Correlation between copy number variation genes (focal) and selected clinical features

Glioblastoma Multiforme (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 (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1Q23X85

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 70 arm-level results and 6 clinical features across 552 patients, 15 significant findings detected with Q value < 0.25.

Amp Peak 8(7p11.2) cnv correlated to 'Time to Death' and 'AGE'.
Amp Peak 9(7q11.21) cnv correlated to 'Time to Death' and 'AGE'.
Amp Peak 10(7q21.2) cnv correlated to 'AGE'.
Del Peak 19(9p21.3) cnv correlated to 'AGE'.
Del Peak 21(10p15.3) cnv correlated to 'Time to Death' and 'AGE'.
Del Peak 22(10p13) cnv correlated to 'Time to Death' and 'AGE'.
Del Peak 23(10p11.23) cnv correlated to 'Time to Death' and 'AGE'.
Del Peak 24(10q23.31) cnv correlated to 'Time to Death' and 'AGE'.
Del Peak 25(10q26.3) cnv correlated to 'AGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 70 arm-level results and 6 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 15 significant findings detected.


		Clinical Features	Time to Death	AGE	GENDER	KARNOFSKY PERFORMANCE SCORE	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	t-test	Fisher's exact test	Fisher's exact test
Amp Peak 8(7p11 2)	0 (0%)	68	4.01e-06 (0.00166)	3.88e-09 (1.63e-06)	0.428 (1.00)	0.0351 (1.00)	0.0463 (1.00)	0.0505 (1.00)
Amp Peak 9(7q11 21)	0 (0%)	108	0.000284 (0.115)	1.32e-07 (5.5e-05)	0.273 (1.00)	0.658 (1.00)	0.0105 (1.00)	0.0629 (1.00)
Del Peak 21(10p15 3)	0 (0%)	102	2.29e-05 (0.00939)	7.27e-08 (3.04e-05)	0.0927 (1.00)	0.596 (1.00)	0.0223 (1.00)	0.41 (1.00)
Del Peak 22(10p13)	0 (0%)	100	1.49e-05 (0.00613)	3.45e-07 (0.000143)	0.0415 (1.00)	0.884 (1.00)	0.0199 (1.00)	0.905 (1.00)
Del Peak 23(10p11 23)	0 (0%)	96	2.23e-06 (0.000927)	2.12e-08 (8.86e-06)	0.109 (1.00)	0.232 (1.00)	0.00327 (1.00)	0.545 (1.00)
Del Peak 24(10q23 31)	0 (0%)	61	6.15e-05 (0.0251)	5.66e-06 (0.00234)	0.677 (1.00)	0.0751 (1.00)	0.00512 (1.00)	0.661 (1.00)
Amp Peak 10(7q21 2)	0 (0%)	94	0.00181 (0.732)	1.54e-05 (0.00635)	0.563 (1.00)	0.49 (1.00)	0.0369 (1.00)	0.143 (1.00)
Del Peak 19(9p21 3)	0 (0%)	149	0.037 (1.00)	0.000356 (0.145)	0.493 (1.00)	0.0926 (1.00)	0.195 (1.00)	0.536 (1.00)
