Correlation between copy number variation genes and molecular subtypes

Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)

23 September 2013 | analyses__2013_09_23

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 (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C147484B

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 52 peak regions and 8 molecular subtypes across 155 patients, 15 significant findings detected with Q value < 0.25.

Amp Peak 3(2q32.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 4(3q26.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(3q28) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(11q22.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 19(17q25.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 21(20q11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.23) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
Del Peak 4(3p22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 5(3p14.2) cnvs correlated to 'CN_CNMF'.
Del Peak 6(4q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 8(5q15) cnvs correlated to 'CN_CNMF'.
Del Peak 15(11q25) cnvs correlated to 'CN_CNMF'.
Del Peak 18(14q32.31) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
Del Peak 21(16q23.1) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 52 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 15 significant findings detected.


		Molecular subtypes	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	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 21(16q23 1)	0 (0%)	124	0.769 (1.00)	0.000524 (0.211)	0.0244 (1.00)	0.000129 (0.0527)	0.0122 (1.00)	0.000849 (0.339)	0.000731 (0.292)	0.00235 (0.915)
Amp Peak 3(2q32 3)	0 (0%)	132	0.000323 (0.131)	0.0219 (1.00)	0.00869 (1.00)	0.00928 (1.00)	0.493 (1.00)	1 (1.00)	0.161 (1.00)	0.181 (1.00)
Amp Peak 4(3q26 2)	0 (0%)	36	3.2e-08 (1.33e-05)	0.0139 (1.00)	0.0366 (1.00)	0.00392 (1.00)	0.0152 (1.00)	0.263 (1.00)	0.0559 (1.00)	0.00609 (1.00)
Amp Peak 5(3q28)	0 (0%)	36	2.27e-08 (9.46e-06)	0.0751 (1.00)	0.0326 (1.00)	0.00392 (1.00)	0.0108 (1.00)	0.373 (1.00)	0.0319 (1.00)	0.00339 (1.00)
Amp Peak 13(11q22 1)	0 (0%)	127	3.64e-06 (0.0015)	0.00215 (0.837)	0.0107 (1.00)	0.776 (1.00)	0.0713 (1.00)	0.0597 (1.00)	0.0766 (1.00)	0.107 (1.00)
Amp Peak 19(17q25 1)	0 (0%)	111	1.83e-05 (0.00756)	0.255 (1.00)	0.00622 (1.00)	0.169 (1.00)	0.631 (1.00)	0.276 (1.00)	0.181 (1.00)	0.15 (1.00)
Amp Peak 21(20q11 21)	0 (0%)	86	0.000129 (0.0527)	0.0484 (1.00)	0.188 (1.00)	0.0798 (1.00)	0.42 (1.00)	0.565 (1.00)	1 (1.00)	0.579 (1.00)
Del Peak 1(1p36 23)	0 (0%)	134	0.202 (1.00)	0.0721 (1.00)	0.0393 (1.00)	0.000328 (0.133)	0.115 (1.00)	0.0149 (1.00)	0.00822 (1.00)	0.00699 (1.00)
Del Peak 4(3p22 1)	0 (0%)	101	3.7e-05 (0.0152)	0.0376 (1.00)	0.154 (1.00)	0.00202 (0.795)	0.049 (1.00)	0.0269 (1.00)	0.114 (1.00)	0.148 (1.00)
Del Peak 5(3p14 2)	0 (0%)	93	3.34e-08 (1.38e-05)	0.00757 (1.00)	0.0475 (1.00)	0.0147 (1.00)	0.00535 (1.00)	0.00295 (1.00)	0.0752 (1.00)	0.0222 (1.00)
