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

Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (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/C18P5Z72

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 57 focal events and 8 molecular subtypes across 206 patients, 38 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_2q32.3 cnv correlated to 'CN_CNMF'.
amp_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q28 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF'.
amp_7p11.2 cnv correlated to 'CN_CNMF'.
amp_11q13.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
amp_11q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q25.1 cnv correlated to 'CN_CNMF'.
amp_19q13.2 cnv correlated to 'CN_CNMF'.
del_2q37.1 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'CN_CNMF'.
del_4q21.3 cnv correlated to 'CN_CNMF'.
del_4q22.1 cnv correlated to 'CN_CNMF'.
del_4q35.2 cnv correlated to 'CN_CNMF'.
del_11q25 cnv correlated to 'CN_CNMF'.
del_17q25.3 cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_18q21.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'METHLYATION_CNMF'.
del_xp11.3 cnv correlated to 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 57 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, 38 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
amp 3q28	160 (78%)	46	1e-05 (0.00456)	4e-05 (0.0175)	0.00195 (0.772)	0.00059 (0.247)	0.0261 (1.00)	0.00041 (0.173)	0.00984 (1.00)	3e-05 (0.0132)
amp 11q22 1	35 (17%)	171	2e-05 (0.00888)	1e-05 (0.00456)	3e-05 (0.0132)	1e-05 (0.00456)	0.0145 (1.00)	0.0586 (1.00)	0.00066 (0.276)	1e-05 (0.00456)
amp 3q26 31	160 (78%)	46	1e-05 (0.00456)	0.00011 (0.0475)	0.00247 (0.971)	0.00035 (0.149)	0.0332 (1.00)	0.00079 (0.327)	0.0113 (1.00)	3e-05 (0.0132)
del 18q21 2	57 (28%)	149	0.00388 (1.00)	4e-05 (0.0175)	1e-05 (0.00456)	0.00022 (0.0944)	0.0587 (1.00)	0.00315 (1.00)	0.0162 (1.00)	0.0001 (0.0433)
del 17q25 3	35 (17%)	171	0.141 (1.00)	0.00743 (1.00)	1e-05 (0.00456)	0.00089 (0.367)	9e-05 (0.0391)	0.00407 (1.00)	0.00019 (0.0817)	0.0254 (1.00)
del 2q37 1	87 (42%)	119	0.00507 (1.00)	0.00921 (1.00)	0.00032 (0.137)	0.00028 (0.12)	0.0118 (1.00)	0.00345 (1.00)	0.00154 (0.627)	0.00526 (1.00)
del 2q37 3	84 (41%)	122	0.00169 (0.678)	0.0143 (1.00)	0.00036 (0.153)	0.00038 (0.161)	0.0149 (1.00)	0.00304 (1.00)	0.00249 (0.976)	0.0037 (1.00)
amp 2q32 3	36 (17%)	170	4e-05 (0.0175)	0.00716 (1.00)	0.00166 (0.667)	0.0129 (1.00)	0.116 (1.00)	0.106 (1.00)	0.315 (1.00)	0.262 (1.00)
amp 5p15 33	88 (43%)	118	1e-05 (0.00456)	0.0575 (1.00)	0.0248 (1.00)	0.104 (1.00)	0.032 (1.00)	0.003 (1.00)	0.00448 (1.00)	0.312 (1.00)
amp 7p11 2	34 (17%)	172	2e-05 (0.00888)	0.0266 (1.00)	0.00282 (1.00)	0.0338 (1.00)	0.0074 (1.00)	0.0833 (1.00)	0.00534 (1.00)	0.413 (1.00)
amp 11q13 3	24 (12%)	182	0.0119 (1.00)	0.0306 (1.00)	0.00451 (1.00)	3e-05 (0.0132)	0.114 (1.00)	0.253 (1.00)	0.172 (1.00)	0.00373 (1.00)
amp 17q25 1	56 (27%)	150	0.00017 (0.0733)	0.0772 (1.00)	0.101 (1.00)	0.101 (1.00)	0.0323 (1.00)	0.252 (1.00)	0.0574 (1.00)	0.737 (1.00)
