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

Liver Hepatocellular Carcinoma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

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/C1J67FKR

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 56 focal events and 8 molecular subtypes across 199 patients, 54 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' and 'METHLYATION_CNMF'.
amp_1q42.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_3q26.31 cnv correlated to 'CN_CNMF' and 'MIRSEQ_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' and 'METHLYATION_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' and 'MRNASEQ_CHIERARCHICAL'.
amp_13q32.3 cnv correlated to 'CN_CNMF'.
amp_17q25.3 cnv correlated to 'CN_CNMF'.
amp_19q13.11 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_20q13.33 cnv correlated to 'MRNASEQ_CNMF'.
amp_xq28 cnv correlated to 'CN_CNMF'.
del_1p36.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_2q37.3 cnv correlated to 'MIRSEQ_CNMF'.
del_3p13 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.
del_4q24 cnv correlated to 'CN_CNMF'.
del_4q34.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_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_MATURE_CNMF'.
del_10q24.33 cnv correlated to 'MRNASEQ_CNMF'.
del_13q12.11 cnv correlated to 'CN_CNMF'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_13q22.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_14q32.33 cnv correlated to 'CN_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_17p11.2 cnv correlated to 'MIRSEQ_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 56 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, 54 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	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test
amp 6p25 2	87 (44%)	112	6.89e-09 (3.06e-06)	0.000173 (0.0711)	8.65e-05 (0.0364)	0.0122 (1.00)	0.42 (1.00)	0.823 (1.00)	0.547 (1.00)	1 (1.00)
amp 19q13 11	54 (27%)	145	0.11 (1.00)	0.00044 (0.176)	0.00031 (0.124)	0.000301 (0.121)	0.252 (1.00)	0.00411 (1.00)	0.00152 (0.588)	0.00405 (1.00)
del 1p36 23	93 (47%)	106	0.000272 (0.11)	1.45e-05 (0.00625)	8e-05 (0.0338)	0.0155 (1.00)	0.602 (1.00)	0.0902 (1.00)	0.0112 (1.00)	0.101 (1.00)
del 13q14 2	94 (47%)	105	5.31e-11 (2.37e-08)	0.0846 (1.00)	0.00174 (0.671)	9.23e-05 (0.0387)	0.262 (1.00)	0.133 (1.00)	0.000219 (0.0889)	0.0466 (1.00)
