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

Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (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/C1J964ZM

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 55 focal events and 8 molecular subtypes across 192 patients, 33 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_2q33.1 cnv correlated to 'MRNASEQ_CNMF'.
amp_3q26.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q28 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF'.
amp_7p11.2 cnv correlated to 'CN_CNMF'.
amp_11q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_17q25.1 cnv correlated to 'CN_CNMF'.
amp_19q13.2 cnv correlated to 'CN_CNMF'.
amp_20q11.21 cnv correlated to 'CN_CNMF'.
del_1p36.31 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'CN_CNMF'.
del_4q21.3 cnv correlated to 'CN_CNMF'.
del_4q35.2 cnv correlated to 'CN_CNMF'.
del_5q13.3 cnv correlated to 'CN_CNMF'.
del_5q35.2 cnv correlated to 'CN_CNMF'.
del_11q25 cnv correlated to 'CN_CNMF'.
del_14q32.31 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.
del_17q25.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 55 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, 33 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	Chi-square 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 17q25 3	32 (17%)	160	0.395 (1.00)	0.000214 (0.0896)	1.93e-05 (0.0083)	0.00265 (1.00)	1.51e-05 (0.00656)	0.0012 (0.472)	2.93e-05 (0.0126)	0.000237 (0.0987)
amp 11q22 1	33 (17%)	159	5.94e-05 (0.0252)	1.69e-05 (0.0073)	0.000284 (0.117)	0.000103 (0.0435)	0.0165 (1.00)	0.0166 (1.00)	0.0132 (1.00)	0.00797 (1.00)
amp 3q26 31	148 (77%)	44	2.63e-09 (1.16e-06)	0.000813 (0.329)	0.017 (1.00)	0.000584 (0.238)	0.0355 (1.00)	0.00464 (1.00)	0.0515 (1.00)	0.000225 (0.0938)
del 18q21 2	53 (28%)	139	0.0158 (1.00)	0.00141 (0.55)	9.61e-05 (0.0407)	0.000583 (0.238)	0.0637 (1.00)	0.000273 (0.113)	0.00136 (0.533)	0.00966 (1.00)
amp 3q28	148 (77%)	44	2.63e-09 (1.16e-06)	0.00305 (1.00)	0.0446 (1.00)	0.00084 (0.339)	0.0225 (1.00)	0.00251 (0.955)	0.0388 (1.00)	0.000133 (0.0562)
del 14q32 31	31 (16%)	161	0.00574 (1.00)	0.262 (1.00)	0.00893 (1.00)	0.000272 (0.112)	0.0381 (1.00)	0.0369 (1.00)	0.00054 (0.221)	0.0361 (1.00)
amp 2q33 1	30 (16%)	162	0.00326 (1.00)	0.0597 (1.00)	0.000145 (0.0607)	0.0584 (1.00)	0.254 (1.00)	0.00822 (1.00)	0.0965 (1.00)	0.155 (1.00)
amp 5p15 33	80 (42%)	112	1.41e-07 (6.14e-05)	0.0257 (1.00)	0.114 (1.00)	0.0164 (1.00)	0.0164 (1.00)	0.011 (1.00)	0.0255 (1.00)	0.0526 (1.00)
amp 7p11 2	34 (18%)	158	3.82e-05 (0.0163)	0.0206 (1.00)	0.0256 (1.00)	0.0492 (1.00)	0.00893 (1.00)	0.0157 (1.00)	0.00747 (1.00)	0.0398 (1.00)
amp 17q25 1	53 (28%)	139	0.000173 (0.0725)	0.0193 (1.00)	0.0984 (1.00)	0.177 (1.00)	0.0511 (1.00)	0.602 (1.00)	0.0285 (1.00)	0.65 (1.00)
amp 19q13 2	59 (31%)	133	7.28e-07 (0.000316)	0.0657 (1.00)	0.402 (1.00)	0.528 (1.00)	0.447 (1.00)	0.435 (1.00)	0.195 (1.00)	0.74 (1.00)