amp 19q13 2	62 (30%)	144	1e-05 (0.00456)	0.0476 (1.00)	0.192 (1.00)	0.17 (1.00)	0.282 (1.00)	0.306 (1.00)	0.449 (1.00)	0.565 (1.00)
del 3p14 2	87 (42%)	119	0.00043 (0.181)	0.00079 (0.327)	0.028 (1.00)	0.00125 (0.511)	0.00826 (1.00)	0.00185 (0.734)	0.0248 (1.00)	0.00226 (0.893)
del 4q21 3	66 (32%)	140	1e-05 (0.00456)	0.427 (1.00)	0.291 (1.00)	0.00547 (1.00)	0.419 (1.00)	0.113 (1.00)	0.452 (1.00)	0.145 (1.00)
del 4q22 1	63 (31%)	143	1e-05 (0.00456)	0.559 (1.00)	0.15 (1.00)	0.00437 (1.00)	0.385 (1.00)	0.151 (1.00)	0.845 (1.00)	0.0304 (1.00)
del 4q35 2	76 (37%)	130	1e-05 (0.00456)	0.365 (1.00)	0.0475 (1.00)	0.0018 (0.718)	0.346 (1.00)	0.226 (1.00)	0.788 (1.00)	0.0223 (1.00)
del 11q25	115 (56%)	91	2e-05 (0.00888)	0.0625 (1.00)	0.0726 (1.00)	0.0426 (1.00)	0.234 (1.00)	0.0301 (1.00)	0.49 (1.00)	0.00363 (1.00)
del 19p13 3	63 (31%)	143	0.00068 (0.284)	0.00047 (0.197)	0.00118 (0.485)	0.00122 (0.5)	0.0699 (1.00)	0.0308 (1.00)	0.267 (1.00)	0.0018 (0.718)
del xp11 3	49 (24%)	157	0.00338 (1.00)	0.00524 (1.00)	0.0407 (1.00)	0.0477 (1.00)	0.00033 (0.141)	0.0291 (1.00)	0.00069 (0.287)	0.018 (1.00)
amp 1p31 3	67 (33%)	139	0.0909 (1.00)	0.523 (1.00)	0.232 (1.00)	0.0999 (1.00)	0.607 (1.00)	0.147 (1.00)	0.982 (1.00)	0.046 (1.00)
amp 1q21 3	108 (52%)	98	0.00134 (0.547)	0.289 (1.00)	0.191 (1.00)	0.358 (1.00)	0.922 (1.00)	0.546 (1.00)	0.851 (1.00)	0.0825 (1.00)
amp 2p24 3	54 (26%)	152	0.0303 (1.00)	0.0321 (1.00)	0.199 (1.00)	0.14 (1.00)	0.28 (1.00)	0.0136 (1.00)	0.357 (1.00)	0.0193 (1.00)
amp 4q12	14 (7%)	192	0.935 (1.00)	0.0481 (1.00)	0.774 (1.00)	0.323 (1.00)	0.343 (1.00)	0.223 (1.00)	0.303 (1.00)	0.535 (1.00)
amp 6p21 33	56 (27%)	150	0.0252 (1.00)	0.0113 (1.00)	0.00351 (1.00)	0.0201 (1.00)	0.354 (1.00)	0.128 (1.00)	0.682 (1.00)	0.0405 (1.00)
amp 8q24 21	84 (41%)	122	0.386 (1.00)	0.388 (1.00)	0.603 (1.00)	0.272 (1.00)	0.0172 (1.00)	0.832 (1.00)	0.172 (1.00)	0.15 (1.00)
amp 9p24 1	43 (21%)	163	0.0252 (1.00)	0.623 (1.00)	0.777 (1.00)	0.261 (1.00)	0.932 (1.00)	0.463 (1.00)	0.976 (1.00)	0.826 (1.00)
amp 11p13	18 (9%)	188	0.118 (1.00)	0.861 (1.00)	0.7 (1.00)	0.251 (1.00)	0.453 (1.00)	0.738 (1.00)	0.475 (1.00)	0.446 (1.00)
amp 13q22 1	45 (22%)	161	0.0371 (1.00)	0.0134 (1.00)	0.953 (1.00)	0.994 (1.00)	0.222 (1.00)	0.225 (1.00)	0.23 (1.00)	0.106 (1.00)
amp 15q26 1	50 (24%)	156	0.83 (1.00)	0.417 (1.00)	0.832 (1.00)	0.784 (1.00)	0.415 (1.00)	1 (1.00)	0.692 (1.00)	0.811 (1.00)
amp 16p13 13	43 (21%)	163	0.297 (1.00)	0.451 (1.00)	0.68 (1.00)	0.289 (1.00)	0.377 (1.00)	0.211 (1.00)	0.257 (1.00)	0.364 (1.00)
amp 17q12	38 (18%)	168	0.0424 (1.00)	0.0162 (1.00)	0.0118 (1.00)	0.0459 (1.00)	0.108 (1.00)	0.0257 (1.00)	0.288 (1.00)	0.291 (1.00)
amp 20q11 21	92 (45%)	114	0.00387 (1.00)	0.0548 (1.00)	0.249 (1.00)	0.0803 (1.00)	0.28 (1.00)	0.011 (1.00)	0.125 (1.00)	0.373 (1.00)
amp xq28	50 (24%)	156	0.934 (1.00)	0.436 (1.00)	0.311 (1.00)	0.685 (1.00)	0.00825 (1.00)	0.126 (1.00)	0.00938 (1.00)	0.696 (1.00)