del 13q22 2	74 (37%)	125	1.31e-08 (5.77e-06)	0.0994 (1.00)	0.0506 (1.00)	0.00059 (0.234)	0.445 (1.00)	0.434 (1.00)	0.000615 (0.243)	0.233 (1.00)
del 16q23 1	83 (42%)	116	6.58e-06 (0.00285)	0.000522 (0.207)	8.84e-06 (0.00382)	0.00113 (0.44)	0.628 (1.00)	0.0413 (1.00)	0.0371 (1.00)	0.0931 (1.00)
amp 1p22 3	48 (24%)	151	0.000206 (0.0844)	0.00281 (1.00)	0.000118 (0.0493)	0.00431 (1.00)	0.217 (1.00)	0.911 (1.00)	0.0655 (1.00)	1 (1.00)
amp 1q22	145 (73%)	54	1.82e-06 (0.000797)	6.77e-08 (2.98e-05)	0.00412 (1.00)	0.0319 (1.00)	0.0602 (1.00)	0.0187 (1.00)	0.246 (1.00)	0.11 (1.00)
amp 1q42 3	139 (70%)	60	0.000296 (0.12)	0.000216 (0.0881)	0.00435 (1.00)	0.056 (1.00)	0.308 (1.00)	0.14 (1.00)	0.413 (1.00)	0.746 (1.00)
amp 3q26 31	42 (21%)	157	0.000216 (0.0881)	0.075 (1.00)	0.588 (1.00)	0.172 (1.00)	0.000516 (0.206)	0.0181 (1.00)	0.0361 (1.00)	0.05 (1.00)
amp 6p21 1	87 (44%)	112	6.89e-09 (3.06e-06)	5.62e-06 (0.00244)	0.000837 (0.329)	0.0085 (1.00)	0.326 (1.00)	0.528 (1.00)	0.359 (1.00)	0.674 (1.00)
amp 8q24 21	119 (60%)	80	3.42e-13 (1.53e-10)	0.0604 (1.00)	0.0834 (1.00)	6.19e-05 (0.0263)	0.145 (1.00)	0.517 (1.00)	0.582 (1.00)	0.709 (1.00)
del 3p13	42 (21%)	157	0.0601 (1.00)	0.0956 (1.00)	0.00531 (1.00)	0.000112 (0.0469)	0.1 (1.00)	0.0847 (1.00)	4.02e-05 (0.0171)	0.0027 (1.00)
del 4q34 3	85 (43%)	114	3.16e-07 (0.000139)	0.000167 (0.0688)	0.00111 (0.435)	0.0458 (1.00)	0.866 (1.00)	0.269 (1.00)	0.269 (1.00)	0.263 (1.00)
del 10q23 31	60 (30%)	139	0.0119 (1.00)	0.302 (1.00)	3.25e-06 (0.00142)	0.00406 (1.00)	0.0947 (1.00)	0.0215 (1.00)	0.000422 (0.169)	0.12 (1.00)
amp 5p15 33	92 (46%)	107	4.5e-06 (0.00196)	0.0599 (1.00)	0.079 (1.00)	0.235 (1.00)	0.389 (1.00)	0.327 (1.00)	0.0934 (1.00)	0.51 (1.00)
amp 5q35 3	65 (33%)	134	2.91e-05 (0.0125)	0.0297 (1.00)	0.664 (1.00)	0.716 (1.00)	1 (1.00)	0.948 (1.00)	0.257 (1.00)	0.744 (1.00)
amp 6q12	63 (32%)	136	1.65e-07 (7.24e-05)	0.0243 (1.00)	0.00542 (1.00)	0.0631 (1.00)	0.192 (1.00)	0.871 (1.00)	0.514 (1.00)	0.906 (1.00)
amp 6q12	46 (23%)	153	0.000131 (0.0544)	0.00679 (1.00)	0.00413 (1.00)	0.0579 (1.00)	0.483 (1.00)	0.963 (1.00)	0.181 (1.00)	0.545 (1.00)
amp 8q11 1	79 (40%)	120	1.75e-10 (7.8e-08)	0.734 (1.00)	0.126 (1.00)	0.00136 (0.529)	0.661 (1.00)	0.257 (1.00)	0.371 (1.00)	0.165 (1.00)
amp 13q32 3	37 (19%)	162	6.9e-05 (0.0292)	0.0141 (1.00)	0.00125 (0.487)	0.026 (1.00)	0.387 (1.00)	0.586 (1.00)	0.0159 (1.00)	0.257 (1.00)