Del Peak 6(4q22 1)	0 (0%)	111	2.88e-05 (0.0118)	0.0238 (1.00)	0.276 (1.00)	0.217 (1.00)	0.732 (1.00)	0.532 (1.00)	0.524 (1.00)	0.401 (1.00)
Del Peak 8(5q15)	0 (0%)	114	0.000384 (0.155)	0.195 (1.00)	0.404 (1.00)	0.518 (1.00)	0.167 (1.00)	0.133 (1.00)	0.703 (1.00)	0.705 (1.00)
Del Peak 15(11q25)	0 (0%)	67	0.000494 (0.199)	0.229 (1.00)	0.0744 (1.00)	0.00635 (1.00)	0.159 (1.00)	0.17 (1.00)	0.0271 (1.00)	0.584 (1.00)
Del Peak 18(14q32 31)	0 (0%)	127	0.158 (1.00)	0.201 (1.00)	0.00757 (1.00)	0.000299 (0.122)	0.0124 (1.00)	0.142 (1.00)	0.00429 (1.00)	0.0135 (1.00)
Amp Peak 1(1q21 3)	0 (0%)	74	0.0163 (1.00)	0.562 (1.00)	0.119 (1.00)	0.319 (1.00)	0.428 (1.00)	0.333 (1.00)	0.854 (1.00)	0.101 (1.00)
Amp Peak 2(2p24 3)	0 (0%)	115	0.00561 (1.00)	0.00206 (0.806)	0.263 (1.00)	0.167 (1.00)	0.484 (1.00)	0.0819 (1.00)	0.458 (1.00)	0.00562 (1.00)
Amp Peak 6(4q12)	0 (0%)	142	0.875 (1.00)	0.466 (1.00)	0.211 (1.00)	0.0113 (1.00)	0.495 (1.00)	0.0428 (1.00)	0.41 (1.00)	0.0824 (1.00)
Amp Peak 7(6p21 33)	0 (0%)	115	0.0441 (1.00)	0.00363 (1.00)	0.0174 (1.00)	0.0256 (1.00)	0.326 (1.00)	0.386 (1.00)	0.211 (1.00)	0.0724 (1.00)
Amp Peak 8(8q24 21)	0 (0%)	91	0.134 (1.00)	0.789 (1.00)	0.954 (1.00)	0.73 (1.00)	0.554 (1.00)	0.699 (1.00)	0.172 (1.00)	0.57 (1.00)
Amp Peak 9(9p24 1)	0 (0%)	122	0.228 (1.00)	0.297 (1.00)	0.45 (1.00)	0.183 (1.00)	0.502 (1.00)	0.475 (1.00)	0.117 (1.00)	0.386 (1.00)
Amp Peak 10(9p24 1)	0 (0%)	120	0.323 (1.00)	0.254 (1.00)	0.617 (1.00)	0.126 (1.00)	0.479 (1.00)	0.351 (1.00)	0.217 (1.00)	0.687 (1.00)
Amp Peak 11(11p13)	0 (0%)	144	0.165 (1.00)	0.138 (1.00)	0.137 (1.00)	0.68 (1.00)	0.859 (1.00)	1 (1.00)	0.619 (1.00)	0.626 (1.00)
Amp Peak 12(11q13 3)	0 (0%)	135	0.0179 (1.00)	0.0505 (1.00)	0.0332 (1.00)	0.119 (1.00)	0.658 (1.00)	0.785 (1.00)	0.178 (1.00)	0.313 (1.00)
Amp Peak 14(13q22 1)	0 (0%)	120	0.169 (1.00)	0.479 (1.00)	0.158 (1.00)	0.757 (1.00)	0.157 (1.00)	0.813 (1.00)	0.792 (1.00)	0.0644 (1.00)
Amp Peak 15(14q24 1)	0 (0%)	125	0.0623 (1.00)	0.0884 (1.00)	0.571 (1.00)	0.14 (1.00)	0.752 (1.00)	1 (1.00)	0.885 (1.00)	0.666 (1.00)
Amp Peak 16(15q26 1)	0 (0%)	117	0.365 (1.00)	0.767 (1.00)	0.639 (1.00)	0.765 (1.00)	0.288 (1.00)	1 (1.00)	0.769 (1.00)	0.361 (1.00)
Amp Peak 17(16p13 13)	0 (0%)	120	0.041 (1.00)	0.0911 (1.00)	0.467 (1.00)	0.435 (1.00)	0.918 (1.00)	0.254 (1.00)	0.932 (1.00)	0.439 (1.00)
Amp Peak 18(17q12)	0 (0%)	128	0.0542 (1.00)	0.333 (1.00)	0.283 (1.00)	0.377 (1.00)	0.367 (1.00)	0.0202 (1.00)	0.16 (1.00)	0.0178 (1.00)
Amp Peak 20(19q13 32)	0 (0%)	105	0.00136 (0.538)	0.328 (1.00)	0.387 (1.00)	0.302 (1.00)	0.671 (1.00)	0.681 (1.00)	0.604 (1.00)	0.865 (1.00)
Amp Peak 22(Xq28)	0 (0%)	112	0.154 (1.00)	0.79 (1.00)	0.392 (1.00)	0.471 (1.00)	0.0331 (1.00)	0.521 (1.00)	0.0189 (1.00)	0.41 (1.00)
Del Peak 2(2q22 1)	0 (0%)	126	0.616 (1.00)	0.771 (1.00)	0.356 (1.00)	0.456 (1.00)	0.39 (1.00)	0.805 (1.00)	0.508 (1.00)	0.669 (1.00)