del 1p36 31	26 (13%)	180	0.0279 (1.00)	0.145 (1.00)	0.00616 (1.00)	0.00298 (1.00)	0.434 (1.00)	0.00173 (0.692)	0.0395 (1.00)	0.0129 (1.00)
del 1p13 2	22 (11%)	184	0.0663 (1.00)	0.018 (1.00)	0.00269 (1.00)	0.254 (1.00)	0.141 (1.00)	0.221 (1.00)	0.0319 (1.00)	0.115 (1.00)
del 2q22 1	41 (20%)	165	0.261 (1.00)	0.942 (1.00)	0.766 (1.00)	0.601 (1.00)	0.905 (1.00)	0.478 (1.00)	0.484 (1.00)	0.873 (1.00)
del 5q22 3	52 (25%)	154	0.0044 (1.00)	0.678 (1.00)	0.449 (1.00)	0.375 (1.00)	0.256 (1.00)	0.27 (1.00)	0.164 (1.00)	0.00349 (1.00)
del 5q35 2	53 (26%)	153	0.00426 (1.00)	0.967 (1.00)	0.567 (1.00)	0.914 (1.00)	0.0632 (1.00)	0.499 (1.00)	0.0308 (1.00)	0.0183 (1.00)
del 6p24 2	30 (15%)	176	0.967 (1.00)	0.225 (1.00)	0.0808 (1.00)	0.685 (1.00)	0.428 (1.00)	0.24 (1.00)	0.772 (1.00)	0.809 (1.00)
del 6q26	70 (34%)	136	0.00271 (1.00)	0.288 (1.00)	0.344 (1.00)	0.511 (1.00)	0.399 (1.00)	0.619 (1.00)	0.293 (1.00)	0.484 (1.00)
del 7q34	45 (22%)	161	0.00439 (1.00)	0.379 (1.00)	0.432 (1.00)	0.653 (1.00)	0.348 (1.00)	0.565 (1.00)	0.442 (1.00)	0.176 (1.00)
del 8p23 3	73 (35%)	133	0.00156 (0.632)	0.0723 (1.00)	0.0238 (1.00)	0.634 (1.00)	0.602 (1.00)	0.824 (1.00)	0.755 (1.00)	0.593 (1.00)
del 10q23 31	60 (29%)	146	0.00259 (1.00)	0.469 (1.00)	0.682 (1.00)	0.633 (1.00)	0.98 (1.00)	0.806 (1.00)	1 (1.00)	0.955 (1.00)
del 11p15 1	68 (33%)	138	0.103 (1.00)	0.0534 (1.00)	0.0912 (1.00)	0.0316 (1.00)	0.0721 (1.00)	0.0711 (1.00)	0.257 (1.00)	0.0975 (1.00)
del 13q12 11	73 (35%)	133	0.0421 (1.00)	0.0245 (1.00)	0.00071 (0.295)	0.0102 (1.00)	0.0511 (1.00)	0.00295 (1.00)	0.0774 (1.00)	0.0611 (1.00)
del 13q14 2	81 (39%)	125	0.0276 (1.00)	0.0106 (1.00)	0.00229 (0.902)	0.0128 (1.00)	0.0385 (1.00)	0.00429 (1.00)	0.1 (1.00)	0.0601 (1.00)
del 14q32 31	32 (16%)	174	0.00717 (1.00)	0.417 (1.00)	0.00494 (1.00)	0.00155 (0.629)	0.138 (1.00)	0.511 (1.00)	0.028 (1.00)	0.302 (1.00)
del 15q21 1	40 (19%)	166	0.0186 (1.00)	0.0926 (1.00)	0.0293 (1.00)	0.146 (1.00)	0.107 (1.00)	0.144 (1.00)	0.236 (1.00)	0.526 (1.00)
del 16q12 1	41 (20%)	165	0.382 (1.00)	0.0498 (1.00)	0.158 (1.00)	0.372 (1.00)	0.168 (1.00)	0.0191 (1.00)	0.06 (1.00)	0.0188 (1.00)
del 16q23 1	41 (20%)	165	0.401 (1.00)	0.00768 (1.00)	0.00634 (1.00)	0.0423 (1.00)	0.239 (1.00)	0.00156 (0.632)	0.0363 (1.00)	0.00569 (1.00)
del 17p12	68 (33%)	138	0.00165 (0.665)	0.346 (1.00)	0.203 (1.00)	0.0455 (1.00)	0.063 (1.00)	0.2 (1.00)	0.121 (1.00)	0.255 (1.00)
del 19q13 33	25 (12%)	181	0.164 (1.00)	0.295 (1.00)	0.266 (1.00)	0.512 (1.00)	0.258 (1.00)	0.634 (1.00)	0.442 (1.00)	0.65 (1.00)
del 20p12 1	27 (13%)	179	0.965 (1.00)	0.247 (1.00)	0.615 (1.00)	1 (1.00)	0.316 (1.00)	0.652 (1.00)	0.417 (1.00)	0.0713 (1.00)
del 21q11 2	40 (19%)	166	0.00545 (1.00)	0.171 (1.00)	0.297 (1.00)	0.00924 (1.00)	0.882 (1.00)	0.711 (1.00)	0.635 (1.00)	0.157 (1.00)
del 22q13 32	57 (28%)	149	0.122 (1.00)	0.268 (1.00)	0.401 (1.00)	0.29 (1.00)	0.852 (1.00)	0.677 (1.00)	0.887 (1.00)	0.618 (1.00)
del xq21 33	43 (21%)	163	0.231 (1.00)	0.014 (1.00)	0.161 (1.00)	0.0529 (1.00)	0.0931 (1.00)	0.101 (1.00)	0.241 (1.00)	0.00847 (1.00)