amp 17q25 3	86 (43%)	113	0.000166 (0.0687)	0.00269 (1.00)	0.0666 (1.00)	0.0929 (1.00)	0.176 (1.00)	0.188 (1.00)	0.116 (1.00)	0.245 (1.00)
amp 20q13 33	69 (35%)	130	0.000651 (0.256)	0.0214 (1.00)	2.1e-05 (0.00905)	0.00724 (1.00)	0.218 (1.00)	0.223 (1.00)	0.00492 (1.00)	0.0831 (1.00)
amp xq28	48 (24%)	151	9.21e-05 (0.0387)	0.0263 (1.00)	0.136 (1.00)	0.317 (1.00)	0.0717 (1.00)	0.00884 (1.00)	0.157 (1.00)	0.089 (1.00)
del 2q37 3	42 (21%)	157	0.00834 (1.00)	0.87 (1.00)	0.00577 (1.00)	0.0179 (1.00)	0.000195 (0.0799)	0.0533 (1.00)	0.253 (1.00)	0.279 (1.00)
del 4q24	93 (47%)	106	6.01e-08 (2.65e-05)	0.00673 (1.00)	0.00198 (0.759)	0.0229 (1.00)	0.262 (1.00)	0.669 (1.00)	0.413 (1.00)	0.614 (1.00)
del 8p23 2	128 (64%)	71	1.61e-11 (7.2e-09)	0.00818 (1.00)	0.0201 (1.00)	0.441 (1.00)	0.855 (1.00)	0.529 (1.00)	0.78 (1.00)	0.495 (1.00)
del 9p21 3	80 (40%)	119	2.93e-05 (0.0125)	0.2 (1.00)	0.117 (1.00)	0.394 (1.00)	0.225 (1.00)	0.158 (1.00)	0.207 (1.00)	0.0889 (1.00)
del 10q24 33	61 (31%)	138	0.0304 (1.00)	0.807 (1.00)	4.7e-05 (0.02)	0.00378 (1.00)	0.0889 (1.00)	0.0304 (1.00)	0.00203 (0.776)	0.212 (1.00)
del 13q12 11	67 (34%)	132	9.67e-05 (0.0404)	0.069 (1.00)	0.0307 (1.00)	0.00648 (1.00)	0.94 (1.00)	0.181 (1.00)	0.0444 (1.00)	0.077 (1.00)
del 14q32 33	70 (35%)	129	5.46e-05 (0.0232)	0.29 (1.00)	0.0642 (1.00)	0.181 (1.00)	0.118 (1.00)	0.0636 (1.00)	0.0411 (1.00)	0.13 (1.00)
del 17p11 2	111 (56%)	88	0.00543 (1.00)	0.115 (1.00)	0.0056 (1.00)	0.0666 (1.00)	0.000151 (0.0626)	0.00259 (0.987)	0.00443 (1.00)	0.00183 (0.705)
del 19p13 3	46 (23%)	153	0.000376 (0.151)	0.0645 (1.00)	0.0167 (1.00)	0.0369 (1.00)	0.331 (1.00)	0.116 (1.00)	0.334 (1.00)	0.214 (1.00)
amp 2p24 1	44 (22%)	155	0.00568 (1.00)	0.62 (1.00)	0.456 (1.00)	0.538 (1.00)	0.416 (1.00)	0.757 (1.00)	0.205 (1.00)	0.916 (1.00)
amp 2q31 2	39 (20%)	160	0.0218 (1.00)	0.951 (1.00)	0.559 (1.00)	0.823 (1.00)	0.0198 (1.00)	0.112 (1.00)	0.551 (1.00)	0.618 (1.00)
amp 4q13 3	17 (9%)	182	0.225 (1.00)	0.556 (1.00)	0.359 (1.00)	0.573 (1.00)	1 (1.00)	0.65 (1.00)	0.648 (1.00)	0.784 (1.00)
amp 7q21 2	70 (35%)	129	0.241 (1.00)	0.206 (1.00)	0.368 (1.00)	0.283 (1.00)	0.214 (1.00)	0.556 (1.00)	0.494 (1.00)	0.352 (1.00)
amp 7q31 2	68 (34%)	131	0.365 (1.00)	0.215 (1.00)	0.351 (1.00)	0.564 (1.00)	0.154 (1.00)	0.409 (1.00)	0.469 (1.00)	0.4 (1.00)