Del Peak 3(2q37 1)	0 (0%)	93	0.102 (1.00)	0.00564 (1.00)	0.0176 (1.00)	0.218 (1.00)	0.156 (1.00)	0.00523 (1.00)	0.11 (1.00)	0.042 (1.00)
Del Peak 7(4q35 2)	0 (0%)	98	0.00278 (1.00)	0.00741 (1.00)	0.431 (1.00)	0.0414 (1.00)	0.656 (1.00)	0.427 (1.00)	0.25 (1.00)	0.512 (1.00)
Del Peak 9(5q35 2)	0 (0%)	113	0.00326 (1.00)	0.0334 (1.00)	0.361 (1.00)	0.549 (1.00)	0.364 (1.00)	0.284 (1.00)	0.799 (1.00)	0.662 (1.00)
Del Peak 10(6p24 2)	0 (0%)	132	0.471 (1.00)	0.116 (1.00)	0.28 (1.00)	0.192 (1.00)	0.768 (1.00)	1 (1.00)	0.768 (1.00)	0.902 (1.00)
Del Peak 11(6q26)	0 (0%)	100	0.147 (1.00)	0.496 (1.00)	0.28 (1.00)	0.63 (1.00)	0.942 (1.00)	1 (1.00)	0.947 (1.00)	0.946 (1.00)
Del Peak 12(7q34)	0 (0%)	121	0.172 (1.00)	0.696 (1.00)	0.385 (1.00)	0.647 (1.00)	0.204 (1.00)	0.642 (1.00)	0.435 (1.00)	0.389 (1.00)
Del Peak 13(10q23 31)	0 (0%)	112	0.477 (1.00)	0.475 (1.00)	0.0764 (1.00)	0.113 (1.00)	0.949 (1.00)	1 (1.00)	0.886 (1.00)	0.809 (1.00)
Del Peak 14(11p15 5)	0 (0%)	106	0.0681 (1.00)	0.133 (1.00)	0.4 (1.00)	0.0357 (1.00)	0.186 (1.00)	0.143 (1.00)	0.0828 (1.00)	0.238 (1.00)
Del Peak 16(13q12 12)	0 (0%)	102	0.00295 (1.00)	0.0268 (1.00)	0.844 (1.00)	0.546 (1.00)	0.24 (1.00)	0.0734 (1.00)	0.0376 (1.00)	0.404 (1.00)
Del Peak 17(13q14 2)	0 (0%)	98	0.00111 (0.441)	0.0428 (1.00)	0.184 (1.00)	0.0433 (1.00)	0.0774 (1.00)	0.168 (1.00)	0.0123 (1.00)	0.324 (1.00)
Del Peak 19(15q15 1)	0 (0%)	121	0.00204 (0.8)	0.13 (1.00)	0.707 (1.00)	0.565 (1.00)	0.0959 (1.00)	1 (1.00)	0.0569 (1.00)	0.0241 (1.00)
Del Peak 20(16q11 2)	0 (0%)	127	0.7 (1.00)	0.0102 (1.00)	0.0875 (1.00)	0.117 (1.00)	0.0654 (1.00)	0.00302 (1.00)	0.00204 (0.8)	0.01 (1.00)
Del Peak 22(17p12)	0 (0%)	108	0.00556 (1.00)	0.893 (1.00)	0.0958 (1.00)	0.478 (1.00)	0.0702 (1.00)	0.153 (1.00)	0.24 (1.00)	0.466 (1.00)
Del Peak 23(17q25 3)	0 (0%)	128	0.114 (1.00)	0.00392 (1.00)	0.000658 (0.264)	0.00295 (1.00)	0.0109 (1.00)	0.0204 (1.00)	0.00451 (1.00)	0.00887 (1.00)
Del Peak 24(19p13 3)	0 (0%)	108	0.00268 (1.00)	0.0104 (1.00)	0.00558 (1.00)	0.257 (1.00)	0.235 (1.00)	0.209 (1.00)	0.187 (1.00)	0.00175 (0.692)
Del Peak 25(19q13 33)	0 (0%)	134	0.047 (1.00)	0.157 (1.00)	0.738 (1.00)	0.659 (1.00)	0.788 (1.00)	0.246 (1.00)	0.75 (1.00)	0.447 (1.00)
Del Peak 26(20p12 1)	0 (0%)	134	0.836 (1.00)	0.689 (1.00)	0.226 (1.00)	0.32 (1.00)	0.552 (1.00)	1 (1.00)	0.18 (1.00)	0.648 (1.00)
Del Peak 27(21q21 1)	0 (0%)	125	0.0623 (1.00)	0.0361 (1.00)	0.885 (1.00)	0.261 (1.00)	0.968 (1.00)	1 (1.00)	0.558 (1.00)	0.519 (1.00)
Del Peak 28(22q13 32)	0 (0%)	111	0.0513 (1.00)	0.176 (1.00)	0.172 (1.00)	0.153 (1.00)	0.506 (1.00)	0.287 (1.00)	0.288 (1.00)	0.285 (1.00)
Del Peak 29(Xp11 3)	0 (0%)	112	0.0116 (1.00)	0.0852 (1.00)	0.189 (1.00)	0.42 (1.00)	0.00111 (0.442)	0.206 (1.00)	0.0391 (1.00)	0.121 (1.00)
Del Peak 30(Xq21 33)	0 (0%)	120	0.0215 (1.00)	0.0146 (1.00)	0.113 (1.00)	0.0626 (1.00)	0.022 (1.00)	0.162 (1.00)	0.309 (1.00)	0.0595 (1.00)