amp 20q11 21	87 (45%)	105	0.00026 (0.108)	0.15 (1.00)	0.156 (1.00)	0.242 (1.00)	0.888 (1.00)	0.319 (1.00)	0.441 (1.00)	0.273 (1.00)
del 1p36 31	26 (14%)	166	0.0314 (1.00)	0.106 (1.00)	0.0425 (1.00)	0.00109 (0.431)	0.0552 (1.00)	8.18e-05 (0.0347)	0.0127 (1.00)	0.00166 (0.641)
del 3p14 2	78 (41%)	114	1.1e-05 (0.00479)	0.000901 (0.36)	0.02 (1.00)	0.00211 (0.814)	0.00526 (1.00)	0.00643 (1.00)	0.0115 (1.00)	0.000854 (0.343)
del 4q21 3	58 (30%)	134	7.73e-08 (3.38e-05)	0.0115 (1.00)	0.581 (1.00)	0.00383 (1.00)	0.317 (1.00)	0.652 (1.00)	0.762 (1.00)	0.436 (1.00)
del 4q35 2	70 (36%)	122	3.9e-08 (1.71e-05)	0.0763 (1.00)	0.0946 (1.00)	0.00174 (0.673)	0.353 (1.00)	0.448 (1.00)	0.97 (1.00)	0.681 (1.00)
del 5q13 3	47 (24%)	145	2.42e-05 (0.0104)	0.0376 (1.00)	0.324 (1.00)	0.38 (1.00)	0.0524 (1.00)	0.476 (1.00)	0.0897 (1.00)	0.392 (1.00)
del 5q35 2	49 (26%)	143	1.88e-05 (0.0081)	0.0632 (1.00)	0.654 (1.00)	0.879 (1.00)	0.0426 (1.00)	0.289 (1.00)	0.0829 (1.00)	0.36 (1.00)
del 11q25	107 (56%)	85	4.37e-05 (0.0186)	0.18 (1.00)	0.323 (1.00)	0.0289 (1.00)	0.0876 (1.00)	0.0327 (1.00)	0.0395 (1.00)	0.00794 (1.00)
del 19p13 3	58 (30%)	134	0.00412 (1.00)	0.000646 (0.263)	0.00286 (1.00)	0.00651 (1.00)	0.433 (1.00)	0.000519 (0.213)	0.25 (1.00)	0.0194 (1.00)
amp 1p31 3	62 (32%)	130	0.683 (1.00)	0.197 (1.00)	0.138 (1.00)	0.0984 (1.00)	0.971 (1.00)	0.156 (1.00)	0.943 (1.00)	0.492 (1.00)
amp 1q21 3	98 (51%)	94	0.00569 (1.00)	0.309 (1.00)	0.367 (1.00)	0.276 (1.00)	0.782 (1.00)	0.475 (1.00)	0.857 (1.00)	0.346 (1.00)
amp 2p24 3	50 (26%)	142	0.0183 (1.00)	0.0173 (1.00)	0.41 (1.00)	0.0475 (1.00)	0.17 (1.00)	0.000899 (0.36)	0.33 (1.00)	0.013 (1.00)
amp 6p21 33	51 (27%)	141	0.0502 (1.00)	0.00436 (1.00)	0.0503 (1.00)	0.0117 (1.00)	0.215 (1.00)	0.0505 (1.00)	0.416 (1.00)	0.554 (1.00)
amp 8q24 21	79 (41%)	113	0.254 (1.00)	0.694 (1.00)	0.868 (1.00)	0.961 (1.00)	0.0131 (1.00)	0.302 (1.00)	0.101 (1.00)	0.239 (1.00)
amp 9p24 1	41 (21%)	151	0.225 (1.00)	0.0578 (1.00)	0.647 (1.00)	0.00884 (1.00)	0.445 (1.00)	0.185 (1.00)	0.828 (1.00)	0.182 (1.00)
amp 11p13	16 (8%)	176	0.241 (1.00)	0.587 (1.00)	0.347 (1.00)	0.92 (1.00)	0.578 (1.00)	0.463 (1.00)	0.773 (1.00)	0.477 (1.00)
amp 11q13 3	24 (12%)	168	0.00314 (1.00)	0.00403 (1.00)	0.00728 (1.00)	0.00715 (1.00)	0.0178 (1.00)	0.00536 (1.00)	0.0162 (1.00)	0.0248 (1.00)
amp 13q22 1	41 (21%)	151	0.011 (1.00)	0.14 (1.00)	0.148 (1.00)	0.934 (1.00)	0.674 (1.00)	0.524 (1.00)	0.687 (1.00)	0.306 (1.00)
amp 13q34	43 (22%)	149	0.00295 (1.00)	0.807 (1.00)	0.934 (1.00)	0.934 (1.00)	0.724 (1.00)	0.154 (1.00)	0.61 (1.00)	0.0815 (1.00)
amp 15q26 1	46 (24%)	146	0.964 (1.00)	0.433 (1.00)	0.761 (1.00)	0.391 (1.00)	0.286 (1.00)	1 (1.00)	0.189 (1.00)	0.787 (1.00)
amp 16p13 13	39 (20%)	153	0.193 (1.00)	0.481 (1.00)	0.358 (1.00)	0.314 (1.00)	0.257 (1.00)	0.427 (1.00)	0.492 (1.00)	0.31 (1.00)
amp 17q12	36 (19%)	156	0.0317 (1.00)	0.0459 (1.00)	0.157 (1.00)	0.136 (1.00)	0.175 (1.00)	0.0779 (1.00)	0.163 (1.00)	0.178 (1.00)
