Correlation between copy number variation genes and molecular subtypes

Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_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/C1MK69Z2

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 33 peak regions and 8 molecular subtypes across 127 patients, 32 significant findings detected with Q value < 0.25.

Amp Peak 1(2q32.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(3p14.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 3(3q26.31) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 4(5q35.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(7q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 8(19p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.31) cnvs correlated to 'CN_CNMF'.
Del Peak 4(3p22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 5(4q33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 7(5q15) cnvs correlated to 'CN_CNMF'.
Del Peak 8(5q35.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 9(6p12.3) cnvs correlated to 'CN_CNMF'.
Del Peak 11(6q26) cnvs correlated to 'CN_CNMF'.
Del Peak 12(9p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 16(14q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 17(14q23.3) cnvs correlated to 'CN_CNMF'.
Del Peak 18(14q32.2) cnvs correlated to 'CN_CNMF'.
Del Peak 23(22q12.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 24(Xq21.31) cnvs correlated to 'CN_CNMF'.
Del Peak 25(Xq28) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 33 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 32 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	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	Fisher's exact test
Amp Peak 2(3p14 1)	0 (0%)	95	4.19e-15 (1.1e-12)	0.0294 (1.00)	0.00279 (0.615)	1.79e-06 (0.000451)	0.00419 (0.905)	1.69e-07 (4.3e-05)	0.327 (1.00)	0.00481 (1.00)
Amp Peak 6(7q22 1)	0 (0%)	56	9.68e-07 (0.000245)	6.15e-05 (0.0151)	0.00172 (0.389)	0.000515 (0.121)	0.0312 (1.00)	0.0063 (1.00)	0.138 (1.00)	0.0252 (1.00)
Del Peak 4(3p22 1)	0 (0%)	117	0.000437 (0.104)	8.4e-05 (0.0203)	0.0206 (1.00)	0.00417 (0.905)	0.00709 (1.00)	0.00948 (1.00)	0.131 (1.00)	6.35e-05 (0.0155)
Del Peak 12(9p21 3)	0 (0%)	108	0.000476 (0.113)	1.18e-05 (0.00296)	3.4e-05 (0.0084)	0.00182 (0.41)	0.0302 (1.00)	0.0959 (1.00)	0.386 (1.00)	0.00202 (0.453)
Amp Peak 3(3q26 31)	0 (0%)	85	1.33e-10 (3.42e-08)	0.155 (1.00)	0.0313 (1.00)	0.00114 (0.261)	0.039 (1.00)	9.19e-05 (0.0222)	0.491 (1.00)	0.0406 (1.00)
Del Peak 5(4q33)	0 (0%)	111	0.000736 (0.171)	0.000168 (0.04)	0.00217 (0.483)	0.0162 (1.00)	0.227 (1.00)	0.474 (1.00)	0.494 (1.00)	0.0487 (1.00)
Del Peak 8(5q35 2)	0 (0%)	118	0.000165 (0.0396)	0.00157 (0.355)	0.000616 (0.145)	0.00116 (0.264)	0.233 (1.00)	0.155 (1.00)	0.424 (1.00)	0.128 (1.00)
Del Peak 23(22q12 2)	0 (0%)	93	0.000694 (0.162)	0.000756 (0.175)	0.519 (1.00)	0.0314 (1.00)	0.0194 (1.00)	0.0322 (1.00)	0.124 (1.00)	0.00731 (1.00)
Amp Peak 1(2q32 1)	0 (0%)	104	0.000867 (0.2)	0.0974 (1.00)	0.942 (1.00)	1 (1.00)	0.317 (1.00)	0.719 (1.00)	0.318 (1.00)	0.13 (1.00)
Amp Peak 4(5q35 2)	0 (0%)	108	1.8e-13 (4.69e-11)	0.0267 (1.00)	0.678 (1.00)	0.0565 (1.00)	0.257 (1.00)	0.183 (1.00)	0.0413 (1.00)	0.345 (1.00)