'Amp Peak 3(2q32.3)' versus 'CN_CNMF'

P value = 0.000323 (Fisher's exact test), Q value = 0.13

Table S1. Gene #3: 'Amp Peak 3(2q32.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	43	58
AMP PEAK 3(2Q32.3) CNV	11	11	1
AMP PEAK 3(2Q32.3) WILD-TYPE	43	32	57

Figure S1. Get High-res Image Gene #3: 'Amp Peak 3(2q32.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(3q26.2)' versus 'CN_CNMF'

P value = 3.2e-08 (Fisher's exact test), Q value = 1.3e-05

Table S2. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	43	58
AMP PEAK 4(3Q26.2) CNV	54	26	39
AMP PEAK 4(3Q26.2) WILD-TYPE	0	17	19

Figure S2. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 5(3q28)' versus 'CN_CNMF'

P value = 2.27e-08 (Fisher's exact test), Q value = 9.5e-06

Table S3. Gene #5: 'Amp Peak 5(3q28)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	43	58
AMP PEAK 5(3Q28) CNV	54	25	40
AMP PEAK 5(3Q28) WILD-TYPE	0	18	18

Figure S3. Get High-res Image Gene #5: 'Amp Peak 5(3q28)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 13(11q22.1)' versus 'CN_CNMF'

P value = 3.64e-06 (Fisher's exact test), Q value = 0.0015

Table S4. Gene #13: 'Amp Peak 13(11q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	43	58
AMP PEAK 13(11Q22.1) CNV	5	19	4
AMP PEAK 13(11Q22.1) WILD-TYPE	49	24	54

Figure S4. Get High-res Image Gene #13: 'Amp Peak 13(11q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 19(17q25.1)' versus 'CN_CNMF'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.0076

Table S5. Gene #19: 'Amp Peak 19(17q25.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	43	58
AMP PEAK 19(17Q25.1) CNV	25	14	5
AMP PEAK 19(17Q25.1) WILD-TYPE	29	29	53

Figure S5. Get High-res Image Gene #19: 'Amp Peak 19(17q25.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 21(20q11.21)' versus 'CN_CNMF'