Del Peak 25(10q26 3)	0 (0%)	60	0.00319 (1.00)	5.33e-05 (0.0218)	0.576 (1.00)	0.0613 (1.00)	0.0188 (1.00)	1 (1.00)
Amp Peak 1(1p36 21)	0 (0%)	465	0.0947 (1.00)	0.348 (1.00)	0.283 (1.00)	0.653 (1.00)	0.314 (1.00)	0.801 (1.00)
Amp Peak 2(1q32 1)	0 (0%)	404	0.48 (1.00)	0.299 (1.00)	0.624 (1.00)	0.279 (1.00)	0.275 (1.00)	0.917 (1.00)
Amp Peak 3(1q44)	0 (0%)	458	0.534 (1.00)	0.857 (1.00)	0.297 (1.00)	0.599 (1.00)	0.627 (1.00)	0.808 (1.00)
Amp Peak 4(2p24 3)	0 (0%)	507	0.0986 (1.00)	0.175 (1.00)	0.341 (1.00)	0.583 (1.00)	0.69 (1.00)	0.867 (1.00)
Amp Peak 5(3q26 33)	0 (0%)	447	0.312 (1.00)	0.0358 (1.00)	0.825 (1.00)	0.688 (1.00)	0.0328 (1.00)	0.907 (1.00)
Amp Peak 6(4p16 3)	0 (0%)	507	0.525 (1.00)	0.514 (1.00)	0.526 (1.00)	0.429 (1.00)	1 (1.00)	0.239 (1.00)
Amp Peak 7(4q12)	0 (0%)	449	0.663 (1.00)	0.575 (1.00)	0.22 (1.00)	0.597 (1.00)	0.416 (1.00)	0.346 (1.00)
Amp Peak 11(7q31 2)	0 (0%)	101	0.0371 (1.00)	0.00184 (0.742)	0.369 (1.00)	0.513 (1.00)	0.143 (1.00)	0.0565 (1.00)
Amp Peak 12(7q36 1)	0 (0%)	96	0.0873 (1.00)	0.00282 (1.00)	0.492 (1.00)	0.732 (1.00)	0.115 (1.00)	0.276 (1.00)
Amp Peak 13(8q24 21)	0 (0%)	489	0.359 (1.00)	0.13 (1.00)	0.275 (1.00)	0.804 (1.00)	0.885 (1.00)	0.472 (1.00)
Amp Peak 14(11p13)	0 (0%)	527	0.958 (1.00)	0.217 (1.00)	0.406 (1.00)	0.316 (1.00)	0.226 (1.00)	0.513 (1.00)
Amp Peak 15(12p13 32)	0 (0%)	473	0.664 (1.00)	0.0932 (1.00)	1 (1.00)	0.695 (1.00)	1 (1.00)	1 (1.00)
Amp Peak 16(12q14 1)	0 (0%)	424	0.201 (1.00)	0.684 (1.00)	0.409 (1.00)	0.808 (1.00)	0.745 (1.00)	0.827 (1.00)
Amp Peak 17(12q15)	0 (0%)	463	0.861 (1.00)	0.679 (1.00)	0.346 (1.00)	0.911 (1.00)	0.683 (1.00)	0.21 (1.00)
Amp Peak 18(13q34)	0 (0%)	522	0.803 (1.00)	0.824 (1.00)	0.339 (1.00)	0.838 (1.00)	0.529 (1.00)	0.688 (1.00)
Amp Peak 19(14q32 33)	0 (0%)	520	0.159 (1.00)	0.0224 (1.00)	0.582 (1.00)	0.254 (1.00)	0.209 (1.00)	1 (1.00)
Amp Peak 20(17p13 2)	0 (0%)	508	0.932 (1.00)	0.541 (1.00)	0.336 (1.00)	0.109 (1.00)	0.685 (1.00)	0.615 (1.00)
Amp Peak 21(17q25 1)	0 (0%)	477	0.139 (1.00)	0.0873 (1.00)	0.255 (1.00)	0.837 (1.00)	1 (1.00)	0.687 (1.00)
Amp Peak 22(19p13 2)	0 (0%)	318	0.101 (1.00)	0.821 (1.00)	1 (1.00)	0.441 (1.00)	0.517 (1.00)	1 (1.00)
Amp Peak 23(19q12)	0 (0%)	353	0.261 (1.00)	0.529 (1.00)	0.587 (1.00)	0.996 (1.00)	0.718 (1.00)	0.774 (1.00)
