WILD-TYPE	52	16	38

Figure S27. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.23' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.012

Table S28. Gene #29: 'del_1p36.23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	31	57	38	40
DEL PEAK 1(1P36.23) MUTATED	18	8	24	31	12
DEL PEAK 1(1P36.23) WILD-TYPE	21	23	33	7	28

Figure S28. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.012

Table S29. Gene #32: 'del_3p13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	84	39
DEL PEAK 4(3P13) MUTATED	30	7	5
DEL PEAK 4(3P13) WILD-TYPE	52	77	34

Figure S29. Get High-res Image Gene #32: 'del_3p13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q24' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S30. Gene #34: 'del_4q24' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
DEL PEAK 6(4Q24) MUTATED	21	20	57
DEL PEAK 6(4Q24) WILD-TYPE	30	62	18

Figure S30. Get High-res Image Gene #34: 'del_4q24' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q24' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.043

Table S31. Gene #34: 'del_4q24' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	31	57	38	40
DEL PEAK 6(4Q24) MUTATED	11	16	30	28	12
DEL PEAK 6(4Q24) WILD-TYPE	28	15	27	10	28

Figure S31. Get High-res Image Gene #34: 'del_4q24' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q34.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S32. Gene #35: 'del_4q34.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
DEL PEAK 7(4Q34.1) MUTATED	20	17	52
DEL PEAK 7(4Q34.1) WILD-TYPE	31	65	23

Figure S32. Get High-res Image Gene #35: 'del_4q34.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S33. Gene #35: 'del_4q34.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	59	50
DEL PEAK 7(4Q34.1) MUTATED	34	40	11
DEL PEAK 7(4Q34.1) WILD-TYPE	56	19	39

Figure S33. Get High-res Image Gene #35: 'del_4q34.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.1' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.066

Table S34. Gene #35: 'del_4q34.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	31	57	38	40
DEL PEAK 7(4Q34.1) MUTATED	10	15	23	28	12
DEL PEAK 7(4Q34.1) WILD-TYPE	29	16	34	10	28

Figure S34. Get High-res Image Gene #35: 'del_4q34.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S35. Gene #36: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
DEL PEAK 8(4Q34.3) MUTATED	20	17	53
DEL PEAK 8(4Q34.3) WILD-TYPE	31	65	22

Figure S35. Get High-res Image Gene #36: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.032

Table S36. Gene #36: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	59	50
DEL PEAK 8(4Q34.3) MUTATED	36	38	11
DEL PEAK 8(4Q34.3) WILD-TYPE	54	21	39

Figure S36. Get High-res Image Gene #36: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.028

Table S37. Gene #36: 'del_4q34.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	31	57	38	40
DEL PEAK 8(4Q34.3) MUTATED	9	13	24	29	14
DEL PEAK 8(4Q34.3) WILD-TYPE	30	18	33	9	26

Figure S37. Get High-res Image Gene #36: 'del_4q34.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S38. Gene #38: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
DEL PEAK 10(8P23.2) MUTATED	48	38	48
DEL PEAK 10(8P23.2) WILD-TYPE	3	44	27

Figure S38. Get High-res Image Gene #38: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.032

Table S39. Gene #39: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
DEL PEAK 11(9P21.3) MUTATED	25	18	40
DEL PEAK 11(9P21.3) WILD-TYPE	26	64	35

Figure S39. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.028

Table S40. Gene #40: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	31	57	38	40
DEL PEAK 12(10Q23.31) MUTATED	12	19	20	4	6
DEL PEAK 12(10Q23.31) WILD-TYPE	27	12	37	34	34

Figure S40. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.051

Table S41. Gene #40: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	53	74	26	24
DEL PEAK 12(10Q23.31) MUTATED	11	24	18	9	0
DEL PEAK 12(10Q23.31) WILD-TYPE	15	29	56	17	24

Figure S41. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q25.2' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.08

Table S42. Gene #41: 'del_10q25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	31	57	38	40
DEL PEAK 13(10Q25.2) MUTATED	14	19	19	5	7
DEL PEAK 13(10Q25.2) WILD-TYPE	25	12	38	33	33

Figure S42. Get High-res Image Gene #41: 'del_10q25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S43. Gene #46: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
DEL PEAK 18(13Q14.2) MUTATED	14	29	57
DEL PEAK 18(13Q14.2) WILD-TYPE	37	53	18

Figure S43. Get High-res Image Gene #46: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.19

Table S44. Gene #46: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	84	39
DEL PEAK 18(13Q14.2) MUTATED	52	36	11
DEL PEAK 18(13Q14.2) WILD-TYPE	30	48	28

Figure S44. Get High-res Image Gene #46: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0042

Table S45. Gene #47: 'del_13q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
DEL PEAK 19(13Q22.2) MUTATED	9	23	48
DEL PEAK 19(13Q22.2) WILD-TYPE	42	59	27

Figure S45. Get High-res Image Gene #47: 'del_13q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.33' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.19

Table S46. Gene #49: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
DEL PEAK 21(14Q32.33) MUTATED	17	18	39
DEL PEAK 21(14Q32.33) WILD-TYPE	34	64	36

Figure S46. Get High-res Image Gene #49: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0081

Table S47. Gene #50: 'del_16q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
DEL PEAK 22(16Q23.2) MUTATED	17	21	50
DEL PEAK 22(16Q23.2) WILD-TYPE	34	61	25

Figure S47. Get High-res Image Gene #50: 'del_16q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.2' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.16

Table S48. Gene #50: 'del_16q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	59	50
DEL PEAK 22(16Q23.2) MUTATED	33	36	13
DEL PEAK 22(16Q23.2) WILD-TYPE	57	23	37

Figure S48. Get High-res Image Gene #50: 'del_16q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0081

Table S49. Gene #50: 'del_16q23.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	31	57	38	40
DEL PEAK 22(16Q23.2) MUTATED	11	17	25	27	8
DEL PEAK 22(16Q23.2) WILD-TYPE	28	14	32	11	32

Figure S49. Get High-res Image Gene #50: 'del_16q23.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.17

Table S50. Gene #50: 'del_16q23.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	84	39
DEL PEAK 22(16Q23.2) MUTATED	47	33	8
DEL PEAK 22(16Q23.2) WILD-TYPE	35	51	31

Figure S50. Get High-res Image Gene #50: 'del_16q23.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.16

Table S51. Gene #51: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
DEL PEAK 23(17P11.2) MUTATED	21	40	55
DEL PEAK 23(17P11.2) WILD-TYPE	30	42	20

Figure S51. Get High-res Image Gene #51: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.032

Table S52. Gene #51: 'del_17p11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	28	35	43	60	37
DEL PEAK 23(17P11.2) MUTATED	15	20	37	25	17
DEL PEAK 23(17P11.2) WILD-TYPE	13	15	6	35	20

Figure S52. Get High-res Image Gene #51: 'del_17p11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.016

Table S53. Gene #52: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	82	75
DEL PEAK 24(19P13.3) MUTATED	13	6	28
DEL PEAK 24(19P13.3) WILD-TYPE	38	76	47

Figure S53. Get High-res Image Gene #52: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = LIHC-TP.transferedmergedcluster.txt
Number of patients = 208
Number of significantly focal cnvs = 53
Number of molecular subtypes = 8
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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