amp 9q34 2	29 (15%)	170	0.144 (1.00)	0.593 (1.00)	0.0576 (1.00)	0.13 (1.00)	0.192 (1.00)	0.61 (1.00)	0.174 (1.00)	0.71 (1.00)
amp 10p15 1	41 (21%)	158	0.523 (1.00)	0.0426 (1.00)	0.213 (1.00)	0.0533 (1.00)	0.145 (1.00)	0.795 (1.00)	0.323 (1.00)	0.388 (1.00)
amp 11q13 3	38 (19%)	161	0.4 (1.00)	0.713 (1.00)	0.0688 (1.00)	0.5 (1.00)	0.101 (1.00)	0.31 (1.00)	0.084 (1.00)	0.74 (1.00)
amp 15q26 3	32 (16%)	167	0.00755 (1.00)	0.218 (1.00)	0.374 (1.00)	0.142 (1.00)	0.39 (1.00)	0.318 (1.00)	0.176 (1.00)	0.0856 (1.00)
amp 16q12 1	20 (10%)	179	0.597 (1.00)	0.919 (1.00)	0.128 (1.00)	0.593 (1.00)	0.835 (1.00)	0.447 (1.00)	0.31 (1.00)	0.477 (1.00)
amp 17p11 2	30 (15%)	169	0.032 (1.00)	0.11 (1.00)	0.643 (1.00)	0.275 (1.00)	0.785 (1.00)	0.897 (1.00)	0.4 (1.00)	0.697 (1.00)
del 2q22 1	25 (13%)	174	0.0195 (1.00)	0.967 (1.00)	0.5 (1.00)	0.882 (1.00)	0.00653 (1.00)	0.375 (1.00)	0.953 (1.00)	0.382 (1.00)
del 4p16 3	44 (22%)	155	0.00315 (1.00)	0.00572 (1.00)	0.0643 (1.00)	0.136 (1.00)	0.743 (1.00)	0.344 (1.00)	0.832 (1.00)	0.296 (1.00)
del 6q16 3	69 (35%)	130	0.0869 (1.00)	0.491 (1.00)	0.18 (1.00)	0.421 (1.00)	0.528 (1.00)	0.502 (1.00)	0.792 (1.00)	0.942 (1.00)
del 6q27	72 (36%)	127	0.007 (1.00)	0.397 (1.00)	0.407 (1.00)	0.41 (1.00)	0.865 (1.00)	0.0404 (1.00)	0.501 (1.00)	0.231 (1.00)
del 9q34 2	64 (32%)	135	0.00809 (1.00)	0.101 (1.00)	0.00982 (1.00)	0.00883 (1.00)	0.392 (1.00)	0.37 (1.00)	0.531 (1.00)	0.285 (1.00)
del 11q14 1	44 (22%)	155	0.094 (1.00)	0.191 (1.00)	0.354 (1.00)	0.338 (1.00)	0.609 (1.00)	0.921 (1.00)	0.522 (1.00)	0.69 (1.00)
del 11q23 3	51 (26%)	148	0.0379 (1.00)	0.00987 (1.00)	0.375 (1.00)	0.479 (1.00)	0.561 (1.00)	0.883 (1.00)	0.144 (1.00)	0.775 (1.00)
del 12p12 1	46 (23%)	153	0.369 (1.00)	0.111 (1.00)	0.00144 (0.558)	0.371 (1.00)	0.0252 (1.00)	0.0467 (1.00)	0.0345 (1.00)	0.00257 (0.983)
del 12q24 33	36 (18%)	163	0.0129 (1.00)	0.189 (1.00)	0.607 (1.00)	0.642 (1.00)	0.888 (1.00)	0.843 (1.00)	0.513 (1.00)	0.597 (1.00)
del 14q23 3	69 (35%)	130	0.00568 (1.00)	0.55 (1.00)	0.008 (1.00)	0.286 (1.00)	0.353 (1.00)	0.0151 (1.00)	0.00974 (1.00)	0.0274 (1.00)
del 20p12 1	14 (7%)	185	0.329 (1.00)	0.491 (1.00)	0.418 (1.00)	0.812 (1.00)	0.593 (1.00)	0.639 (1.00)	0.662 (1.00)	0.387 (1.00)
del 22q13 32	59 (30%)	140	0.606 (1.00)	0.89 (1.00)	0.0244 (1.00)	0.0636 (1.00)	0.64 (1.00)	0.745 (1.00)	0.507 (1.00)	0.599 (1.00)

