Correlation between copy number variation genes and molecular subtypes

Cervical Squamous Cell Carcinoma (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/C1MK6B2T

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 48 peak regions and 6 molecular subtypes across 114 patients, 16 significant findings detected with Q value < 0.25.

Amp Peak 3(3q26.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 4(3q28) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(5p15.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 20(19q13.31) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.22) cnvs correlated to 'MIRSEQ_CHIERARCHICAL'.
Del Peak 4(3p11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 5(4q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 6(4q35.2) cnvs correlated to 'CN_CNMF'.
Del Peak 13(11q25) cnvs correlated to 'CN_CNMF'.
Del Peak 17(14q32.31) cnvs correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 19(16q23.1) cnvs correlated to 'MIRSEQ_CHIERARCHICAL'.
Del Peak 22(19p13.3) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 48 regions and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 16 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ 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
Del Peak 22(19p13 3)	34 (30%)	80	0.0857 (1.00)	0.000705 (0.193)	0.00016 (0.0449)	0.000182 (0.0508)	0.0318 (1.00)	3.54e-05 (0.0101)
Del Peak 17(14q32 31)	21 (18%)	93	0.141 (1.00)	0.00953 (1.00)	0.000549 (0.151)	0.000172 (0.048)	0.024 (1.00)	0.0052 (1.00)
Amp Peak 3(3q26 2)	89 (78%)	25	4.55e-05 (0.0129)	0.0251 (1.00)	0.234 (1.00)	0.0251 (1.00)	0.85 (1.00)	0.105 (1.00)
Amp Peak 4(3q28)	88 (77%)	26	3.78e-05 (0.0107)	0.00424 (1.00)	0.131 (1.00)	0.00472 (1.00)	0.818 (1.00)	0.063 (1.00)
Amp Peak 6(5p15 33)	50 (44%)	64	2.88e-05 (0.00822)	0.898 (1.00)	0.54 (1.00)	0.676 (1.00)	0.382 (1.00)	0.0889 (1.00)
Amp Peak 20(19q13 31)	38 (33%)	76	0.000819 (0.224)	0.19 (1.00)	0.365 (1.00)	0.0966 (1.00)	0.0995 (1.00)	0.874 (1.00)
Del Peak 1(1p36 22)	18 (16%)	96	0.0405 (1.00)	0.023 (1.00)	0.02 (1.00)	0.00911 (1.00)	0.474 (1.00)	0.000203 (0.0561)
Del Peak 4(3p11 2)	47 (41%)	67	0.000374 (0.103)	0.137 (1.00)	0.56 (1.00)	0.374 (1.00)	0.129 (1.00)	0.00706 (1.00)
Del Peak 5(4q22 1)	34 (30%)	80	3.23e-08 (9.3e-06)	0.534 (1.00)	0.0713 (1.00)	0.21 (1.00)	0.2 (1.00)	0.297 (1.00)
Del Peak 6(4q35 2)	42 (37%)	72	3.04e-06 (0.000871)	0.479 (1.00)	0.0675 (1.00)	0.0638 (1.00)	0.575 (1.00)	0.323 (1.00)
Del Peak 13(11q25)	68 (60%)	46	8.43e-05 (0.0238)	0.629 (1.00)	0.245 (1.00)	0.219 (1.00)	0.0267 (1.00)	0.447 (1.00)
Del Peak 19(16q23 1)	24 (21%)	90	0.956 (1.00)	0.0191 (1.00)	0.0697 (1.00)	0.121 (1.00)	0.143 (1.00)	0.000197 (0.0549)
Amp Peak 1(1q21 3)	60 (53%)	54	0.0585 (1.00)	0.387 (1.00)	0.318 (1.00)	0.0186 (1.00)	0.58 (1.00)	0.566 (1.00)
Amp Peak 2(2p24 3)	29 (25%)	85	0.147 (1.00)	0.22 (1.00)	0.428 (1.00)	0.421 (1.00)	0.0869 (1.00)	0.0056 (1.00)
Amp Peak 5(4q12)	12 (11%)	102	1 (1.00)	0.131 (1.00)	0.427 (1.00)	0.0901 (1.00)	0.216 (1.00)	0.0208 (1.00)
Amp Peak 7(6q12)	21 (18%)	93	0.605 (1.00)	0.435 (1.00)	0.188 (1.00)	0.057 (1.00)	0.239 (1.00)	0.181 (1.00)
Amp Peak 8(7p11 2)	23 (20%)	91	0.0718 (1.00)	0.249 (1.00)	0.06 (1.00)	0.944 (1.00)	0.0647 (1.00)	0.0577 (1.00)
Amp Peak 9(8q24 21)	47 (41%)	67	0.173 (1.00)	0.706 (1.00)	0.771 (1.00)	0.887 (1.00)	0.0891 (1.00)	0.491 (1.00)
