Correlation between copy number variation genes and molecular subtypes

Thyroid Adenocarcinoma (Primary solid tumor)

22 February 2013 | analyses__2013_02_22

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/C1X0658C

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 25 peak regions and 8 molecular subtypes across 430 patients, 44 significant findings detected with Q value < 0.25.

Del Peak 2(2p22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 3(2q35) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 5(6q22.31) cnvs correlated to 'CN_CNMF'.
Del Peak 6(6q27) cnvs correlated to 'CN_CNMF'.
Del Peak 9(8p12) cnvs correlated to 'CN_CNMF'.
Del Peak 10(8q24.22) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 11(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 12(9q22.32) cnvs correlated to 'CN_CNMF'.
Del Peak 14(10q23.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 15(11p15.1) cnvs correlated to 'CN_CNMF'.
Del Peak 17(13q14.3) cnvs correlated to 'CN_CNMF'.
Del Peak 22(18p11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 23(19p13.2) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 26(21q21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 27(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 28(22q13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 29(22q13.32) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 25 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 44 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ 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
Del Peak 3(2q35)	11 (3%)	419	3.56e-11 (6.81e-09)	3.39e-05 (0.00587)	0.895 (1.00)	0.00145 (0.224)	1.89e-05 (0.00338)	1.95e-05 (0.00342)	9.77e-07 (0.00018)	3.2e-07 (5.94e-05)
Del Peak 2(2p22 3)	11 (3%)	419	1.79e-09 (3.4e-07)	8.28e-05 (0.014)	0.773 (1.00)	0.00799 (1.00)	1.89e-05 (0.00338)	1.95e-05 (0.00342)	9.77e-07 (0.00018)	3.2e-07 (5.94e-05)
Del Peak 10(8q24 22)	7 (2%)	423	8.01e-05 (0.0137)	0.00251 (0.369)	0.683 (1.00)	0.0398 (1.00)	0.00217 (0.326)	0.00122 (0.191)	0.000164 (0.0275)	8.14e-05 (0.0138)
Del Peak 23(19p13 2)	7 (2%)	423	0.0143 (1.00)	0.00103 (0.163)	0.0349 (1.00)	0.114 (1.00)	0.00217 (0.326)	0.00122 (0.191)	0.000579 (0.0949)	0.000319 (0.0533)
Del Peak 27(22q13 31)	74 (17%)	356	2.45e-77 (4.81e-75)	0.000881 (0.143)	0.241 (1.00)	0.0925 (1.00)	3.04e-07 (5.72e-05)	1.91e-05 (0.00339)	0.0118 (1.00)	0.012 (1.00)
Del Peak 28(22q13 2)	74 (17%)	356	2.45e-77 (4.81e-75)	0.000881 (0.143)	0.241 (1.00)	0.0925 (1.00)	3.04e-07 (5.72e-05)	1.91e-05 (0.00339)	0.0118 (1.00)	0.012 (1.00)