'amp_1p22.3' versus 'CN_CNMF'

P value = 0.000206 (Fisher's exact test), Q value = 0.084

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 1(1P22.3) MUTATED	11	9	28
AMP PEAK 1(1P22.3) WILD-TYPE	41	69	41

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 = 0.000118 (Chi-square test), Q value = 0.049

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	44	32	51	27	33
AMP PEAK 1(1P22.3) MUTATED	17	15	9	2	3
AMP PEAK 1(1P22.3) WILD-TYPE	27	17	42	25	30

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

'amp_1q22' versus 'CN_CNMF'

P value = 1.82e-06 (Fisher's exact test), Q value = 8e-04

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 2(1Q22) MUTATED	46	41	58
AMP PEAK 2(1Q22) WILD-TYPE	6	37	11

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

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 6.77e-08 (Fisher's exact test), Q value = 3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	52	89
AMP PEAK 2(1Q22) MUTATED	25	45	75
AMP PEAK 2(1Q22) WILD-TYPE	32	7	14

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

'amp_1q42.3' versus 'CN_CNMF'

P value = 0.000296 (Fisher's exact test), Q value = 0.12

Table S5. Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 3(1Q42.3) MUTATED	44	42	53
AMP PEAK 3(1Q42.3) WILD-TYPE	8	36	16

Figure S5. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.3' versus 'METHLYATION_CNMF'

P value = 0.000216 (Fisher's exact test), Q value = 0.088

Table S6. Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	52	89
AMP PEAK 3(1Q42.3) MUTATED	28	39	72
AMP PEAK 3(1Q42.3) WILD-TYPE	29	13	17

Figure S6. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.31' versus 'CN_CNMF'

P value = 0.000216 (Fisher's exact test), Q value = 0.088

Table S7. Gene #6: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 6(3Q26.31) MUTATED	5	11	26
AMP PEAK 6(3Q26.31) WILD-TYPE	47	67	43

Figure S7. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.31' versus 'MIRSEQ_CNMF'

P value = 0.000516 (Fisher's exact test), Q value = 0.21

Table S8. Gene #6: 'amp_3q26.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	48	73
AMP PEAK 6(3Q26.31) MUTATED	12	20	9
AMP PEAK 6(3Q26.31) WILD-TYPE	61	28	64

Figure S8. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 4.5e-06 (Fisher's exact test), Q value = 0.002

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 8(5P15.33) MUTATED	35	20	37
AMP PEAK 8(5P15.33) WILD-TYPE	17	58	32

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 = 2.91e-05 (Fisher's exact test), Q value = 0.012

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 9(5Q35.3) MUTATED	27	12	26
AMP PEAK 9(5Q35.3) WILD-TYPE	25	66	43

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 = 6.89e-09 (Fisher's exact test), Q value = 3.1e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 10(6P25.2) MUTATED	25	15	47
AMP PEAK 10(6P25.2) WILD-TYPE	27	63	22

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 = 0.000173 (Fisher's exact test), Q value = 0.071

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	52	89
AMP PEAK 10(6P25.2) MUTATED	12	29	45
AMP PEAK 10(6P25.2) WILD-TYPE	45	23	44

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 = 8.65e-05 (Chi-square test), Q value = 0.036

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	44	32	51	27	33
AMP PEAK 10(6P25.2) MUTATED	31	16	18	4	16
AMP PEAK 10(6P25.2) WILD-TYPE	13	16	33	23	17

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 = 6.89e-09 (Fisher's exact test), Q value = 3.1e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 11(6P21.1) MUTATED	25	15	47
AMP PEAK 11(6P21.1) WILD-TYPE	27	63	22

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 = 5.62e-06 (Fisher's exact test), Q value = 0.0024

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	52	89
AMP PEAK 11(6P21.1) MUTATED	10	25	51
AMP PEAK 11(6P21.1) WILD-TYPE	47	27	38

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

'amp_6q12' versus 'CN_CNMF'

P value = 1.65e-07 (Fisher's exact test), Q value = 7.2e-05

Table S16. Gene #12: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 12(6Q12) MUTATED	17	9	37
AMP PEAK 12(6Q12) WILD-TYPE	35	69	32

Figure S16. Get High-res Image Gene #12: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 0.000131 (Fisher's exact test), Q value = 0.054

Table S17. Gene #13: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 13(6Q12) MUTATED	13	7	26
AMP PEAK 13(6Q12) WILD-TYPE	39	71	43

Figure S17. Get High-res Image Gene #13: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.1' versus 'CN_CNMF'