amp xq28	47 (24%)	145	0.782 (1.00)	0.992 (1.00)	0.753 (1.00)	0.581 (1.00)	0.00479 (1.00)	0.0368 (1.00)	0.0308 (1.00)	0.0812 (1.00)
del 2q22 1	37 (19%)	155	0.792 (1.00)	0.915 (1.00)	0.383 (1.00)	0.279 (1.00)	0.73 (1.00)	0.761 (1.00)	0.862 (1.00)	0.731 (1.00)
del 2q37 1	81 (42%)	111	0.172 (1.00)	0.00824 (1.00)	0.00833 (1.00)	0.000736 (0.299)	0.0183 (1.00)	0.00713 (1.00)	0.0144 (1.00)	0.00291 (1.00)
del 6p24 2	29 (15%)	163	0.556 (1.00)	0.0932 (1.00)	0.244 (1.00)	0.523 (1.00)	0.196 (1.00)	0.833 (1.00)	0.865 (1.00)	0.556 (1.00)
del 6q26	65 (34%)	127	0.00982 (1.00)	0.419 (1.00)	0.746 (1.00)	0.639 (1.00)	0.602 (1.00)	0.227 (1.00)	0.705 (1.00)	0.225 (1.00)
del 7q34	43 (22%)	149	0.00505 (1.00)	0.965 (1.00)	0.683 (1.00)	0.696 (1.00)	0.453 (1.00)	0.528 (1.00)	0.603 (1.00)	0.676 (1.00)
del 8p23 3	66 (34%)	126	0.00344 (1.00)	0.136 (1.00)	0.0915 (1.00)	0.851 (1.00)	0.831 (1.00)	0.157 (1.00)	0.829 (1.00)	0.273 (1.00)
del 10q23 31	55 (29%)	137	0.0314 (1.00)	0.197 (1.00)	0.242 (1.00)	0.65 (1.00)	0.669 (1.00)	1 (1.00)	0.973 (1.00)	1 (1.00)
del 11p15 1	62 (32%)	130	0.0146 (1.00)	0.046 (1.00)	0.0596 (1.00)	0.0372 (1.00)	0.187 (1.00)	0.0821 (1.00)	0.168 (1.00)	0.0615 (1.00)
del 13q12 12	68 (35%)	124	0.000866 (0.347)	0.0143 (1.00)	0.167 (1.00)	0.00308 (1.00)	0.0108 (1.00)	0.021 (1.00)	0.0106 (1.00)	0.0148 (1.00)
del 13q14 2	74 (39%)	118	0.00231 (0.884)	0.00853 (1.00)	0.0679 (1.00)	0.00147 (0.573)	0.00354 (1.00)	0.00276 (1.00)	0.00286 (1.00)	0.0067 (1.00)
del 15q21 1	38 (20%)	154	0.0185 (1.00)	0.0526 (1.00)	0.414 (1.00)	0.213 (1.00)	0.27 (1.00)	0.0232 (1.00)	0.124 (1.00)	0.113 (1.00)
del 16q12 1	39 (20%)	153	0.575 (1.00)	0.0175 (1.00)	0.173 (1.00)	0.347 (1.00)	0.146 (1.00)	0.0787 (1.00)	0.0102 (1.00)	0.154 (1.00)
del 16q23 1	39 (20%)	153	0.511 (1.00)	0.000931 (0.37)	0.00398 (1.00)	0.00388 (1.00)	0.055 (1.00)	0.00161 (0.623)	0.00106 (0.421)	0.00474 (1.00)
del 17p12	61 (32%)	131	0.00332 (1.00)	0.442 (1.00)	0.217 (1.00)	0.11 (1.00)	0.0357 (1.00)	0.375 (1.00)	0.0637 (1.00)	0.0959 (1.00)
del 19q13 33	22 (11%)	170	0.244 (1.00)	0.241 (1.00)	0.102 (1.00)	0.487 (1.00)	0.467 (1.00)	0.109 (1.00)	0.488 (1.00)	0.171 (1.00)
del 20p12 1	25 (13%)	167	0.802 (1.00)	0.446 (1.00)	0.271 (1.00)	0.75 (1.00)	0.334 (1.00)	0.16 (1.00)	0.236 (1.00)	0.732 (1.00)
del 21q21 1	35 (18%)	157	0.0383 (1.00)	0.387 (1.00)	0.848 (1.00)	0.00237 (0.904)	0.756 (1.00)	0.671 (1.00)	0.929 (1.00)	0.744 (1.00)
del 22q13 32	52 (27%)	140	0.166 (1.00)	0.13 (1.00)	0.257 (1.00)	0.385 (1.00)	0.886 (1.00)	0.203 (1.00)	0.54 (1.00)	0.365 (1.00)
del xp21 1	42 (22%)	150	0.00104 (0.414)	0.0907 (1.00)	0.131 (1.00)	0.286 (1.00)	0.0124 (1.00)	0.0171 (1.00)	0.0104 (1.00)	0.00277 (1.00)
del xp11 3	46 (24%)	146	0.00141 (0.55)	0.0688 (1.00)	0.0865 (1.00)	0.139 (1.00)	0.00106 (0.42)	0.0103 (1.00)	0.000824 (0.333)	0.00214 (0.823)
del xq21 33	39 (20%)	153	0.063 (1.00)	0.0253 (1.00)	0.303 (1.00)	0.0258 (1.00)	0.0733 (1.00)	0.0129 (1.00)	0.15 (1.00)	0.00715 (1.00)