Del Peak 29(22q13 32)	75 (17%)	355	1.72e-75 (3.34e-73)	0.000467 (0.077)	0.241 (1.00)	0.0925 (1.00)	1.62e-07 (3.06e-05)	1.06e-05 (0.00191)	0.00708 (0.956)	0.00658 (0.895)
Del Peak 14(10q23 31)	10 (2%)	420	0.000762 (0.124)	0.0516 (1.00)	0.0349 (1.00)	0.0692 (1.00)	0.00411 (0.592)	0.00117 (0.183)	0.0257 (1.00)	0.0123 (1.00)
Del Peak 5(6q22 31)	6 (1%)	424	0.000943 (0.151)	0.00735 (0.978)	0.0374 (1.00)	0.776 (1.00)	0.0175 (1.00)	0.00936 (1.00)	0.038 (1.00)	0.0221 (1.00)
Del Peak 6(6q27)	6 (1%)	424	0.000943 (0.151)	0.00735 (0.978)	0.0374 (1.00)	0.776 (1.00)	0.0175 (1.00)	0.00936 (1.00)	0.038 (1.00)	0.0221 (1.00)
Del Peak 9(8p12)	4 (1%)	426	3.73e-05 (0.00641)	0.0419 (1.00)			0.0373 (1.00)	0.0348 (1.00)	0.00712 (0.956)	0.0048 (0.677)
Del Peak 11(9p21 3)	17 (4%)	413	1.88e-12 (3.63e-10)	0.334 (1.00)	0.444 (1.00)	0.189 (1.00)	0.116 (1.00)	0.515 (1.00)	0.00246 (0.364)	0.00278 (0.406)
Del Peak 12(9q22 32)	22 (5%)	408	1.86e-11 (3.57e-09)	0.497 (1.00)	0.181 (1.00)	0.00487 (0.682)	0.244 (1.00)	0.774 (1.00)	0.0326 (1.00)	0.0653 (1.00)
Del Peak 15(11p15 1)	5 (1%)	425	2.71e-06 (0.000494)	0.057 (1.00)	0.504 (1.00)	1 (1.00)	0.0498 (1.00)	0.132 (1.00)	0.038 (1.00)	0.0221 (1.00)
Del Peak 17(13q14 3)	18 (4%)	412	0.00155 (0.237)	0.0682 (1.00)	0.0985 (1.00)	1 (1.00)	0.00998 (1.00)	0.0251 (1.00)	0.0724 (1.00)	0.0643 (1.00)
Del Peak 22(18p11 21)	4 (1%)	426	0.00034 (0.0565)	0.175 (1.00)	1 (1.00)	0.182 (1.00)	0.244 (1.00)	0.0895 (1.00)	0.0726 (1.00)	0.0383 (1.00)
Del Peak 26(21q21 1)	8 (2%)	422	3.11e-06 (0.000563)	0.396 (1.00)	0.15 (1.00)	0.074 (1.00)	0.29 (1.00)	0.46 (1.00)	0.0847 (1.00)	0.084 (1.00)
Del Peak 8(7q34)	4 (1%)	426	0.655 (1.00)	0.781 (1.00)			0.748 (1.00)	0.589 (1.00)	0.687 (1.00)	0.823 (1.00)
Del Peak 13(10q21 2)	10 (2%)	420	0.00578 (0.803)	0.0398 (1.00)	0.195 (1.00)	1 (1.00)	0.0519 (1.00)	0.148 (1.00)	0.372 (1.00)	0.61 (1.00)
Del Peak 16(13q12 3)	15 (3%)	415	0.00608 (0.833)	0.00603 (0.832)	0.385 (1.00)	0.397 (1.00)	0.00956 (1.00)	0.0452 (1.00)	0.194 (1.00)	0.112 (1.00)
Del Peak 18(15q25 3)	7 (2%)	423	0.0018 (0.273)	0.0333 (1.00)	0.444 (1.00)	0.0385 (1.00)	0.0782 (1.00)	0.0674 (1.00)	0.00286 (0.415)	0.00204 (0.308)
Del Peak 20(16q23 3)	6 (1%)	424	0.0598 (1.00)	0.136 (1.00)	0.444 (1.00)	0.114 (1.00)	0.128 (1.00)	0.112 (1.00)	0.25 (1.00)	0.293 (1.00)
Del Peak 21(17p13 1)	8 (2%)	422	0.00434 (0.619)	0.883 (1.00)	1 (1.00)	1 (1.00)	0.711 (1.00)	0.642 (1.00)	0.0796 (1.00)	0.306 (1.00)
Del Peak 30(Xq22 1)	6 (1%)	424	0.015 (1.00)	0.396 (1.00)	0.102 (1.00)	0.146 (1.00)	0.672 (1.00)	0.861 (1.00)	0.452 (1.00)	0.386 (1.00)
Del Peak 31(Xq22 3)	4 (1%)	426	0.00433 (0.619)	0.0419 (1.00)	0.286 (1.00)	0.348 (1.00)	0.13 (1.00)	0.401 (1.00)	0.0726 (1.00)	0.0383 (1.00)