P value = 1.75e-10 (Fisher's exact test), Q value = 7.8e-08

Table S18. Gene #16: 'amp_8q11.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 16(8Q11.1) MUTATED	41	20	18
AMP PEAK 16(8Q11.1) WILD-TYPE	11	58	51

Figure S18. Get High-res Image Gene #16: 'amp_8q11.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 3.42e-13 (Fisher's exact test), Q value = 1.5e-10

Table S19. Gene #17: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 17(8Q24.21) MUTATED	51	30	38
AMP PEAK 17(8Q24.21) WILD-TYPE	1	48	31

Figure S19. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.19e-05 (Fisher's exact test), Q value = 0.026

Table S20. Gene #17: 'amp_8q24.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	35	69	52
AMP PEAK 17(8Q24.21) MUTATED	20	23	51	17
AMP PEAK 17(8Q24.21) WILD-TYPE	11	12	18	35

Figure S20. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_13q32.3' versus 'CN_CNMF'

P value = 6.9e-05 (Fisher's exact test), Q value = 0.029

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 21(13Q32.3) MUTATED	11	4	22
AMP PEAK 21(13Q32.3) WILD-TYPE	41	74	47

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

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.000166 (Fisher's exact test), Q value = 0.069

Table S22. Gene #25: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 25(17Q25.3) MUTATED	23	21	42
AMP PEAK 25(17Q25.3) WILD-TYPE	29	57	27

Figure S22. Get High-res Image Gene #25: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.11' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.18

Table S23. Gene #26: 'amp_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	52	89
AMP PEAK 26(19Q13.11) MUTATED	12	25	16
AMP PEAK 26(19Q13.11) WILD-TYPE	45	27	73

Figure S23. Get High-res Image Gene #26: 'amp_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Chi-square test), Q value = 0.12

Table S24. Gene #26: 'amp_19q13.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	32	51	27	33
AMP PEAK 26(19Q13.11) MUTATED	23	9	8	5	5
AMP PEAK 26(19Q13.11) WILD-TYPE	21	23	43	22	28

Figure S24. Get High-res Image Gene #26: 'amp_19q13.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000301 (Fisher's exact test), Q value = 0.12

Table S25. Gene #26: 'amp_19q13.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	35	69	52
AMP PEAK 26(19Q13.11) MUTATED	9	5	30	6
AMP PEAK 26(19Q13.11) WILD-TYPE	22	30	39	46

Figure S25. Get High-res Image Gene #26: 'amp_19q13.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 2.1e-05 (Chi-square test), Q value = 0.009

Table S26. Gene #27: 'amp_20q13.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	32	51	27	33
AMP PEAK 27(20Q13.33) MUTATED	26	14	19	4	3
AMP PEAK 27(20Q13.33) WILD-TYPE	18	18	32	23	30

Figure S26. Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 9.21e-05 (Fisher's exact test), Q value = 0.039

Table S27. Gene #28: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
AMP PEAK 28(XQ28) MUTATED	24	10	14
AMP PEAK 28(XQ28) WILD-TYPE	28	68	55

Figure S27. Get High-res Image Gene #28: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.23' versus 'CN_CNMF'

P value = 0.000272 (Fisher's exact test), Q value = 0.11

Table S28. Gene #29: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
DEL PEAK 1(1P36.23) MUTATED	23	25	45
DEL PEAK 1(1P36.23) WILD-TYPE	29	53	24

Figure S28. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.23' versus 'METHLYATION_CNMF'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.0062

Table S29. Gene #29: 'del_1p36.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	52	89
DEL PEAK 1(1P36.23) MUTATED	17	38	37
DEL PEAK 1(1P36.23) WILD-TYPE	40	14	52

Figure S29. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.23' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Chi-square test), Q value = 0.034

Table S30. Gene #29: 'del_1p36.23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	32	51	27	33
DEL PEAK 1(1P36.23) MUTATED	33	9	24	11	9
DEL PEAK 1(1P36.23) WILD-TYPE	11	23	27	16	24