'amp_2q32.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S1. Gene #4: 'amp_2q32.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	44	96
AMP PEAK 4(2Q32.3) MUTATED	13	17	6
AMP PEAK 4(2Q32.3) WILD-TYPE	53	27	90

Figure S1. Get High-res Image Gene #4: 'amp_2q32.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S2. Gene #5: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	44	96
AMP PEAK 5(3Q26.31) MUTATED	66	35	59
AMP PEAK 5(3Q26.31) WILD-TYPE	0	9	37

Figure S2. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.31' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.048

Table S3. Gene #5: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	51	34	39	38	32	12
AMP PEAK 5(3Q26.31) MUTATED	32	27	34	24	31	12
AMP PEAK 5(3Q26.31) WILD-TYPE	19	7	5	14	1	0

Figure S3. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.15

Table S4. Gene #5: 'amp_3q26.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	27	21	53
AMP PEAK 5(3Q26.31) MUTATED	86	25	12	34
AMP PEAK 5(3Q26.31) WILD-TYPE	14	2	9	19

Figure S4. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S5. Gene #5: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	25	38	16	32	34	28	33
AMP PEAK 5(3Q26.31) MUTATED	14	35	16	18	29	18	30
AMP PEAK 5(3Q26.31) WILD-TYPE	11	3	0	14	5	10	3

Figure S5. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S6. Gene #6: 'amp_3q28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	44	96
AMP PEAK 6(3Q28) MUTATED	66	35	59
AMP PEAK 6(3Q28) WILD-TYPE	0	9	37

Figure S6. Get High-res Image Gene #6: 'amp_3q28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q28' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S7. Gene #6: 'amp_3q28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	51	34	39	38	32	12
AMP PEAK 6(3Q28) MUTATED	31	27	33	25	32	12
AMP PEAK 6(3Q28) WILD-TYPE	20	7	6	13	0	0

Figure S7. Get High-res Image Gene #6: 'amp_3q28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.25

Table S8. Gene #6: 'amp_3q28' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	27	21	53
AMP PEAK 6(3Q28) MUTATED	87	24	13	33
AMP PEAK 6(3Q28) WILD-TYPE	13	3	8	20