'Del Peak 2(2p22.3) mutation analysis' versus 'CN_CNMF'

P value = 1.79e-09 (Fisher's exact test), Q value = 3.4e-07

Table S1. Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 2(2P22.3) MUTATED	9	1	1
DEL PEAK 2(2P22.3) WILD-TYPE	26	329	64

Figure S1. Get High-res Image Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 2(2p22.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.28e-05 (Fisher's exact test), Q value = 0.014

Table S2. Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	135	55	240
DEL PEAK 2(2P22.3) MUTATED	9	2	0
DEL PEAK 2(2P22.3) WILD-TYPE	126	53	240

Figure S2. Get High-res Image Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 2(2p22.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0034

Table S3. Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	50	89	137
DEL PEAK 2(2P22.3) MUTATED	11	0	0	0
DEL PEAK 2(2P22.3) WILD-TYPE	118	50	89	137

Figure S3. Get High-res Image Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 2(2p22.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.95e-05 (Fisher's exact test), Q value = 0.0034

Table S4. Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	190	74
DEL PEAK 2(2P22.3) MUTATED	11	0	0
DEL PEAK 2(2P22.3) WILD-TYPE	130	190	74

Figure S4. Get High-res Image Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(2p22.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.77e-07 (Fisher's exact test), Q value = 0.00018

Table S5. Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	143	144
DEL PEAK 2(2P22.3) MUTATED	11	0	0
DEL PEAK 2(2P22.3) WILD-TYPE	108	143	144

Figure S5. Get High-res Image Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 2(2p22.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.2e-07 (Fisher's exact test), Q value = 5.9e-05

Table S6. Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	129
DEL PEAK 2(2P22.3) MUTATED	11	0	0
DEL PEAK 2(2P22.3) WILD-TYPE	97	169	129

Figure S6. Get High-res Image Gene #1: 'Del Peak 2(2p22.3) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 3(2q35) mutation analysis' versus 'CN_CNMF'

P value = 3.56e-11 (Fisher's exact test), Q value = 6.8e-09

Table S7. Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 3(2Q35) MUTATED	10	1	0
DEL PEAK 3(2Q35) WILD-TYPE	25	329	65

Figure S7. Get High-res Image Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 3(2q35) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.0059

Table S8. Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	135	55	240
DEL PEAK 3(2Q35) MUTATED	10	1	0
DEL PEAK 3(2Q35) WILD-TYPE	125	54	240

Figure S8. Get High-res Image Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 3(2q35) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.22

Table S9. Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	97	97
DEL PEAK 3(2Q35) MUTATED	4	0	3
DEL PEAK 3(2Q35) WILD-TYPE	23	97	94

Figure S9. Get High-res Image Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'Del Peak 3(2q35) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0034

Table S10. Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	50	89	137
DEL PEAK 3(2Q35) MUTATED	11	0	0	0
DEL PEAK 3(2Q35) WILD-TYPE	118	50	89	137

Figure S10. Get High-res Image Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 3(2q35) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.95e-05 (Fisher's exact test), Q value = 0.0034

Table S11. Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	190	74
DEL PEAK 3(2Q35) MUTATED	11	0	0
DEL PEAK 3(2Q35) WILD-TYPE	130	190	74

Figure S11. Get High-res Image Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q35) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.77e-07 (Fisher's exact test), Q value = 0.00018

Table S12. Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	143	144
DEL PEAK 3(2Q35) MUTATED	11	0	0
DEL PEAK 3(2Q35) WILD-TYPE	108	143	144

Figure S12. Get High-res Image Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 3(2q35) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.2e-07 (Fisher's exact test), Q value = 5.9e-05

Table S13. Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	129
DEL PEAK 3(2Q35) MUTATED	11	0	0
DEL PEAK 3(2Q35) WILD-TYPE	97	169	129