Amp Peak 24(21q21 1)	0 (0%)	488	0.526 (1.00)	0.0198 (1.00)	0.684 (1.00)	0.549 (1.00)	0.374 (1.00)	0.566 (1.00)
Del Peak 1(1p36 32)	0 (0%)	457	0.374 (1.00)	0.867 (1.00)	0.0508 (1.00)	0.999 (1.00)	0.43 (1.00)	0.808 (1.00)
Del Peak 2(1p36 23)	0 (0%)	421	0.943 (1.00)	0.0255 (1.00)	0.0104 (1.00)	0.193 (1.00)	0.263 (1.00)	0.665 (1.00)
Del Peak 3(1p32 3)	0 (0%)	493	0.735 (1.00)	0.0677 (1.00)	0.159 (1.00)	0.687 (1.00)	1 (1.00)	0.101 (1.00)
Del Peak 4(1p22 1)	0 (0%)	506	0.257 (1.00)	0.345 (1.00)	1 (1.00)	0.585 (1.00)	0.0899 (1.00)	1 (1.00)
Del Peak 5(1q42 11)	0 (0%)	507	0.0965 (1.00)	0.0679 (1.00)	1 (1.00)	0.0102 (1.00)	1 (1.00)	0.181 (1.00)
Del Peak 6(1q44)	0 (0%)	521	0.315 (1.00)	0.301 (1.00)	0.851 (1.00)	0.0669 (1.00)	1 (1.00)	0.844 (1.00)
Del Peak 7(2q22 1)	0 (0%)	509	0.33 (1.00)	0.102 (1.00)	0.198 (1.00)	0.686 (1.00)	0.816 (1.00)	0.123 (1.00)
Del Peak 8(2q37 1)	0 (0%)	497	0.73 (1.00)	0.327 (1.00)	0.146 (1.00)	0.657 (1.00)	1 (1.00)	0.36 (1.00)
Del Peak 9(3p21 1)	0 (0%)	500	0.021 (1.00)	0.0109 (1.00)	0.883 (1.00)	0.698 (1.00)	0.501 (1.00)	0.0591 (1.00)
Del Peak 10(3q13 31)	0 (0%)	497	0.504 (1.00)	0.0586 (1.00)	0.384 (1.00)	0.306 (1.00)	0.872 (1.00)	0.128 (1.00)
Del Peak 11(3q22 1)	0 (0%)	497	0.625 (1.00)	0.128 (1.00)	1 (1.00)	0.49 (1.00)	0.872 (1.00)	0.442 (1.00)
Del Peak 12(3q29)	0 (0%)	489	0.277 (1.00)	0.233 (1.00)	1 (1.00)	0.459 (1.00)	1 (1.00)	0.246 (1.00)
Del Peak 13(4p16 3)	0 (0%)	476	0.295 (1.00)	0.0281 (1.00)	0.255 (1.00)	0.154 (1.00)	0.507 (1.00)	0.084 (1.00)
Del Peak 14(4q34 3)	0 (0%)	463	0.149 (1.00)	0.0849 (1.00)	0.0585 (1.00)	0.66 (1.00)	0.561 (1.00)	0.105 (1.00)
Del Peak 15(5q35 3)	0 (0%)	500	0.0167 (1.00)	0.171 (1.00)	1 (1.00)	0.564 (1.00)	1 (1.00)	0.431 (1.00)
Del Peak 16(6q22 31)	0 (0%)	400	0.0543 (1.00)	0.353 (1.00)	0.0974 (1.00)	0.454 (1.00)	0.122 (1.00)	0.838 (1.00)
Del Peak 17(6q26)	0 (0%)	380	0.214 (1.00)	0.713 (1.00)	0.189 (1.00)	0.702 (1.00)	0.128 (1.00)	0.692 (1.00)
Del Peak 18(8p23 2)	0 (0%)	486	0.171 (1.00)	0.0355 (1.00)	0.595 (1.00)	0.634 (1.00)	0.782 (1.00)	0.571 (1.00)
Del Peak 20(9q34 2)	0 (0%)	482	0.417 (1.00)	0.768 (1.00)	1 (1.00)	0.498 (1.00)	0.615 (1.00)	0.681 (1.00)