Amp Peak 8(19p13 2)	0 (0%)	113	3.65e-08 (9.34e-06)	0.132 (1.00)	0.0683 (1.00)	0.765 (1.00)	0.938 (1.00)	0.444 (1.00)	0.704 (1.00)	0.667 (1.00)
Del Peak 1(1p36 31)	0 (0%)	100	3.09e-07 (7.86e-05)	0.009 (1.00)	0.0725 (1.00)	0.0861 (1.00)	0.183 (1.00)	0.227 (1.00)	0.213 (1.00)	0.0896 (1.00)
Del Peak 7(5q15)	0 (0%)	117	2.07e-05 (0.00516)	0.053 (1.00)	0.0129 (1.00)	0.0506 (1.00)	0.783 (1.00)	0.206 (1.00)	0.772 (1.00)	0.667 (1.00)
Del Peak 9(6p12 3)	0 (0%)	115	6.35e-05 (0.0155)	0.0263 (1.00)	0.697 (1.00)	0.675 (1.00)	0.639 (1.00)	0.889 (1.00)	1 (1.00)	0.911 (1.00)
Del Peak 11(6q26)	0 (0%)	112	7.23e-05 (0.0176)	0.00303 (0.664)	0.399 (1.00)	0.303 (1.00)	0.537 (1.00)	0.507 (1.00)	0.632 (1.00)	0.192 (1.00)
Del Peak 16(14q11 2)	0 (0%)	98	1.86e-10 (4.78e-08)	0.276 (1.00)	0.0934 (1.00)	0.177 (1.00)	0.826 (1.00)	0.79 (1.00)	1 (1.00)	0.324 (1.00)
Del Peak 17(14q23 3)	0 (0%)	99	6.82e-13 (1.77e-10)	0.122 (1.00)	0.0351 (1.00)	0.0295 (1.00)	0.855 (1.00)	0.742 (1.00)	0.958 (1.00)	0.324 (1.00)
Del Peak 18(14q32 2)	0 (0%)	99	6.48e-13 (1.68e-10)	0.23 (1.00)	0.0775 (1.00)	0.0648 (1.00)	0.855 (1.00)	0.742 (1.00)	0.958 (1.00)	0.442 (1.00)
Del Peak 24(Xq21 31)	0 (0%)	109	7.17e-06 (0.0018)	0.00341 (0.743)	0.00278 (0.615)	0.0354 (1.00)	0.208 (1.00)	0.899 (1.00)	0.325 (1.00)	0.228 (1.00)
Del Peak 25(Xq28)	0 (0%)	110	2.93e-05 (0.00726)	0.0608 (1.00)	0.0436 (1.00)	0.253 (1.00)	0.317 (1.00)	0.844 (1.00)	0.688 (1.00)	0.753 (1.00)
Amp Peak 5(6p12 3)	0 (0%)	123	0.0634 (1.00)	0.137 (1.00)	0.114 (1.00)	0.35 (1.00)	0.282 (1.00)	0.457 (1.00)	0.379 (1.00)	0.516 (1.00)
Amp Peak 7(17q25 2)	0 (0%)	40	0.00112 (0.257)	0.0949 (1.00)	0.28 (1.00)	0.0388 (1.00)	0.417 (1.00)	0.304 (1.00)	0.375 (1.00)	0.961 (1.00)
Amp Peak 9(19q13 11)	0 (0%)	123	0.927 (1.00)	0.137 (1.00)	0.201 (1.00)	0.13 (1.00)	0.415 (1.00)	0.457 (1.00)	0.455 (1.00)	0.25 (1.00)
Del Peak 2(2p11 2)	0 (0%)	124	0.613 (1.00)	0.8 (1.00)			0.024 (1.00)	0.036 (1.00)	0.0553 (1.00)	0.028 (1.00)
Del Peak 3(2q37 3)	0 (0%)	122	0.959 (1.00)	0.139 (1.00)	0.684 (1.00)	0.35 (1.00)	0.612 (1.00)	0.913 (1.00)	0.372 (1.00)	0.0539 (1.00)
Del Peak 6(5p15 2)	0 (0%)	120	0.00642 (1.00)	0.0362 (1.00)	0.0395 (1.00)	0.017 (1.00)	0.221 (1.00)	0.218 (1.00)	0.289 (1.00)	0.36 (1.00)
Del Peak 10(6q22 31)	0 (0%)	113	0.00555 (1.00)	0.0212 (1.00)	0.0976 (1.00)	0.175 (1.00)	0.166 (1.00)	0.479 (1.00)	0.933 (1.00)	0.0813 (1.00)
Del Peak 13(10p15 3)	0 (0%)	119	0.0609 (1.00)	0.0111 (1.00)	0.435 (1.00)	0.232 (1.00)	0.00689 (1.00)	0.581 (1.00)	0.527 (1.00)	0.197 (1.00)
Del Peak 14(11q22 3)	0 (0%)	113	0.00848 (1.00)	0.00257 (0.57)	0.0772 (1.00)	0.0114 (1.00)	0.109 (1.00)	0.665 (1.00)	0.494 (1.00)	0.513 (1.00)
Del Peak 19(15q14)	0 (0%)	111	0.00506 (1.00)	0.00849 (1.00)	0.112 (1.00)	0.301 (1.00)	0.129 (1.00)	0.52 (1.00)	0.369 (1.00)	0.0896 (1.00)
Del Peak 20(19p13 3)	0 (0%)	114	0.00729 (1.00)	0.231 (1.00)	0.43 (1.00)	0.0871 (1.00)	0.976 (1.00)	0.801 (1.00)	0.217 (1.00)	0.703 (1.00)
Del Peak 21(19q13 2)	0 (0%)	116	0.179 (1.00)	0.136 (1.00)	0.732 (1.00)	0.0493 (1.00)	0.166 (1.00)	0.805 (1.00)	0.375 (1.00)	0.516 (1.00)
Del Peak 22(19q13 42)	0 (0%)	115	0.186 (1.00)	0.3 (1.00)	0.732 (1.00)	0.232 (1.00)	0.82 (1.00)	0.94 (1.00)	0.863 (1.00)	0.493 (1.00)