Amp Peak 10(9p24 1)	26 (23%)	88	0.455 (1.00)	0.256 (1.00)	1 (1.00)	0.653 (1.00)	0.234 (1.00)	0.685 (1.00)
Amp Peak 11(11p13)	8 (7%)	106	0.629 (1.00)	0.388 (1.00)	0.318 (1.00)	0.0767 (1.00)	0.73 (1.00)	0.894 (1.00)
Amp Peak 12(11q13 3)	16 (14%)	98	0.0186 (1.00)	0.214 (1.00)	0.0345 (1.00)	0.0308 (1.00)	0.107 (1.00)	0.885 (1.00)
Amp Peak 13(11q22 1)	24 (21%)	90	0.00443 (1.00)	0.00156 (0.424)	0.0176 (1.00)	0.232 (1.00)	0.0132 (1.00)	0.123 (1.00)
Amp Peak 14(13q22 1)	24 (21%)	90	0.0576 (1.00)	0.039 (1.00)	0.234 (1.00)	0.0356 (1.00)	0.162 (1.00)	0.0195 (1.00)
Amp Peak 15(14q24 1)	23 (20%)	91	0.753 (1.00)	0.643 (1.00)	0.514 (1.00)	0.109 (1.00)	0.705 (1.00)	0.955 (1.00)
Amp Peak 16(15q26 3)	29 (25%)	85	0.0692 (1.00)	0.765 (1.00)	0.2 (1.00)	0.538 (1.00)	0.928 (1.00)	1 (1.00)
Amp Peak 17(16p13 13)	28 (25%)	86	0.152 (1.00)	0.561 (1.00)	0.667 (1.00)	0.474 (1.00)	0.682 (1.00)	0.465 (1.00)
Amp Peak 18(17q12)	19 (17%)	95	0.197 (1.00)	0.0724 (1.00)	0.0399 (1.00)	0.016 (1.00)	0.112 (1.00)	0.065 (1.00)
Amp Peak 19(17q25 1)	30 (26%)	84	0.22 (1.00)	0.0345 (1.00)	0.022 (1.00)	0.019 (1.00)	0.48 (1.00)	0.607 (1.00)
Amp Peak 21(20q11 21)	57 (50%)	57	0.0346 (1.00)	0.337 (1.00)	0.523 (1.00)	0.0411 (1.00)	0.532 (1.00)	0.722 (1.00)
Amp Peak 22(Xq28)	34 (30%)	80	0.448 (1.00)	0.502 (1.00)	0.248 (1.00)	0.913 (1.00)	0.0433 (1.00)	0.133 (1.00)
Del Peak 2(2q22 1)	21 (18%)	93	0.443 (1.00)	0.341 (1.00)	0.136 (1.00)	0.419 (1.00)	0.911 (1.00)	0.953 (1.00)
Del Peak 3(2q37 1)	46 (40%)	68	0.683 (1.00)	0.146 (1.00)	0.00237 (0.634)	0.0262 (1.00)	0.172 (1.00)	0.0766 (1.00)
Del Peak 7(5q15)	33 (29%)	81	0.018 (1.00)	0.368 (1.00)	0.666 (1.00)	0.21 (1.00)	0.216 (1.00)	0.346 (1.00)
Del Peak 8(6p24 3)	18 (16%)	96	0.107 (1.00)	0.239 (1.00)	0.0652 (1.00)	0.404 (1.00)	0.499 (1.00)	1 (1.00)
Del Peak 9(6p12 1)	19 (17%)	95	0.679 (1.00)	0.354 (1.00)	0.303 (1.00)	0.137 (1.00)	0.819 (1.00)	0.135 (1.00)
Del Peak 10(6q26)	43 (38%)	71	0.746 (1.00)	0.163 (1.00)	0.685 (1.00)	0.662 (1.00)	0.545 (1.00)	0.495 (1.00)
Del Peak 11(7q34)	26 (23%)	88	0.0718 (1.00)	0.923 (1.00)	0.242 (1.00)	0.0237 (1.00)	0.0683 (1.00)	0.198 (1.00)
Del Peak 12(10q23 31)	35 (31%)	79	0.541 (1.00)	0.572 (1.00)	0.694 (1.00)	0.363 (1.00)	0.739 (1.00)	0.87 (1.00)
Del Peak 14(13q12 12)	45 (39%)	69	0.0161 (1.00)	0.515 (1.00)	0.212 (1.00)	0.471 (1.00)	0.141 (1.00)	0.161 (1.00)
Del Peak 15(13q13 3)	47 (41%)	67	0.0102 (1.00)	0.248 (1.00)	0.318 (1.00)	0.507 (1.00)	0.0197 (1.00)	0.107 (1.00)
Del Peak 16(14q31 1)	18 (16%)	96	0.197 (1.00)	0.0598 (1.00)	0.00616 (1.00)	0.00188 (0.507)	0.118 (1.00)	0.031 (1.00)
Del Peak 18(16q11 2)	21 (18%)	93	0.464 (1.00)	0.025 (1.00)	0.59 (1.00)	0.217 (1.00)	0.139 (1.00)	0.00188 (0.507)
Del Peak 20(17p12)	38 (33%)	76	0.00119 (0.323)	0.426 (1.00)	0.252 (1.00)	0.716 (1.00)	0.0932 (1.00)	0.044 (1.00)
Del Peak 21(17q25 3)	19 (17%)	95	0.0305 (1.00)	0.0803 (1.00)	0.0179 (1.00)	0.0848 (1.00)	0.033 (1.00)	0.0738 (1.00)
Del Peak 23(20p12 1)	13 (11%)	101	0.803 (1.00)	0.95 (1.00)	0.693 (1.00)	1 (1.00)	0.434 (1.00)	0.451 (1.00)
Del Peak 24(21q21 1)	24 (21%)	90	0.00522 (1.00)	0.197 (1.00)	0.524 (1.00)	0.122 (1.00)	0.527 (1.00)	0.8 (1.00)
Del Peak 25(Xp11 3)	34 (30%)	80	0.0957 (1.00)	0.0066 (1.00)	0.0171 (1.00)	0.0352 (1.00)	0.0119 (1.00)	0.00375 (1.00)
Del Peak 26(Xq21 33)	27 (24%)	87	0.532 (1.00)	0.0371 (1.00)	0.0918 (1.00)	0.142 (1.00)	0.101 (1.00)	0.00955 (1.00)