Del Peak 26(11p15 5)	0 (0%)	427	0.0326 (1.00)	0.00539 (1.00)	0.177 (1.00)	0.242 (1.00)	0.436 (1.00)	0.742 (1.00)
Del Peak 27(11p11 2)	0 (0%)	452	0.0771 (1.00)	0.64 (1.00)	0.144 (1.00)	0.796 (1.00)	0.197 (1.00)	0.812 (1.00)
Del Peak 28(11q14 1)	0 (0%)	458	0.763 (1.00)	0.815 (1.00)	0.297 (1.00)	0.538 (1.00)	0.382 (1.00)	0.0658 (1.00)
Del Peak 29(12p13 1)	0 (0%)	478	0.356 (1.00)	0.859 (1.00)	0.523 (1.00)	0.846 (1.00)	0.713 (1.00)	0.893 (1.00)
Del Peak 30(12q12)	0 (0%)	477	0.667 (1.00)	0.736 (1.00)	1 (1.00)	0.81 (1.00)	1 (1.00)	0.227 (1.00)
Del Peak 31(12q15)	0 (0%)	476	0.635 (1.00)	0.717 (1.00)	0.451 (1.00)	0.186 (1.00)	0.394 (1.00)	0.181 (1.00)
Del Peak 32(13q14 2)	0 (0%)	320	0.55 (1.00)	0.648 (1.00)	0.792 (1.00)	0.828 (1.00)	0.515 (1.00)	0.577 (1.00)
Del Peak 33(14q13 1)	0 (0%)	379	0.817 (1.00)	0.591 (1.00)	0.223 (1.00)	0.262 (1.00)	0.162 (1.00)	0.767 (1.00)
Del Peak 34(14q24 2)	0 (0%)	384	0.806 (1.00)	0.397 (1.00)	0.395 (1.00)	0.605 (1.00)	0.112 (1.00)	0.484 (1.00)
Del Peak 35(14q31 3)	0 (0%)	397	0.977 (1.00)	0.663 (1.00)	0.628 (1.00)	0.647 (1.00)	0.0532 (1.00)	0.609 (1.00)
Del Peak 36(15q14)	0 (0%)	405	0.447 (1.00)	0.0681 (1.00)	0.695 (1.00)	0.808 (1.00)	0.77 (1.00)	0.211 (1.00)
Del Peak 37(16p12 2)	0 (0%)	463	0.359 (1.00)	0.339 (1.00)	0.238 (1.00)	0.808 (1.00)	0.287 (1.00)	0.534 (1.00)
Del Peak 38(16q23 3)	0 (0%)	459	0.243 (1.00)	0.91 (1.00)	0.486 (1.00)	0.266 (1.00)	0.569 (1.00)	0.0141 (1.00)
Del Peak 39(17p13 2)	0 (0%)	470	0.626 (1.00)	0.504 (1.00)	0.272 (1.00)	0.189 (1.00)	1 (1.00)	0.519 (1.00)
Del Peak 40(17p13 1)	0 (0%)	460	0.807 (1.00)	0.164 (1.00)	0.0802 (1.00)	0.797 (1.00)	1 (1.00)	0.0832 (1.00)
Del Peak 41(17q11 2)	0 (0%)	484	0.585 (1.00)	0.518 (1.00)	0.895 (1.00)	0.245 (1.00)	1 (1.00)	0.035 (1.00)
Del Peak 42(18q22 3)	0 (0%)	473	0.744 (1.00)	0.63 (1.00)	0.805 (1.00)	0.128 (1.00)	1 (1.00)	0.896 (1.00)
Del Peak 43(19q13 41)	0 (0%)	454	0.058 (1.00)	0.415 (1.00)	1 (1.00)	0.264 (1.00)	0.441 (1.00)	1 (1.00)
Del Peak 44(21q22 3)	0 (0%)	493	0.699 (1.00)	0.0576 (1.00)	0.325 (1.00)	0.198 (1.00)	0.883 (1.00)	0.882 (1.00)
Del Peak 45(22q13 32)	0 (0%)	346	0.634 (1.00)	0.307 (1.00)	0.928 (1.00)	0.518 (1.00)	0.79 (1.00)	1 (1.00)
Del Peak 46(Xp22 2)	0 (0%)	430	0.252 (1.00)	0.429 (1.00)	0.676 (1.00)	0.825 (1.00)	0.308 (1.00)	0.438 (1.00)