'Amp Peak 1(2q32.1)' versus 'CN_CNMF'

P value = 0.000867 (Chi-square test), Q value = 0.2

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
AMP PEAK 1(2Q32.1) CNV	10	1	1	7	4
AMP PEAK 1(2Q32.1) WILD-TYPE	14	43	12	19	16

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

'Amp Peak 2(3p14.1)' versus 'CN_CNMF'

P value = 4.19e-15 (Chi-square test), Q value = 1.1e-12

Table S2. Gene #2: 'Amp Peak 2(3p14.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
AMP PEAK 2(3P14.1) CNV	2	2	3	5	20
AMP PEAK 2(3P14.1) WILD-TYPE	22	42	10	21	0

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(3p14.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 2(3p14.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.79e-06 (Fisher's exact test), Q value = 0.00045

Table S3. Gene #2: 'Amp Peak 2(3p14.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	37	21
AMP PEAK 2(3P14.1) CNV	1	19	0
AMP PEAK 2(3P14.1) WILD-TYPE	17	18	21

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(3p14.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 2(3p14.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.69e-07 (Fisher's exact test), Q value = 4.3e-05

Table S4. Gene #2: 'Amp Peak 2(3p14.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	33	11	35
AMP PEAK 2(3P14.1) CNV	6	3	10	13
AMP PEAK 2(3P14.1) WILD-TYPE	42	30	1	22

Figure S4. Get High-res Image Gene #2: 'Amp Peak 2(3p14.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 3(3q26.31)' versus 'CN_CNMF'