Figure S8. Get High-res Image Gene #6: 'amp_3q28' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3q28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.17

Table S9. Gene #6: 'amp_3q28' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	123	41
AMP PEAK 6(3Q28) MUTATED	25	96	39
AMP PEAK 6(3Q28) WILD-TYPE	17	27	2

Figure S9. Get High-res Image Gene #6: 'amp_3q28' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_3q28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S10. Gene #6: 'amp_3q28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	25	38	16	32	34	28	33
AMP PEAK 6(3Q28) MUTATED	14	35	16	19	29	17	30
AMP PEAK 6(3Q28) WILD-TYPE	11	3	0	13	5	11	3

Figure S10. Get High-res Image Gene #6: 'amp_3q28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S11. Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	44	96
AMP PEAK 8(5P15.33) MUTATED	32	32	24
AMP PEAK 8(5P15.33) WILD-TYPE	34	12	72

Figure S11. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S12. Gene #10: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	44	96
AMP PEAK 10(7P11.2) MUTATED	7	18	9
AMP PEAK 10(7P11.2) WILD-TYPE	59	26	87

Figure S12. Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S13. Gene #14: 'amp_11q13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	27	21	53
AMP PEAK 14(11Q13.3) MUTATED	9	0	10	5
AMP PEAK 14(11Q13.3) WILD-TYPE	91	27	11	48

Figure S13. Get High-res Image Gene #14: 'amp_11q13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_11q22.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S14. Gene #15: 'amp_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	44	96
AMP PEAK 15(11Q22.1) MUTATED	5	19	11
AMP PEAK 15(11Q22.1) WILD-TYPE	61	25	85

Figure S14. Get High-res Image Gene #15: 'amp_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S15. Gene #15: 'amp_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	51	34	39	38	32	12
AMP PEAK 15(11Q22.1) MUTATED	3	1	8	18	3	2
AMP PEAK 15(11Q22.1) WILD-TYPE	48	33	31	20	29	10

Figure S15. Get High-res Image Gene #15: 'amp_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q22.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S16. Gene #15: 'amp_11q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	50	65
AMP PEAK 15(11Q22.1) MUTATED	10	20	5
AMP PEAK 15(11Q22.1) WILD-TYPE	76	30	60

Figure S16. Get High-res Image Gene #15: 'amp_11q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_11q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S17. Gene #15: 'amp_11q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	27	21	53
AMP PEAK 15(11Q22.1) MUTATED	12	5	15	3
AMP PEAK 15(11Q22.1) WILD-TYPE	88	22	6	50

Figure S17. Get High-res Image Gene #15: 'amp_11q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_11q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S18. Gene #15: 'amp_11q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	25	38	16	32	34	28	33
AMP PEAK 15(11Q22.1) MUTATED	2	6	6	16	2	1	2
AMP PEAK 15(11Q22.1) WILD-TYPE	23	32	10	16	32	27	31

Figure S18. Get High-res Image Gene #15: 'amp_11q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.073

Table S19. Gene #20: 'amp_17q25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	44	96
AMP PEAK 20(17Q25.1) MUTATED	29	13	14
AMP PEAK 20(17Q25.1) WILD-TYPE	37	31	82

Figure S19. Get High-res Image Gene #20: 'amp_17q25.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S20. Gene #21: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	44	96
AMP PEAK 21(19Q13.2) MUTATED	16	28	18
AMP PEAK 21(19Q13.2) WILD-TYPE	50	16	78

Figure S20. Get High-res Image Gene #21: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.1' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.14

Table S21. Gene #27: 'del_2q37.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	50	65
DEL PEAK 4(2Q37.1) MUTATED	41	29	15
DEL PEAK 4(2Q37.1) WILD-TYPE	45	21	50

Figure S21. Get High-res Image Gene #27: 'del_2q37.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q37.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.12

Table S22. Gene #27: 'del_2q37.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	27	21	53
DEL PEAK 4(2Q37.1) MUTATED	48	11	15	11
DEL PEAK 4(2Q37.1) WILD-TYPE	52	16	6	42

Figure S22. Get High-res Image Gene #27: 'del_2q37.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.15

Table S23. Gene #28: 'del_2q37.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	50	65
DEL PEAK 5(2Q37.3) MUTATED	38	29	15
DEL PEAK 5(2Q37.3) WILD-TYPE	48	21	50