'Amp Peak 8(7p11.2)' versus 'Time to Death'

P value = 4.01e-06 (logrank test), Q value = 0.0017

Table S1. Gene #8: 'Amp Peak 8(7p11.2)' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	552	419	0.1 - 127.6 (9.6)
AMP PEAK 8(7P11.2) CNV	484	373	0.1 - 127.6 (9.2)
AMP PEAK 8(7P11.2) WILD-TYPE	68	46	0.2 - 108.8 (13.2)

Figure S1. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 8(7p11.2)' versus 'AGE'

P value = 3.88e-09 (t-test), Q value = 1.6e-06

Table S2. Gene #8: 'Amp Peak 8(7p11.2)' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	552	57.9 (14.4)
AMP PEAK 8(7P11.2) CNV	484	59.8 (12.5)
AMP PEAK 8(7P11.2) WILD-TYPE	68	44.2 (18.8)

Figure S2. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Clinical Feature #2: 'AGE'

'Amp Peak 9(7q11.21)' versus 'Time to Death'

P value = 0.000284 (logrank test), Q value = 0.12

Table S3. Gene #9: 'Amp Peak 9(7q11.21)' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	552	419	0.1 - 127.6 (9.6)
AMP PEAK 9(7Q11.21) CNV	444	338	0.1 - 127.6 (9.2)
AMP PEAK 9(7Q11.21) WILD-TYPE	108	81	0.2 - 108.8 (11.9)

Figure S3. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 9(7q11.21)' versus 'AGE'

P value = 1.32e-07 (t-test), Q value = 5.5e-05

Table S4. Gene #9: 'Amp Peak 9(7q11.21)' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	552	57.9 (14.4)
AMP PEAK 9(7Q11.21) CNV	444	59.9 (12.4)
AMP PEAK 9(7Q11.21) WILD-TYPE	108	49.6 (18.3)

Figure S4. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Clinical Feature #2: 'AGE'

'Amp Peak 10(7q21.2)' versus 'AGE'

P value = 1.54e-05 (t-test), Q value = 0.0063

Table S5. Gene #10: 'Amp Peak 10(7q21.2)' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	552	57.9 (14.4)
AMP PEAK 10(7Q21.2) CNV	458	59.5 (12.4)
AMP PEAK 10(7Q21.2) WILD-TYPE	94	49.9 (19.9)

Figure S5. Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Clinical Feature #2: 'AGE'

'Del Peak 19(9p21.3)' versus 'AGE'

P value = 0.000356 (t-test), Q value = 0.14

Table S6. Gene #43: 'Del Peak 19(9p21.3)' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	552	57.9 (14.4)
DEL PEAK 19(9P21.3) CNV	403	59.3 (13.6)
DEL PEAK 19(9P21.3) WILD-TYPE	149	54.0 (15.8)

Figure S6. Get High-res Image Gene #43: 'Del Peak 19(9p21.3)' versus Clinical Feature #2: 'AGE'

'Del Peak 21(10p15.3)' versus 'Time to Death'

P value = 2.29e-05 (logrank test), Q value = 0.0094

Table S7. Gene #45: 'Del Peak 21(10p15.3)' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	552	419	0.1 - 127.6 (9.6)
DEL PEAK 21(10P15.3) CNV	450	347	0.1 - 92.6 (9.4)
DEL PEAK 21(10P15.3) WILD-TYPE	102	72	0.1 - 127.6 (10.6)

Figure S7. Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 21(10p15.3)' versus 'AGE'