Figure S30. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.08

Table S31. Gene #31: 'del_2q37.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	48	73
DEL PEAK 3(2Q37.3) MUTATED	5	17	19
DEL PEAK 3(2Q37.3) WILD-TYPE	68	31	54

Figure S31. Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000112 (Fisher's exact test), Q value = 0.047

Table S32. Gene #32: 'del_3p13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	35	69	52
DEL PEAK 4(3P13) MUTATED	2	4	26	5
DEL PEAK 4(3P13) WILD-TYPE	29	31	43	47

Figure S32. Get High-res Image Gene #32: 'del_3p13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.02e-05 (Chi-square test), Q value = 0.017

Table S33. Gene #32: 'del_3p13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	19	21	35	30	40	49
DEL PEAK 4(3P13) MUTATED	5	3	18	5	3	6
DEL PEAK 4(3P13) WILD-TYPE	14	18	17	25	37	43

Figure S33. Get High-res Image Gene #32: 'del_3p13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4q24' versus 'CN_CNMF'

P value = 6.01e-08 (Fisher's exact test), Q value = 2.7e-05

Table S34. Gene #34: 'del_4q24' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
DEL PEAK 6(4Q24) MUTATED	20	22	51
DEL PEAK 6(4Q24) WILD-TYPE	32	56	18

Figure S34. Get High-res Image Gene #34: 'del_4q24' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'CN_CNMF'

P value = 3.16e-07 (Fisher's exact test), Q value = 0.00014

Table S35. Gene #35: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
DEL PEAK 7(4Q34.3) MUTATED	19	19	47
DEL PEAK 7(4Q34.3) WILD-TYPE	33	59	22

Figure S35. Get High-res Image Gene #35: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.069

Table S36. Gene #35: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	52	89
DEL PEAK 7(4Q34.3) MUTATED	15	34	36
DEL PEAK 7(4Q34.3) WILD-TYPE	42	18	53

Figure S36. Get High-res Image Gene #35: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1.61e-11 (Fisher's exact test), Q value = 7.2e-09

Table S37. Gene #38: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
DEL PEAK 10(8P23.2) MUTATED	50	31	47
DEL PEAK 10(8P23.2) WILD-TYPE	2	47	22

Figure S37. Get High-res Image Gene #38: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 2.93e-05 (Fisher's exact test), Q value = 0.013

Table S38. Gene #39: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
DEL PEAK 11(9P21.3) MUTATED	23	17	40
DEL PEAK 11(9P21.3) WILD-TYPE	29	61	29

Figure S38. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 3.25e-06 (Chi-square test), Q value = 0.0014

Table S39. Gene #41: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	32	51	27	33
DEL PEAK 13(10Q23.31) MUTATED	10	21	17	4	3
DEL PEAK 13(10Q23.31) WILD-TYPE	34	11	34	23	30

Figure S39. Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000422 (Chi-square test), Q value = 0.17

Table S40. Gene #41: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	19	21	35	30	40	49
DEL PEAK 13(10Q23.31) MUTATED	4	10	11	6	22	7
DEL PEAK 13(10Q23.31) WILD-TYPE	15	11	24	24	18	42

Figure S40. Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_10q24.33' versus 'MRNASEQ_CNMF'

P value = 4.7e-05 (Chi-square test), Q value = 0.02

Table S41. Gene #42: 'del_10q24.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	32	51	27	33
DEL PEAK 14(10Q24.33) MUTATED	10	20	17	6	3
DEL PEAK 14(10Q24.33) WILD-TYPE	34	12	34	21	30

Figure S41. Get High-res Image Gene #42: 'del_10q24.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'CN_CNMF'

P value = 9.67e-05 (Fisher's exact test), Q value = 0.04

Table S42. Gene #47: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
DEL PEAK 19(13Q12.11) MUTATED	11	19	37
DEL PEAK 19(13Q12.11) WILD-TYPE	41	59	32

Figure S42. Get High-res Image Gene #47: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 5.31e-11 (Fisher's exact test), Q value = 2.4e-08