Figure S13. Get High-res Image Gene #2: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(6q22.31) mutation analysis' versus 'CN_CNMF'

P value = 0.000943 (Fisher's exact test), Q value = 0.15

Table S14. Gene #3: 'Del Peak 5(6q22.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 5(6Q22.31) MUTATED	4	2	0
DEL PEAK 5(6Q22.31) WILD-TYPE	31	328	65

Figure S14. Get High-res Image Gene #3: 'Del Peak 5(6q22.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 6(6q27) mutation analysis' versus 'CN_CNMF'

P value = 0.000943 (Fisher's exact test), Q value = 0.15

Table S15. Gene #4: 'Del Peak 6(6q27) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 6(6Q27) MUTATED	4	2	0
DEL PEAK 6(6Q27) WILD-TYPE	31	328	65

Figure S15. Get High-res Image Gene #4: 'Del Peak 6(6q27) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(8p12) mutation analysis' versus 'CN_CNMF'

P value = 3.73e-05 (Fisher's exact test), Q value = 0.0064

Table S16. Gene #6: 'Del Peak 9(8p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 9(8P12) MUTATED	4	0	0
DEL PEAK 9(8P12) WILD-TYPE	31	330	65

Figure S16. Get High-res Image Gene #6: 'Del Peak 9(8p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(8q24.22) mutation analysis' versus 'CN_CNMF'

P value = 8.01e-05 (Fisher's exact test), Q value = 0.014

Table S17. Gene #7: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 10(8Q24.22) MUTATED	5	2	0
DEL PEAK 10(8Q24.22) WILD-TYPE	30	328	65

Figure S17. Get High-res Image Gene #7: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(8q24.22) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.19

Table S18. Gene #7: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	190	74
DEL PEAK 10(8Q24.22) MUTATED	7	0	0
DEL PEAK 10(8Q24.22) WILD-TYPE	134	190	74

Figure S18. Get High-res Image Gene #7: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(8q24.22) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000164 (Fisher's exact test), Q value = 0.027

Table S19. Gene #7: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	143	144
DEL PEAK 10(8Q24.22) MUTATED	7	0	0
DEL PEAK 10(8Q24.22) WILD-TYPE	112	143	144

Figure S19. Get High-res Image Gene #7: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 10(8q24.22) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.14e-05 (Fisher's exact test), Q value = 0.014

Table S20. Gene #7: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	129
DEL PEAK 10(8Q24.22) MUTATED	7	0	0
DEL PEAK 10(8Q24.22) WILD-TYPE	101	169	129

Figure S20. Get High-res Image Gene #7: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 1.88e-12 (Fisher's exact test), Q value = 3.6e-10

Table S21. Gene #8: 'Del Peak 11(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 11(9P21.3) MUTATED	13	3	1
DEL PEAK 11(9P21.3) WILD-TYPE	22	327	64

Figure S21. Get High-res Image Gene #8: 'Del Peak 11(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 12(9q22.32) mutation analysis' versus 'CN_CNMF'

P value = 1.86e-11 (Fisher's exact test), Q value = 3.6e-09

Table S22. Gene #9: 'Del Peak 12(9q22.32) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 12(9Q22.32) MUTATED	14	7	1
DEL PEAK 12(9Q22.32) WILD-TYPE	21	323	64

Figure S22. Get High-res Image Gene #9: 'Del Peak 12(9q22.32) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 14(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 0.000762 (Fisher's exact test), Q value = 0.12

Table S23. Gene #11: 'Del Peak 14(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 14(10Q23.31) MUTATED	5	5	0
DEL PEAK 14(10Q23.31) WILD-TYPE	30	325	65

Figure S23. Get High-res Image Gene #11: 'Del Peak 14(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 14(10q23.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.18