'amp_2q33.1' versus 'MRNASEQ_CNMF'

P value = 0.000145 (Fisher's exact test), Q value = 0.061

Table S1. Gene #4: 'amp_2q33.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	34	45	37
AMP PEAK 4(2Q33.1) MUTATED	1	11	7	7
AMP PEAK 4(2Q33.1) WILD-TYPE	63	23	38	30

Figure S1. Get High-res Image Gene #4: 'amp_2q33.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3q26.31' versus 'CN_CNMF'

P value = 2.63e-09 (Fisher's exact test), Q value = 1.2e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
AMP PEAK 5(3Q26.31) MUTATED	60	33	55
AMP PEAK 5(3Q26.31) WILD-TYPE	0	9	35

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

'amp_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000584 (Fisher's exact test), Q value = 0.24

Table S3. Gene #5: 'amp_3q26.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	112	49
AMP PEAK 5(3Q26.31) MUTATED	10	96	32
AMP PEAK 5(3Q26.31) WILD-TYPE	9	16	17

Figure S3. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000225 (Fisher's exact test), Q value = 0.094

Table S4. Gene #5: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	70	55
AMP PEAK 5(3Q26.31) MUTATED	62	51	35
AMP PEAK 5(3Q26.31) WILD-TYPE	5	19	20

Figure S4. Get High-res Image Gene #5: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q28' versus 'CN_CNMF'

P value = 2.63e-09 (Fisher's exact test), Q value = 1.2e-06

Table S5. Gene #6: 'amp_3q28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
AMP PEAK 6(3Q28) MUTATED	60	33	55
AMP PEAK 6(3Q28) WILD-TYPE	0	9	35

Figure S5. Get High-res Image Gene #6: 'amp_3q28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000133 (Fisher's exact test), Q value = 0.056

Table S6. Gene #6: 'amp_3q28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	70	55
AMP PEAK 6(3Q28) MUTATED	62	52	34
AMP PEAK 6(3Q28) WILD-TYPE	5	18	21

Figure S6. Get High-res Image Gene #6: 'amp_3q28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1.41e-07 (Fisher's exact test), Q value = 6.1e-05

Table S7. Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
AMP PEAK 7(5P15.33) MUTATED	28	31	21
AMP PEAK 7(5P15.33) WILD-TYPE	32	11	69

Figure S7. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'CN_CNMF'

