Stomach Adenocarcinoma: Correlation between copy number variations of arm-level result and selected clinical features<BR>(primary solid tumor cohort)

Stomach Adenocarcinoma: Correlation between copy number variations of arm-level result and selected clinical features
(primary solid tumor cohort)

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 74 arm-level results and 11 clinical features across 177 patients, 5 significant findings detected with Q value < 0.25.

2p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
2q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
20p gain cnv correlated to 'GENDER'.
20q gain cnv correlated to 'GENDER'.
3q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 74 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 5 significant findings detected.


		Clinical Features	Time to Death	AGE	GENDER	HISTOLOGICAL TYPE	PATHOLOGY T	PATHOLOGY N	PATHOLOGICSPREAD(M)	TUMOR STAGE	RADIATIONS RADIATION REGIMENINDICATION	COMPLETENESS OF RESECTION	NUMBER OF LYMPH NODES
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	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	t-test
2p gain	11 (6%)	166	0.695 (1.00)	0.288 (1.00)	0.53 (1.00)	0.537 (1.00)	0.278 (1.00)	0.171 (1.00)	1 (1.00)	0.0193 (1.00)	1 (1.00)	0.511 (1.00)	3.37e-05 (0.0269)
2q gain	13 (7%)	164	0.344 (1.00)	0.648 (1.00)	0.57 (1.00)	0.508 (1.00)	0.491 (1.00)	0.108 (1.00)	1 (1.00)	0.0555 (1.00)	1 (1.00)	0.928 (1.00)	3.85e-07 (0.000308)
20p gain	67 (38%)	110	0.181 (1.00)	0.143 (1.00)	7.09e-05 (0.0564)	0.756 (1.00)	0.026 (1.00)	0.424 (1.00)	0.117 (1.00)	0.12 (1.00)	0.651 (1.00)	0.204 (1.00)	0.528 (1.00)
20q gain	81 (46%)	96	0.147 (1.00)	0.0703 (1.00)	6e-05 (0.0478)	0.339 (1.00)	0.000551 (0.437)	0.251 (1.00)	0.0306 (1.00)	0.105 (1.00)	1 (1.00)	0.508 (1.00)	0.129 (1.00)
3q loss	9 (5%)	168	0.633 (1.00)	0.865 (1.00)	0.0897 (1.00)	0.968 (1.00)	0.826 (1.00)	0.749 (1.00)	0.484 (1.00)	0.81 (1.00)	1 (1.00)	0.626 (1.00)	0.000145 (0.115)
1p gain	9 (5%)	168	0.686 (1.00)	0.292 (1.00)	0.486 (1.00)	0.407 (1.00)	0.66 (1.00)	0.822 (1.00)	0.484 (1.00)	0.75 (1.00)	1 (1.00)	0.136 (1.00)	0.625 (1.00)
1q gain	24 (14%)	153	0.975 (1.00)	0.155 (1.00)	0.177 (1.00)	0.398 (1.00)	0.536 (1.00)	0.252 (1.00)	0.103 (1.00)	0.773 (1.00)	0.137 (1.00)	0.611 (1.00)	0.229 (1.00)
3p gain	3 (2%)	174		0.719 (1.00)	1 (1.00)	0.811 (1.00)	1 (1.00)	0.863 (1.00)	1 (1.00)	0.493 (1.00)	1 (1.00)	0.17 (1.00)	0.901 (1.00)
3q gain	14 (8%)	163	0.373 (1.00)	0.0236 (1.00)	0.0094 (1.00)	0.568 (1.00)	1 (1.00)	0.577 (1.00)	0.54 (1.00)	1 (1.00)	1 (1.00)	0.732 (1.00)	0.453 (1.00)