Table S24. Gene #11: 'Del Peak 14(10q23.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	190	74
DEL PEAK 14(10Q23.31) MUTATED	8	0	2
DEL PEAK 14(10Q23.31) WILD-TYPE	133	190	72

Figure S24. Get High-res Image Gene #11: 'Del Peak 14(10q23.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(11p15.1) mutation analysis' versus 'CN_CNMF'

P value = 2.71e-06 (Fisher's exact test), Q value = 0.00049

Table S25. Gene #12: 'Del Peak 15(11p15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 15(11P15.1) MUTATED	5	0	0
DEL PEAK 15(11P15.1) WILD-TYPE	30	330	65

Figure S25. Get High-res Image Gene #12: 'Del Peak 15(11p15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 17(13q14.3) mutation analysis' versus 'CN_CNMF'

P value = 0.00155 (Fisher's exact test), Q value = 0.24

Table S26. Gene #14: 'Del Peak 17(13q14.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 17(13Q14.3) MUTATED	6	9	3
DEL PEAK 17(13Q14.3) WILD-TYPE	29	321	62

Figure S26. Get High-res Image Gene #14: 'Del Peak 17(13q14.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 22(18p11.21) mutation analysis' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.056

Table S27. Gene #18: 'Del Peak 22(18p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 22(18P11.21) MUTATED	3	0	1
DEL PEAK 22(18P11.21) WILD-TYPE	32	330	64

Figure S27. Get High-res Image Gene #18: 'Del Peak 22(18p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 23(19p13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.16

Table S28. Gene #19: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	135	55	240
DEL PEAK 23(19P13.2) MUTATED	7	0	0
DEL PEAK 23(19P13.2) WILD-TYPE	128	55	240

Figure S28. Get High-res Image Gene #19: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 23(19p13.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.19

Table S29. Gene #19: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	190	74
DEL PEAK 23(19P13.2) MUTATED	7	0	0
DEL PEAK 23(19P13.2) WILD-TYPE	134	190	74

Figure S29. Get High-res Image Gene #19: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 23(19p13.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000579 (Fisher's exact test), Q value = 0.095

Table S30. Gene #19: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	143	144
DEL PEAK 23(19P13.2) MUTATED	6	0	0
DEL PEAK 23(19P13.2) WILD-TYPE	113	143	144

Figure S30. Get High-res Image Gene #19: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 23(19p13.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000319 (Fisher's exact test), Q value = 0.053

Table S31. Gene #19: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	129
DEL PEAK 23(19P13.2) MUTATED	6	0	0
DEL PEAK 23(19P13.2) WILD-TYPE	102	169	129

Figure S31. Get High-res Image Gene #19: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(21q21.1) mutation analysis' versus 'CN_CNMF'

P value = 3.11e-06 (Fisher's exact test), Q value = 0.00056

Table S32. Gene #20: 'Del Peak 26(21q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 26(21Q21.1) MUTATED	6	1	1
DEL PEAK 26(21Q21.1) WILD-TYPE	29	329	64

Figure S32. Get High-res Image Gene #20: 'Del Peak 26(21q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(22q13.31) mutation analysis' versus 'CN_CNMF'

P value = 2.45e-77 (Fisher's exact test), Q value = 4.8e-75

Table S33. Gene #21: 'Del Peak 27(22q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 27(22Q13.31) MUTATED	9	0	65
DEL PEAK 27(22Q13.31) WILD-TYPE	26	330	0

Figure S33. Get High-res Image Gene #21: 'Del Peak 27(22q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(22q13.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000881 (Fisher's exact test), Q value = 0.14

Table S34. Gene #21: 'Del Peak 27(22q13.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	135	55	240
DEL PEAK 27(22Q13.31) MUTATED	37	5	32
DEL PEAK 27(22Q13.31) WILD-TYPE	98	50	208

Figure S34. Get High-res Image Gene #21: 'Del Peak 27(22q13.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 27(22q13.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.04e-07 (Fisher's exact test), Q value = 5.7e-05