P value = 1.33e-10 (Chi-square test), Q value = 3.4e-08

Table S5. Gene #3: 'Amp Peak 3(3q26.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
AMP PEAK 3(3Q26.31) CNV	5	5	3	9	20
AMP PEAK 3(3Q26.31) WILD-TYPE	19	39	10	17	0

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(3q26.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(3q26.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.19e-05 (Fisher's exact test), Q value = 0.022

Table S6. Gene #3: 'Amp Peak 3(3q26.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	33	11	35
AMP PEAK 3(3Q26.31) CNV	10	8	10	14
AMP PEAK 3(3Q26.31) WILD-TYPE	38	25	1	21

Figure S6. Get High-res Image Gene #3: 'Amp Peak 3(3q26.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 4(5q35.2)' versus 'CN_CNMF'

P value = 1.8e-13 (Chi-square test), Q value = 4.7e-11

Table S7. Gene #4: 'Amp Peak 4(5q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
AMP PEAK 4(5Q35.2) CNV	0	2	0	17	0
AMP PEAK 4(5Q35.2) WILD-TYPE	24	42	13	9	20

Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(5q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(7q22.1)' versus 'CN_CNMF'

P value = 9.68e-07 (Chi-square test), Q value = 0.00024

Table S8. Gene #6: 'Amp Peak 6(7q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
AMP PEAK 6(7Q22.1) CNV	7	22	13	10	19
AMP PEAK 6(7Q22.1) WILD-TYPE	17	22	0	16	1

Figure S8. Get High-res Image Gene #6: 'Amp Peak 6(7q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(7q22.1)' versus 'METHLYATION_CNMF'

P value = 6.15e-05 (Fisher's exact test), Q value = 0.015

Table S9. Gene #6: 'Amp Peak 6(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	53	31
AMP PEAK 6(7Q22.1) CNV	10	40	10
AMP PEAK 6(7Q22.1) WILD-TYPE	17	13	21

Figure S9. Get High-res Image Gene #6: 'Amp Peak 6(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 6(7q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000515 (Fisher's exact test), Q value = 0.12

Table S10. Gene #6: 'Amp Peak 6(7q22.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	37	21
AMP PEAK 6(7Q22.1) CNV	8	29	6
AMP PEAK 6(7Q22.1) WILD-TYPE	10	8	15

Figure S10. Get High-res Image Gene #6: 'Amp Peak 6(7q22.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 8(19p13.2)' versus 'CN_CNMF'

P value = 3.65e-08 (Chi-square test), Q value = 9.3e-06

Table S11. Gene #8: 'Amp Peak 8(19p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
AMP PEAK 8(19P13.2) CNV	3	0	8	2	1
AMP PEAK 8(19P13.2) WILD-TYPE	21	44	5	24	19

Figure S11. Get High-res Image Gene #8: 'Amp Peak 8(19p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 1(1p36.31)' versus 'CN_CNMF'

P value = 3.09e-07 (Chi-square test), Q value = 7.9e-05

Table S12. Gene #10: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 1(1P36.31) CNV	12	3	0	12	0
DEL PEAK 1(1P36.31) WILD-TYPE	12	41	13	14	20

Figure S12. Get High-res Image Gene #10: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000437 (Chi-square test), Q value = 0.1

Table S13. Gene #13: 'Del Peak 4(3p22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 4(3P22.1) CNV	3	0	0	7	0
DEL PEAK 4(3P22.1) WILD-TYPE	21	44	13	19	20

Figure S13. Get High-res Image Gene #13: 'Del Peak 4(3p22.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 8.4e-05 (Fisher's exact test), Q value = 0.02

Table S14. Gene #13: 'Del Peak 4(3p22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	53	31
DEL PEAK 4(3P22.1) CNV	1	0	8
DEL PEAK 4(3P22.1) WILD-TYPE	26	53	23