'Amp Peak 3(3q26.2) mutation analysis' versus 'CN_CNMF'

P value = 4.55e-05 (Fisher's exact test), Q value = 0.013

Table S1. Gene #3: 'Amp Peak 3(3q26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	25	54
AMP PEAK 3(3Q26.2) MUTATED	35	19	35
AMP PEAK 3(3Q26.2) WILD-TYPE	0	6	19

Figure S1. Get High-res Image Gene #3: 'Amp Peak 3(3q26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 4(3q28) mutation analysis' versus 'CN_CNMF'

P value = 3.78e-05 (Fisher's exact test), Q value = 0.011

Table S2. Gene #4: 'Amp Peak 4(3q28) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	25	54
AMP PEAK 4(3Q28) MUTATED	35	18	35
AMP PEAK 4(3Q28) WILD-TYPE	0	7	19

Figure S2. Get High-res Image Gene #4: 'Amp Peak 4(3q28) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 6(5p15.33) mutation analysis' versus 'CN_CNMF'

P value = 2.88e-05 (Fisher's exact test), Q value = 0.0082

Table S3. Gene #6: 'Amp Peak 6(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	25	54
AMP PEAK 6(5P15.33) MUTATED	16	20	14
AMP PEAK 6(5P15.33) WILD-TYPE	19	5	40

Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 20(19q13.31) mutation analysis' versus 'CN_CNMF'

P value = 0.000819 (Fisher's exact test), Q value = 0.22

Table S4. Gene #20: 'Amp Peak 20(19q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	25	54
AMP PEAK 20(19Q13.31) MUTATED	11	16	11
AMP PEAK 20(19Q13.31) WILD-TYPE	24	9	43

Figure S4. Get High-res Image Gene #20: 'Amp Peak 20(19q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 1(1p36.22) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000203 (Fisher's exact test), Q value = 0.056

Table S5. Gene #23: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	52	32
DEL PEAK 1(1P36.22) MUTATED	9	1	8
DEL PEAK 1(1P36.22) WILD-TYPE	21	51	24

Figure S5. Get High-res Image Gene #23: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(3p11.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000374 (Fisher's exact test), Q value = 0.1