P value = 0.000129 (Fisher's exact test), Q value = 0.053

Table S6. Gene #21: 'Amp Peak 21(20q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	43	58
AMP PEAK 21(20Q11.21) CNV	34	21	14
AMP PEAK 21(20Q11.21) WILD-TYPE	20	22	44

Figure S6. Get High-res Image Gene #21: 'Amp Peak 21(20q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 1(1p36.23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000328 (Fisher's exact test), Q value = 0.13

Table S7. Gene #23: 'Del Peak 1(1p36.23)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	73	20
DEL PEAK 1(1P36.23) CNV	14	3	3
DEL PEAK 1(1P36.23) WILD-TYPE	33	70	17

Figure S7. Get High-res Image Gene #23: 'Del Peak 1(1p36.23)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 4(3p22.1)' versus 'CN_CNMF'

P value = 3.7e-05 (Fisher's exact test), Q value = 0.015

Table S8. Gene #26: 'Del Peak 4(3p22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	43	58
DEL PEAK 4(3P22.1) CNV	18	26	10
DEL PEAK 4(3P22.1) WILD-TYPE	36	17	48

Figure S8. Get High-res Image Gene #26: 'Del Peak 4(3p22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 5(3p14.2)' versus 'CN_CNMF'

P value = 3.34e-08 (Fisher's exact test), Q value = 1.4e-05

Table S9. Gene #27: 'Del Peak 5(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	43	58
DEL PEAK 5(3P14.2) CNV	22	31	9
DEL PEAK 5(3P14.2) WILD-TYPE	32	12	49

Figure S9. Get High-res Image Gene #27: 'Del Peak 5(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(4q22.1)' versus 'CN_CNMF'

P value = 2.88e-05 (Fisher's exact test), Q value = 0.012

Table S10. Gene #28: 'Del Peak 6(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	43	58
DEL PEAK 6(4Q22.1) CNV	16	22	6
DEL PEAK 6(4Q22.1) WILD-TYPE	38	21	52

Figure S10. Get High-res Image Gene #28: 'Del Peak 6(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 8(5q15)' versus 'CN_CNMF'

P value = 0.000384 (Fisher's exact test), Q value = 0.16

Table S11. Gene #30: 'Del Peak 8(5q15)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	43	58
DEL PEAK 8(5Q15) CNV	16	19	6
DEL PEAK 8(5Q15) WILD-TYPE	38	24	52

Figure S11. Get High-res Image Gene #30: 'Del Peak 8(5q15)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(11q25)' versus 'CN_CNMF'

P value = 0.000494 (Fisher's exact test), Q value = 0.2

Table S12. Gene #37: 'Del Peak 15(11q25)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	43	58
DEL PEAK 15(11Q25) CNV	40	26	22
DEL PEAK 15(11Q25) WILD-TYPE	14	17	36

Figure S12. Get High-res Image Gene #37: 'Del Peak 15(11q25)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 18(14q32.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000299 (Fisher's exact test), Q value = 0.12

Table S13. Gene #40: 'Del Peak 18(14q32.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	73	20
DEL PEAK 18(14Q32.31) CNV	14	4	6
DEL PEAK 18(14Q32.31) WILD-TYPE	33	69	14

Figure S13. Get High-res Image Gene #40: 'Del Peak 18(14q32.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 21(16q23.1)' versus 'METHLYATION_CNMF'

P value = 0.000524 (Chi-square test), Q value = 0.21

Table S14. Gene #43: 'Del Peak 21(16q23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	25	24	17	25	28	26	10
DEL PEAK 21(16Q23.1) CNV	0	6	6	4	2	12	1
DEL PEAK 21(16Q23.1) WILD-TYPE	25	18	11	21	26	14	9

Figure S14. Get High-res Image Gene #43: 'Del Peak 21(16q23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 21(16q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000129 (Fisher's exact test), Q value = 0.053

Table S15. Gene #43: 'Del Peak 21(16q23.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	73	20
DEL PEAK 21(16Q23.1) CNV	16	5	7
DEL PEAK 21(16Q23.1) WILD-TYPE	31	68	13

Figure S15. Get High-res Image Gene #43: 'Del Peak 21(16q23.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = CESC-TP.transferedmergedcluster.txt
Number of patients = 155
Number of copy number variation regions = 52
Number of molecular subtypes = 8
Exclude regions 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)

[4] GISTIC_version2

Made with Nozzle