P value = 3.82e-05 (Fisher's exact test), Q value = 0.016

Table S8. Gene #9: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
AMP PEAK 9(7P11.2) MUTATED	7	18	9
AMP PEAK 9(7P11.2) WILD-TYPE	53	24	81

Figure S8. Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q22.1' versus 'CN_CNMF'

P value = 5.94e-05 (Fisher's exact test), Q value = 0.025

Table S9. Gene #14: 'amp_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
AMP PEAK 14(11Q22.1) MUTATED	4	17	12
AMP PEAK 14(11Q22.1) WILD-TYPE	56	25	78

Figure S9. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q22.1' versus 'METHLYATION_CNMF'

P value = 1.69e-05 (Chi-square test), Q value = 0.0073

Table S10. Gene #14: 'amp_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	27	21	32	31	34	15
AMP PEAK 14(11Q22.1) MUTATED	8	0	2	15	2	3	3
AMP PEAK 14(11Q22.1) WILD-TYPE	24	27	19	17	29	31	12

Figure S10. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q22.1' versus 'MRNASEQ_CNMF'

P value = 0.000284 (Fisher's exact test), Q value = 0.12

Table S11. Gene #14: 'amp_11q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	34	45	37
AMP PEAK 14(11Q22.1) MUTATED	9	1	5	15
AMP PEAK 14(11Q22.1) WILD-TYPE	55	33	40	22

Figure S11. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_11q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000103 (Fisher's exact test), Q value = 0.044

Table S12. Gene #14: 'amp_11q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	112	49
AMP PEAK 14(11Q22.1) MUTATED	10	17	3
AMP PEAK 14(11Q22.1) WILD-TYPE	9	95	46

Figure S12. Get High-res Image Gene #14: 'amp_11q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'CN_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.072

Table S13. Gene #20: 'amp_17q25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
AMP PEAK 20(17Q25.1) MUTATED	27	13	13
AMP PEAK 20(17Q25.1) WILD-TYPE	33	29	77

Figure S13. Get High-res Image Gene #20: 'amp_17q25.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.2' versus 'CN_CNMF'

P value = 7.28e-07 (Fisher's exact test), Q value = 0.00032

Table S14. Gene #21: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
AMP PEAK 21(19Q13.2) MUTATED	16	27	16
AMP PEAK 21(19Q13.2) WILD-TYPE	44	15	74

Figure S14. Get High-res Image Gene #21: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.11

Table S15. Gene #22: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
AMP PEAK 22(20Q11.21) MUTATED	34	26	27
AMP PEAK 22(20Q11.21) WILD-TYPE	26	16	63

Figure S15. Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.18e-05 (Fisher's exact test), Q value = 0.035

Table S16. Gene #24: 'del_1p36.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	61	60
DEL PEAK 1(1P36.31) MUTATED	1	10	15
DEL PEAK 1(1P36.31) WILD-TYPE	70	51	45

Figure S16. Get High-res Image Gene #24: 'del_1p36.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0048

Table S17. Gene #27: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
DEL PEAK 4(3P14.2) MUTATED	26	29	23
DEL PEAK 4(3P14.2) WILD-TYPE	34	13	67

Figure S17. Get High-res Image Gene #27: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'CN_CNMF'

P value = 7.73e-08 (Fisher's exact test), Q value = 3.4e-05

Table S18. Gene #28: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
DEL PEAK 5(4Q21.3) MUTATED	18	27	13
DEL PEAK 5(4Q21.3) WILD-TYPE	42	15	77

Figure S18. Get High-res Image Gene #28: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.2' versus 'CN_CNMF'

P value = 3.9e-08 (Fisher's exact test), Q value = 1.7e-05

Table S19. Gene #29: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
DEL PEAK 6(4Q35.2) MUTATED	20	31	19
DEL PEAK 6(4Q35.2) WILD-TYPE	40	11	71

Figure S19. Get High-res Image Gene #29: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q13.3' versus 'CN_CNMF'

P value = 2.42e-05 (Fisher's exact test), Q value = 0.01

Table S20. Gene #30: 'del_5q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
DEL PEAK 7(5Q13.3) MUTATED	15	21	11
DEL PEAK 7(5Q13.3) WILD-TYPE	45	21	79

Figure S20. Get High-res Image Gene #30: 'del_5q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.2' versus 'CN_CNMF'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.0081