Figure S14. Get High-res Image Gene #13: 'Del Peak 4(3p22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 6.35e-05 (Fisher's exact test), Q value = 0.016

Table S15. Gene #13: 'Del Peak 4(3p22.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	16	48
DEL PEAK 4(3P22.1) CNV	0	6	3
DEL PEAK 4(3P22.1) WILD-TYPE	47	10	45

Figure S15. Get High-res Image Gene #13: 'Del Peak 4(3p22.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 5(4q33)' versus 'CN_CNMF'

P value = 0.000736 (Chi-square test), Q value = 0.17

Table S16. Gene #14: 'Del Peak 5(4q33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 5(4Q33) CNV	8	1	0	6	1
DEL PEAK 5(4Q33) WILD-TYPE	16	43	13	20	19

Figure S16. Get High-res Image Gene #14: 'Del Peak 5(4q33)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 5(4q33)' versus 'METHLYATION_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.04

Table S17. Gene #14: 'Del Peak 5(4q33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	53	31
DEL PEAK 5(4Q33) CNV	2	1	10
DEL PEAK 5(4Q33) WILD-TYPE	25	52	21

Figure S17. Get High-res Image Gene #14: 'Del Peak 5(4q33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(5q15)' versus 'CN_CNMF'

P value = 2.07e-05 (Chi-square test), Q value = 0.0052

Table S18. Gene #16: 'Del Peak 7(5q15)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 7(5Q15) CNV	8	1	0	0	1
DEL PEAK 7(5Q15) WILD-TYPE	16	43	13	26	19

Figure S18. Get High-res Image Gene #16: 'Del Peak 7(5q15)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 8(5q35.2)' versus 'CN_CNMF'

P value = 0.000165 (Chi-square test), Q value = 0.04

Table S19. Gene #17: 'Del Peak 8(5q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 8(5Q35.2) CNV	7	1	0	0	1
DEL PEAK 8(5Q35.2) WILD-TYPE	17	43	13	26	19

Figure S19. Get High-res Image Gene #17: 'Del Peak 8(5q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 8(5q35.2)' versus 'MRNASEQ_CNMF'

P value = 0.000616 (Fisher's exact test), Q value = 0.14

Table S20. Gene #17: 'Del Peak 8(5q35.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	24	25
DEL PEAK 8(5Q35.2) CNV	0	6	0
DEL PEAK 8(5Q35.2) WILD-TYPE	27	18	25

Figure S20. Get High-res Image Gene #17: 'Del Peak 8(5q35.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 9(6p12.3)' versus 'CN_CNMF'

P value = 6.35e-05 (Chi-square test), Q value = 0.016

Table S21. Gene #18: 'Del Peak 9(6p12.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 9(6P12.3) CNV	1	1	0	9	1
DEL PEAK 9(6P12.3) WILD-TYPE	23	43	13	17	19

Figure S21. Get High-res Image Gene #18: 'Del Peak 9(6p12.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(6q26)' versus 'CN_CNMF'

P value = 7.23e-05 (Chi-square test), Q value = 0.018

Table S22. Gene #20: 'Del Peak 11(6q26)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 11(6Q26) CNV	3	1	0	10	1
DEL PEAK 11(6Q26) WILD-TYPE	21	43	13	16	19

Figure S22. Get High-res Image Gene #20: 'Del Peak 11(6q26)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(9p21.3)' versus 'CN_CNMF'

P value = 0.000476 (Chi-square test), Q value = 0.11

Table S23. Gene #21: 'Del Peak 12(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 12(9P21.3) CNV	9	2	0	7	1
DEL PEAK 12(9P21.3) WILD-TYPE	15	42	13	19	19

Figure S23. Get High-res Image Gene #21: 'Del Peak 12(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(9p21.3)' versus 'METHLYATION_CNMF'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.003

Table S24. Gene #21: 'Del Peak 12(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	53	31
DEL PEAK 12(9P21.3) CNV	6	0	10
DEL PEAK 12(9P21.3) WILD-TYPE	21	53	21