Table S35. Gene #21: 'Del Peak 27(22q13.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	50	89	137
DEL PEAK 27(22Q13.31) MUTATED	36	4	21	7
DEL PEAK 27(22Q13.31) WILD-TYPE	93	46	68	130

Figure S35. Get High-res Image Gene #21: 'Del Peak 27(22q13.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 27(22q13.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.0034

Table S36. Gene #21: 'Del Peak 27(22q13.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	190	74
DEL PEAK 27(22Q13.31) MUTATED	36	15	17
DEL PEAK 27(22Q13.31) WILD-TYPE	105	175	57

Figure S36. Get High-res Image Gene #21: 'Del Peak 27(22q13.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(22q13.2) mutation analysis' versus 'CN_CNMF'

P value = 2.45e-77 (Fisher's exact test), Q value = 4.8e-75

Table S37. Gene #22: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 28(22Q13.2) MUTATED	9	0	65
DEL PEAK 28(22Q13.2) WILD-TYPE	26	330	0

Figure S37. Get High-res Image Gene #22: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 28(22q13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000881 (Fisher's exact test), Q value = 0.14

Table S38. Gene #22: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	135	55	240
DEL PEAK 28(22Q13.2) MUTATED	37	5	32
DEL PEAK 28(22Q13.2) WILD-TYPE	98	50	208

Figure S38. Get High-res Image Gene #22: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 28(22q13.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.04e-07 (Fisher's exact test), Q value = 5.7e-05

Table S39. Gene #22: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	50	89	137
DEL PEAK 28(22Q13.2) MUTATED	36	4	21	7
DEL PEAK 28(22Q13.2) WILD-TYPE	93	46	68	130

Figure S39. Get High-res Image Gene #22: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 28(22q13.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.0034

Table S40. Gene #22: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	190	74
DEL PEAK 28(22Q13.2) MUTATED	36	15	17
DEL PEAK 28(22Q13.2) WILD-TYPE	105	175	57

Figure S40. Get High-res Image Gene #22: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(22q13.32) mutation analysis' versus 'CN_CNMF'

P value = 1.72e-75 (Fisher's exact test), Q value = 3.3e-73

Table S41. Gene #23: 'Del Peak 29(22q13.32) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	330	65
DEL PEAK 29(22Q13.32) MUTATED	9	1	65
DEL PEAK 29(22Q13.32) WILD-TYPE	26	329	0

Figure S41. Get High-res Image Gene #23: 'Del Peak 29(22q13.32) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 29(22q13.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000467 (Fisher's exact test), Q value = 0.077

Table S42. Gene #23: 'Del Peak 29(22q13.32) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	135	55	240
DEL PEAK 29(22Q13.32) MUTATED	38	5	32
DEL PEAK 29(22Q13.32) WILD-TYPE	97	50	208

Figure S42. Get High-res Image Gene #23: 'Del Peak 29(22q13.32) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 29(22q13.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.62e-07 (Fisher's exact test), Q value = 3.1e-05

Table S43. Gene #23: 'Del Peak 29(22q13.32) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	50	89	137
DEL PEAK 29(22Q13.32) MUTATED	37	4	21	7
DEL PEAK 29(22Q13.32) WILD-TYPE	92	46	68	130

Figure S43. Get High-res Image Gene #23: 'Del Peak 29(22q13.32) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 29(22q13.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0019

Table S44. Gene #23: 'Del Peak 29(22q13.32) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	190	74
DEL PEAK 29(22Q13.32) MUTATED	37	15	17
DEL PEAK 29(22Q13.32) WILD-TYPE	104	175	57

Figure S44. Get High-res Image Gene #23: 'Del Peak 29(22q13.32) mutation analysis' versus Clinical Feature #6: '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 = THCA-TP.transferedmergedcluster.txt
Number of patients = 430
Number of copy number variation regions = 25
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

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] 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)

[3] GISTIC_version2

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