P value = 7.27e-08 (t-test), Q value = 3e-05

Table S8. Gene #45: 'Del Peak 21(10p15.3)' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	552	57.9 (14.4)
DEL PEAK 21(10P15.3) CNV	450	59.9 (12.4)
DEL PEAK 21(10P15.3) WILD-TYPE	102	48.9 (18.4)

Figure S8. Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Clinical Feature #2: 'AGE'

'Del Peak 22(10p13)' versus 'Time to Death'

P value = 1.49e-05 (logrank test), Q value = 0.0061

Table S9. Gene #46: 'Del Peak 22(10p13)' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	552	419	0.1 - 127.6 (9.6)
DEL PEAK 22(10P13) CNV	452	348	0.1 - 92.6 (9.4)
DEL PEAK 22(10P13) WILD-TYPE	100	71	0.1 - 127.6 (10.2)

Figure S9. Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 22(10p13)' versus 'AGE'

P value = 3.45e-07 (t-test), Q value = 0.00014

Table S10. Gene #46: 'Del Peak 22(10p13)' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	552	57.9 (14.4)
DEL PEAK 22(10P13) CNV	452	59.8 (12.4)
DEL PEAK 22(10P13) WILD-TYPE	100	49.1 (18.9)

Figure S10. Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Clinical Feature #2: 'AGE'

'Del Peak 23(10p11.23)' versus 'Time to Death'

P value = 2.23e-06 (logrank test), Q value = 0.00093

Table S11. Gene #47: 'Del Peak 23(10p11.23)' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	552	419	0.1 - 127.6 (9.6)
DEL PEAK 23(10P11.23) CNV	456	350	0.1 - 92.6 (9.4)
DEL PEAK 23(10P11.23) WILD-TYPE	96	69	0.1 - 127.6 (11.7)

Figure S11. Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 23(10p11.23)' versus 'AGE'

P value = 2.12e-08 (t-test), Q value = 8.9e-06

Table S12. Gene #47: 'Del Peak 23(10p11.23)' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	552	57.9 (14.4)
DEL PEAK 23(10P11.23) CNV	456	60.0 (12.3)
DEL PEAK 23(10P11.23) WILD-TYPE	96	47.9 (18.8)

Figure S12. Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Clinical Feature #2: 'AGE'

'Del Peak 24(10q23.31)' versus 'Time to Death'

P value = 6.15e-05 (logrank test), Q value = 0.025

Table S13. Gene #48: 'Del Peak 24(10q23.31)' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	552	419	0.1 - 127.6 (9.6)
DEL PEAK 24(10Q23.31) CNV	491	377	0.1 - 127.6 (9.5)
DEL PEAK 24(10Q23.31) WILD-TYPE	61	42	0.2 - 108.8 (10.7)

Figure S13. Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 24(10q23.31)' versus 'AGE'

P value = 5.66e-06 (t-test), Q value = 0.0023

Table S14. Gene #48: 'Del Peak 24(10q23.31)' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	552	57.9 (14.4)
DEL PEAK 24(10Q23.31) CNV	491	59.3 (13.1)
DEL PEAK 24(10Q23.31) WILD-TYPE	61	47.0 (18.9)

Figure S14. Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Clinical Feature #2: 'AGE'

'Del Peak 25(10q26.3)' versus 'AGE'

P value = 5.33e-05 (t-test), Q value = 0.022

Table S15. Gene #49: 'Del Peak 25(10q26.3)' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	552	57.9 (14.4)
DEL PEAK 25(10Q26.3) CNV	492	59.1 (13.3)
DEL PEAK 25(10Q26.3) WILD-TYPE	60	48.2 (19.0)

Figure S15. Get High-res Image Gene #49: 'Del Peak 25(10q26.3)' versus Clinical Feature #2: 'AGE'

Methods & Data

Input

Mutation data file = all_lesions.conf_99.cnv.cluster.txt
Clinical data file = GBM-TP.clin.merged.picked.txt
Number of patients = 552
Number of significantly arm-level cnvs = 70
Number of selected clinical features = 6
Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.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] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)

[3] 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)

[4] 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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