Table S6. Gene #26: 'Del Peak 4(3p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	25	54
DEL PEAK 4(3P11.2) MUTATED	12	19	16
DEL PEAK 4(3P11.2) WILD-TYPE	23	6	38

Figure S6. Get High-res Image Gene #26: 'Del Peak 4(3p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 5(4q22.1) mutation analysis' versus 'CN_CNMF'

P value = 3.23e-08 (Fisher's exact test), Q value = 9.3e-06

Table S7. Gene #27: 'Del Peak 5(4q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	25	54
DEL PEAK 5(4Q22.1) MUTATED	9	19	6
DEL PEAK 5(4Q22.1) WILD-TYPE	26	6	48

Figure S7. Get High-res Image Gene #27: 'Del Peak 5(4q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 6(4q35.2) mutation analysis' versus 'CN_CNMF'

P value = 3.04e-06 (Fisher's exact test), Q value = 0.00087

Table S8. Gene #28: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	25	54
DEL PEAK 6(4Q35.2) MUTATED	10	20	12
DEL PEAK 6(4Q35.2) WILD-TYPE	25	5	42

Figure S8. Get High-res Image Gene #28: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 13(11q25) mutation analysis' versus 'CN_CNMF'

P value = 8.43e-05 (Fisher's exact test), Q value = 0.024

Table S9. Gene #35: 'Del Peak 13(11q25) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	25	54
DEL PEAK 13(11Q25) MUTATED	30	16	22
DEL PEAK 13(11Q25) WILD-TYPE	5	9	32

Figure S9. Get High-res Image Gene #35: 'Del Peak 13(11q25) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 17(14q32.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000549 (Fisher's exact test), Q value = 0.15

Table S10. Gene #39: 'Del Peak 17(14q32.31) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	25	27
DEL PEAK 17(14Q32.31) MUTATED	2	3	11
DEL PEAK 17(14Q32.31) WILD-TYPE	39	22	16

Figure S10. Get High-res Image Gene #39: 'Del Peak 17(14q32.31) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 17(14q32.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000172 (Fisher's exact test), Q value = 0.048

Table S11. Gene #39: 'Del Peak 17(14q32.31) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	24	49
DEL PEAK 17(14Q32.31) MUTATED	2	11	3
DEL PEAK 17(14Q32.31) WILD-TYPE	18	13	46

Figure S11. Get High-res Image Gene #39: 'Del Peak 17(14q32.31) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(16q23.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000197 (Fisher's exact test), Q value = 0.055

Table S12. Gene #41: 'Del Peak 19(16q23.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	52	32
DEL PEAK 19(16Q23.1) MUTATED	14	4	6
DEL PEAK 19(16Q23.1) WILD-TYPE	16	48	26

Figure S12. Get High-res Image Gene #41: 'Del Peak 19(16q23.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 22(19p13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000705 (Chi-square test), Q value = 0.19

Table S13. Gene #44: 'Del Peak 22(19p13.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	20	22	24	26
DEL PEAK 22(19P13.3) MUTATED	1	12	3	8	10
DEL PEAK 22(19P13.3) WILD-TYPE	21	8	19	16	16

Figure S13. Get High-res Image Gene #44: 'Del Peak 22(19p13.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 22(19p13.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.045

Table S14. Gene #44: 'Del Peak 22(19p13.3) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	25	27
DEL PEAK 22(19P13.3) MUTATED	5	14	13
DEL PEAK 22(19P13.3) WILD-TYPE	36	11	14

Figure S14. Get High-res Image Gene #44: 'Del Peak 22(19p13.3) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 22(19p13.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000182 (Fisher's exact test), Q value = 0.051

Table S15. Gene #44: 'Del Peak 22(19p13.3) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	24	49
DEL PEAK 22(19P13.3) MUTATED	13	11	8
DEL PEAK 22(19P13.3) WILD-TYPE	7	13	41

Figure S15. Get High-res Image Gene #44: 'Del Peak 22(19p13.3) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 22(19p13.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.54e-05 (Fisher's exact test), Q value = 0.01

Table S16. Gene #44: 'Del Peak 22(19p13.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	52	32
DEL PEAK 22(19P13.3) MUTATED	13	5	16
DEL PEAK 22(19P13.3) WILD-TYPE	17	47	16

Figure S16. Get High-res Image Gene #44: 'Del Peak 22(19p13.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_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 = 114
Number of copy number variation regions = 48
Number of molecular subtypes = 6
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

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] 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

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