4p gain	3 (2%)	174		0.119 (1.00)	0.279 (1.00)		0.0374 (1.00)	0.863 (1.00)	1 (1.00)	0.22 (1.00)	1 (1.00)	0.239 (1.00)
5p gain	26 (15%)	151	0.973 (1.00)	0.517 (1.00)	0.194 (1.00)	0.409 (1.00)	0.826 (1.00)	0.872 (1.00)	0.211 (1.00)	0.0172 (1.00)	0.157 (1.00)	0.233 (1.00)	0.33 (1.00)
5q gain	7 (4%)	170	0.145 (1.00)	0.691 (1.00)	0.247 (1.00)	0.104 (1.00)	0.844 (1.00)	0.671 (1.00)	1 (1.00)	0.5 (1.00)	1 (1.00)	0.832 (1.00)	0.00991 (1.00)
6p gain	13 (7%)	164	0.755 (1.00)	0.866 (1.00)	0.769 (1.00)	0.64 (1.00)	0.586 (1.00)	0.599 (1.00)	1 (1.00)	0.343 (1.00)	0.32 (1.00)	0.426 (1.00)	0.111 (1.00)
6q gain	13 (7%)	164	0.755 (1.00)	0.866 (1.00)	0.769 (1.00)	0.64 (1.00)	0.586 (1.00)	0.599 (1.00)	1 (1.00)	0.343 (1.00)	0.32 (1.00)	0.426 (1.00)	0.111 (1.00)
7p gain	53 (30%)	124	0.454 (1.00)	0.0135 (1.00)	0.131 (1.00)	0.365 (1.00)	0.357 (1.00)	0.382 (1.00)	0.62 (1.00)	0.187 (1.00)	0.636 (1.00)	0.763 (1.00)	0.984 (1.00)
7q gain	48 (27%)	129	0.645 (1.00)	0.00698 (1.00)	0.388 (1.00)	0.367 (1.00)	0.165 (1.00)	0.459 (1.00)	0.201 (1.00)	0.169 (1.00)	1 (1.00)	0.786 (1.00)	0.711 (1.00)
8p gain	49 (28%)	128	0.681 (1.00)	0.00825 (1.00)	0.232 (1.00)	0.491 (1.00)	0.0291 (1.00)	0.67 (1.00)	0.125 (1.00)	0.472 (1.00)	0.131 (1.00)	0.0783 (1.00)	0.51 (1.00)
8q gain	69 (39%)	108	0.514 (1.00)	0.00427 (1.00)	0.432 (1.00)	0.416 (1.00)	0.00382 (1.00)	0.209 (1.00)	0.32 (1.00)	0.222 (1.00)	0.379 (1.00)	0.0656 (1.00)	0.314 (1.00)
9p gain	14 (8%)	163	0.513 (1.00)	0.977 (1.00)	0.41 (1.00)	0.7 (1.00)	0.113 (1.00)	0.358 (1.00)	0.634 (1.00)	0.0285 (1.00)	0.341 (1.00)	0.591 (1.00)	0.224 (1.00)
9q gain	18 (10%)	159	0.53 (1.00)	0.664 (1.00)	0.8 (1.00)	0.895 (1.00)	0.29 (1.00)	0.355 (1.00)	0.548 (1.00)	0.252 (1.00)	0.419 (1.00)	0.765 (1.00)	0.742 (1.00)
10p gain	26 (15%)	151	0.891 (1.00)	0.211 (1.00)	0.667 (1.00)	0.128 (1.00)	0.624 (1.00)	0.56 (1.00)	0.588 (1.00)	0.0768 (1.00)	1 (1.00)	0.281 (1.00)	0.685 (1.00)
10q gain	14 (8%)	163	0.754 (1.00)	0.454 (1.00)	1 (1.00)	0.342 (1.00)	0.841 (1.00)	0.735 (1.00)	0.742 (1.00)	0.716 (1.00)	1 (1.00)	0.518 (1.00)	0.838 (1.00)
11p gain	5 (3%)	172	0.54 (1.00)	0.792 (1.00)	0.649 (1.00)	0.54 (1.00)	0.389 (1.00)	0.529 (1.00)	1 (1.00)	0.75 (1.00)	1 (1.00)	0.218 (1.00)	0.599 (1.00)
11q gain	9 (5%)	168	0.193 (1.00)	0.85 (1.00)	1 (1.00)	0.701 (1.00)	0.826 (1.00)	0.749 (1.00)	0.802 (1.00)	0.867 (1.00)	1 (1.00)	0.567 (1.00)	0.0791 (1.00)
12p gain	17 (10%)	160	0.257 (1.00)	0.493 (1.00)	0.0677 (1.00)	0.996 (1.00)	0.465 (1.00)	0.539 (1.00)	0.255 (1.00)	0.715 (1.00)	1 (1.00)	0.35 (1.00)	0.204 (1.00)