Figure S24. Get High-res Image Gene #21: 'Del Peak 12(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 12(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 3.4e-05 (Fisher's exact test), Q value = 0.0084

Table S25. Gene #21: 'Del Peak 12(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	24	25
DEL PEAK 12(9P21.3) CNV	1	12	2
DEL PEAK 12(9P21.3) WILD-TYPE	26	12	23

Figure S25. Get High-res Image Gene #21: 'Del Peak 12(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 16(14q11.2)' versus 'CN_CNMF'

P value = 1.86e-10 (Chi-square test), Q value = 4.8e-08

Table S26. Gene #24: 'Del Peak 16(14q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 16(14Q11.2) CNV	18	2	0	7	2
DEL PEAK 16(14Q11.2) WILD-TYPE	6	42	13	19	18

Figure S26. Get High-res Image Gene #24: 'Del Peak 16(14q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(14q23.3)' versus 'CN_CNMF'

P value = 6.82e-13 (Chi-square test), Q value = 1.8e-10

Table S27. Gene #25: 'Del Peak 17(14q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 17(14Q23.3) CNV	19	1	0	7	1
DEL PEAK 17(14Q23.3) WILD-TYPE	5	43	13	19	19

Figure S27. Get High-res Image Gene #25: 'Del Peak 17(14q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 18(14q32.2)' versus 'CN_CNMF'

P value = 6.48e-13 (Chi-square test), Q value = 1.7e-10

Table S28. Gene #26: 'Del Peak 18(14q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 18(14Q32.2) CNV	19	2	0	7	0
DEL PEAK 18(14Q32.2) WILD-TYPE	5	42	13	19	20

Figure S28. Get High-res Image Gene #26: 'Del Peak 18(14q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(22q12.2)' versus 'CN_CNMF'

P value = 0.000694 (Chi-square test), Q value = 0.16

Table S29. Gene #31: 'Del Peak 23(22q12.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 23(22Q12.2) CNV	9	9	1	14	1
DEL PEAK 23(22Q12.2) WILD-TYPE	15	35	12	12	19

Figure S29. Get High-res Image Gene #31: 'Del Peak 23(22q12.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(22q12.2)' versus 'METHLYATION_CNMF'

P value = 0.000756 (Fisher's exact test), Q value = 0.18

Table S30. Gene #31: 'Del Peak 23(22q12.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	53	31
DEL PEAK 23(22Q12.2) CNV	5	9	17
DEL PEAK 23(22Q12.2) WILD-TYPE	22	44	14

Figure S30. Get High-res Image Gene #31: 'Del Peak 23(22q12.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 24(Xq21.31)' versus 'CN_CNMF'

P value = 7.17e-06 (Chi-square test), Q value = 0.0018

Table S31. Gene #32: 'Del Peak 24(Xq21.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 24(XQ21.31) CNV	10	0	0	7	1
DEL PEAK 24(XQ21.31) WILD-TYPE	14	44	13	19	19

Figure S31. Get High-res Image Gene #32: 'Del Peak 24(Xq21.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 25(Xq28)' versus 'CN_CNMF'

P value = 2.93e-05 (Chi-square test), Q value = 0.0073

Table S32. Gene #33: 'Del Peak 25(Xq28)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	24	44	13	26	20
DEL PEAK 25(XQ28) CNV	9	0	0	7	1
DEL PEAK 25(XQ28) WILD-TYPE	15	44	13	19	19

Figure S32. Get High-res Image Gene #33: 'Del Peak 25(Xq28)' versus Molecular Subtype #1: 'CN_CNMF'

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 = KIRP-TP.transferedmergedcluster.txt
Number of patients = 127
Number of copy number variation regions = 33
Number of molecular subtypes = 8
Exclude regions that fewer than K tumors have alterations, K = 3

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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[2] 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)

[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

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