Table S43. Gene #48: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
DEL PEAK 20(13Q14.2) MUTATED	13	26	55
DEL PEAK 20(13Q14.2) WILD-TYPE	39	52	14

Figure S43. Get High-res Image Gene #48: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.039

Table S44. Gene #48: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	35	69	52
DEL PEAK 20(13Q14.2) MUTATED	9	9	46	25
DEL PEAK 20(13Q14.2) WILD-TYPE	22	26	23	27

Figure S44. Get High-res Image Gene #48: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000219 (Chi-square test), Q value = 0.089

Table S45. Gene #48: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	19	21	35	30	40	49
DEL PEAK 20(13Q14.2) MUTATED	7	14	25	12	22	12
DEL PEAK 20(13Q14.2) WILD-TYPE	12	7	10	18	18	37

Figure S45. Get High-res Image Gene #48: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_13q22.2' versus 'CN_CNMF'

P value = 1.31e-08 (Fisher's exact test), Q value = 5.8e-06

Table S46. Gene #49: 'del_13q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
DEL PEAK 21(13Q22.2) MUTATED	9	20	45
DEL PEAK 21(13Q22.2) WILD-TYPE	43	58	24

Figure S46. Get High-res Image Gene #49: 'del_13q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.23

Table S47. Gene #49: 'del_13q22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	35	69	52
DEL PEAK 21(13Q22.2) MUTATED	6	6	36	21
DEL PEAK 21(13Q22.2) WILD-TYPE	25	29	33	31

Figure S47. Get High-res Image Gene #49: 'del_13q22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000615 (Chi-square test), Q value = 0.24

Table S48. Gene #49: 'del_13q22.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	19	21	35	30	40	49
DEL PEAK 21(13Q22.2) MUTATED	5	10	22	10	17	8
DEL PEAK 21(13Q22.2) WILD-TYPE	14	11	13	20	23	41

Figure S48. Get High-res Image Gene #49: 'del_13q22.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_14q32.33' versus 'CN_CNMF'

P value = 5.46e-05 (Fisher's exact test), Q value = 0.023

Table S49. Gene #51: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
DEL PEAK 23(14Q32.33) MUTATED	16	16	38
DEL PEAK 23(14Q32.33) WILD-TYPE	36	62	31

Figure S49. Get High-res Image Gene #51: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 6.58e-06 (Fisher's exact test), Q value = 0.0028

Table S50. Gene #52: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
DEL PEAK 24(16Q23.1) MUTATED	15	23	45
DEL PEAK 24(16Q23.1) WILD-TYPE	37	55	24

Figure S50. Get High-res Image Gene #52: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.000522 (Fisher's exact test), Q value = 0.21

Table S51. Gene #52: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	52	89
DEL PEAK 24(16Q23.1) MUTATED	16	33	33
DEL PEAK 24(16Q23.1) WILD-TYPE	41	19	56

Figure S51. Get High-res Image Gene #52: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 8.84e-06 (Chi-square test), Q value = 0.0038

Table S52. Gene #52: 'del_16q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	32	51	27	33
DEL PEAK 24(16Q23.1) MUTATED	27	20	23	6	4
DEL PEAK 24(16Q23.1) WILD-TYPE	17	12	28	21	29

Figure S52. Get High-res Image Gene #52: 'del_16q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p11.2' versus 'MIRSEQ_CNMF'

P value = 0.000151 (Fisher's exact test), Q value = 0.063

Table S53. Gene #53: 'del_17p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	48	73
DEL PEAK 25(17P11.2) MUTATED	37	39	33
DEL PEAK 25(17P11.2) WILD-TYPE	36	9	40

Figure S53. Get High-res Image Gene #53: 'del_17p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.000376 (Fisher's exact test), Q value = 0.15

Table S54. Gene #54: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	78	69
DEL PEAK 26(19P13.3) MUTATED	12	8	26
DEL PEAK 26(19P13.3) WILD-TYPE	40	70	43

Figure S54. Get High-res Image Gene #54: '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 = 199
Number of significantly focal cnvs = 56
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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] 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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