Figure S23. Get High-res Image Gene #28: 'del_2q37.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.16

Table S24. Gene #28: 'del_2q37.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	27	21	53
DEL PEAK 5(2Q37.3) MUTATED	45	11	15	11
DEL PEAK 5(2Q37.3) WILD-TYPE	55	16	6	42

Figure S24. Get High-res Image Gene #28: 'del_2q37.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.18

Table S25. Gene #29: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	44	96
DEL PEAK 6(3P14.2) MUTATED	31	28	28
DEL PEAK 6(3P14.2) WILD-TYPE	35	16	68

Figure S25. Get High-res Image Gene #29: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S26. Gene #30: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	44	96
DEL PEAK 7(4Q21.3) MUTATED	23	31	12
DEL PEAK 7(4Q21.3) WILD-TYPE	43	13	84

Figure S26. Get High-res Image Gene #30: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S27. Gene #31: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	44	96
DEL PEAK 8(4Q22.1) MUTATED	21	33	9
DEL PEAK 8(4Q22.1) WILD-TYPE	45	11	87

Figure S27. Get High-res Image Gene #31: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S28. Gene #32: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	44	96
DEL PEAK 9(4Q35.2) MUTATED	24	35	17
DEL PEAK 9(4Q35.2) WILD-TYPE	42	9	79

Figure S28. Get High-res Image Gene #32: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S29. Gene #41: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	44	96
DEL PEAK 18(11Q25) MUTATED	48	30	37
DEL PEAK 18(11Q25) WILD-TYPE	18	14	59

Figure S29. Get High-res Image Gene #41: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S30. Gene #49: 'del_17q25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	50	65
DEL PEAK 26(17Q25.3) MUTATED	14	18	2
DEL PEAK 26(17Q25.3) WILD-TYPE	72	32	63

Figure S30. Get High-res Image Gene #49: 'del_17q25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17q25.3' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.039

Table S31. Gene #49: 'del_17q25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	57	77
DEL PEAK 26(17Q25.3) MUTATED	4	7	24
DEL PEAK 26(17Q25.3) WILD-TYPE	68	50	53

Figure S31. Get High-res Image Gene #49: 'del_17q25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17q25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.082

Table S32. Gene #49: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	62	70
DEL PEAK 26(17Q25.3) MUTATED	4	9	22
DEL PEAK 26(17Q25.3) WILD-TYPE	70	53	48

Figure S32. Get High-res Image Gene #49: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S33. Gene #50: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	51	34	39	38	32	12
DEL PEAK 27(18Q21.2) MUTATED	22	6	7	18	2	2
DEL PEAK 27(18Q21.2) WILD-TYPE	29	28	32	20	30	10

Figure S33. Get High-res Image Gene #50: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0046

Table S34. Gene #50: 'del_18q21.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	50	65
DEL PEAK 27(18Q21.2) MUTATED	7	24	25
DEL PEAK 27(18Q21.2) WILD-TYPE	79	26	40

Figure S34. Get High-res Image Gene #50: 'del_18q21.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.094

Table S35. Gene #50: 'del_18q21.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	27	21	53
DEL PEAK 27(18Q21.2) MUTATED	18	4	11	23
DEL PEAK 27(18Q21.2) WILD-TYPE	82	23	10	30

Figure S35. Get High-res Image Gene #50: 'del_18q21.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.043

Table S36. Gene #50: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	25	38	16	32	34	28	33
DEL PEAK 27(18Q21.2) MUTATED	15	10	2	15	4	7	4
DEL PEAK 27(18Q21.2) WILD-TYPE	10	28	14	17	30	21	29

Figure S36. Get High-res Image Gene #50: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.2

Table S37. Gene #51: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	51	34	39	38	32	12
DEL PEAK 28(19P13.3) MUTATED	16	9	4	22	8	4
DEL PEAK 28(19P13.3) WILD-TYPE	35	25	35	16	24	8

Figure S37. Get High-res Image Gene #51: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp11.3' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.14

Table S38. Gene #56: 'del_xp11.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	57	77
DEL PEAK 33(XP11.3) MUTATED	12	7	30
DEL PEAK 33(XP11.3) WILD-TYPE	60	50	47

Figure S38. Get High-res Image Gene #56: 'del_xp11.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = CESC-TP.transferedmergedcluster.txt
Number of patients = 206
Number of significantly focal cnvs = 57
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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