Table S21. Gene #31: 'del_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
DEL PEAK 8(5Q35.2) MUTATED	15	22	12
DEL PEAK 8(5Q35.2) WILD-TYPE	45	20	78

Figure S21. Get High-res Image Gene #31: 'del_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'CN_CNMF'

P value = 4.37e-05 (Fisher's exact test), Q value = 0.019

Table S22. Gene #38: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	42	90
DEL PEAK 15(11Q25) MUTATED	44	28	35
DEL PEAK 15(11Q25) WILD-TYPE	16	14	55

Figure S22. Get High-res Image Gene #38: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S23. Gene #41: 'del_14q32.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	112	49
DEL PEAK 18(14Q32.31) MUTATED	8	10	13
DEL PEAK 18(14Q32.31) WILD-TYPE	11	102	36

Figure S23. Get High-res Image Gene #41: 'del_14q32.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.22

Table S24. Gene #41: 'del_14q32.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	52	68
DEL PEAK 18(14Q32.31) MUTATED	4	7	20
DEL PEAK 18(14Q32.31) WILD-TYPE	68	45	48

Figure S24. Get High-res Image Gene #41: 'del_14q32.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_17q25.3' versus 'METHLYATION_CNMF'

P value = 0.000214 (Chi-square test), Q value = 0.09

Table S25. Gene #46: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	27	21	32	31	34	15
DEL PEAK 23(17Q25.3) MUTATED	5	2	2	10	12	0	1
DEL PEAK 23(17Q25.3) WILD-TYPE	27	25	19	22	19	34	14

Figure S25. Get High-res Image Gene #46: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q25.3' versus 'MRNASEQ_CNMF'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.0083

Table S26. Gene #46: 'del_17q25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	34	45	37
DEL PEAK 23(17Q25.3) MUTATED	12	1	1	14
DEL PEAK 23(17Q25.3) WILD-TYPE	52	33	44	23

Figure S26. Get High-res Image Gene #46: 'del_17q25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17q25.3' versus 'MIRSEQ_CNMF'

P value = 1.51e-05 (Fisher's exact test), Q value = 0.0066

Table S27. Gene #46: 'del_17q25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	52	67
DEL PEAK 23(17Q25.3) MUTATED	23	7	2
DEL PEAK 23(17Q25.3) WILD-TYPE	50	45	65

Figure S27. Get High-res Image Gene #46: 'del_17q25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17q25.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S28. Gene #46: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	52	68
DEL PEAK 23(17Q25.3) MUTATED	22	8	2
DEL PEAK 23(17Q25.3) WILD-TYPE	50	44	66

Figure S28. Get High-res Image Gene #46: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_17q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000237 (Fisher's exact test), Q value = 0.099

Table S29. Gene #46: 'del_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	70	55
DEL PEAK 23(17Q25.3) MUTATED	9	21	2
DEL PEAK 23(17Q25.3) WILD-TYPE	58	49	53

Figure S29. Get High-res Image Gene #46: 'del_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 9.61e-05 (Fisher's exact test), Q value = 0.041

Table S30. Gene #47: 'del_18q21.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	34	45	37
DEL PEAK 24(18Q21.2) MUTATED	7	7	20	16
DEL PEAK 24(18Q21.2) WILD-TYPE	57	27	25	21

Figure S30. Get High-res Image Gene #47: 'del_18q21.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000583 (Fisher's exact test), Q value = 0.24

Table S31. Gene #47: 'del_18q21.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	112	49
DEL PEAK 24(18Q21.2) MUTATED	9	20	21
DEL PEAK 24(18Q21.2) WILD-TYPE	10	92	28

Figure S31. Get High-res Image Gene #47: 'del_18q21.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000273 (Fisher's exact test), Q value = 0.11

Table S32. Gene #47: 'del_18q21.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	61	60
DEL PEAK 24(18Q21.2) MUTATED	8	22	23
DEL PEAK 24(18Q21.2) WILD-TYPE	63	39	37

Figure S32. Get High-res Image Gene #47: 'del_18q21.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000519 (Fisher's exact test), Q value = 0.21

Table S33. Gene #48: 'del_19p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	61	60
DEL PEAK 25(19P13.3) MUTATED	10	26	22
DEL PEAK 25(19P13.3) WILD-TYPE	61	35	38

Figure S33. Get High-res Image Gene #48: 'del_19p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = CESC-TP.transferedmergedcluster.txt
Number of patients = 192
Number of significantly focal cnvs = 55
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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