12q gain	12 (7%)	165	0.673 (1.00)	0.0312 (1.00)	0.369 (1.00)	0.285 (1.00)	0.718 (1.00)	0.0866 (1.00)	1 (1.00)	0.885 (1.00)	0.299 (1.00)	0.324 (1.00)	0.795 (1.00)
13q gain	34 (19%)	143	0.586 (1.00)	0.784 (1.00)	0.436 (1.00)	0.346 (1.00)	0.838 (1.00)	0.326 (1.00)	0.45 (1.00)	0.866 (1.00)	1 (1.00)	0.86 (1.00)	0.326 (1.00)
15q gain	7 (4%)	170	0.151 (1.00)	0.4 (1.00)	0.0431 (1.00)	0.944 (1.00)	1 (1.00)	0.0623 (1.00)	0.747 (1.00)	0.616 (1.00)	1 (1.00)	0.804 (1.00)	0.561 (1.00)
16p gain	12 (7%)	165	0.572 (1.00)	0.801 (1.00)	0.766 (1.00)	0.563 (1.00)	0.546 (1.00)	0.0924 (1.00)	0.15 (1.00)	0.00573 (1.00)	0.299 (1.00)	1 (1.00)	0.237 (1.00)
16q gain	8 (5%)	169	0.685 (1.00)	0.998 (1.00)	1 (1.00)	0.836 (1.00)	0.132 (1.00)	0.471 (1.00)	0.193 (1.00)	0.00909 (1.00)	1 (1.00)	0.86 (1.00)	0.796 (1.00)
17p gain	5 (3%)	172	0.00798 (1.00)	0.724 (1.00)	1 (1.00)	0.577 (1.00)	0.878 (1.00)	0.0131 (1.00)	0.012 (1.00)	0.0775 (1.00)	1 (1.00)	0.00862 (1.00)	0.179 (1.00)
17q gain	10 (6%)	167	0.276 (1.00)	0.416 (1.00)	0.742 (1.00)	0.969 (1.00)	0.761 (1.00)	0.234 (1.00)	0.0231 (1.00)	0.198 (1.00)	1 (1.00)	0.0502 (1.00)	0.325 (1.00)
18p gain	16 (9%)	161	0.657 (1.00)	0.262 (1.00)	1 (1.00)	0.842 (1.00)	0.869 (1.00)	0.0618 (1.00)	0.507 (1.00)	0.31 (1.00)	0.381 (1.00)	0.364 (1.00)	0.261 (1.00)
18q gain	9 (5%)	168	0.635 (1.00)	0.95 (1.00)	0.741 (1.00)	0.369 (1.00)	0.75 (1.00)	0.308 (1.00)	0.0607 (1.00)	0.709 (1.00)	1 (1.00)	0.123 (1.00)	0.603 (1.00)
19p gain	10 (6%)	167	0.943 (1.00)	0.274 (1.00)	0.015 (1.00)	0.645 (1.00)	0.725 (1.00)	0.0501 (1.00)	0.0231 (1.00)	0.0341 (1.00)	1 (1.00)	0.00116 (0.916)	0.033 (1.00)
19q gain	17 (10%)	160	0.257 (1.00)	0.108 (1.00)	0.117 (1.00)	0.603 (1.00)	0.43 (1.00)	0.106 (1.00)	0.129 (1.00)	0.0124 (1.00)	0.4 (1.00)	0.0101 (1.00)	0.0375 (1.00)
22q gain	3 (2%)	174	0.745 (1.00)	0.348 (1.00)	1 (1.00)	0.955 (1.00)	0.805 (1.00)	0.443 (1.00)	1 (1.00)	0.22 (1.00)	1 (1.00)	1 (1.00)
1p loss	8 (5%)	169	0.121 (1.00)	0.522 (1.00)	0.267 (1.00)	0.889 (1.00)	0.3 (1.00)	0.4 (1.00)	0.000648 (0.513)	0.00324 (1.00)	1 (1.00)	0.00292 (1.00)	0.374 (1.00)
1q loss	3 (2%)	174	0.585 (1.00)	0.098 (1.00)	0.563 (1.00)	0.245 (1.00)	1 (1.00)	0.605 (1.00)	0.0421 (1.00)	0.177 (1.00)	1 (1.00)	0.357 (1.00)	0.535 (1.00)
2q loss	3 (2%)	174			0.563 (1.00)		0.805 (1.00)	0.384 (1.00)	0.231 (1.00)	0.313 (1.00)	0.0828 (1.00)
3p loss	15 (8%)	162	0.78 (1.00)	0.586 (1.00)	0.41 (1.00)	0.993 (1.00)	1 (1.00)	0.243 (1.00)	0.563 (1.00)	0.749 (1.00)	1 (1.00)	0.317 (1.00)	0.0332 (1.00)
4p loss	27 (15%)	150	0.341 (1.00)	0.33 (1.00)	0.527 (1.00)	0.13 (1.00)	0.0247 (1.00)	0.739 (1.00)	0.412 (1.00)	0.0475 (1.00)	0.167 (1.00)	0.144 (1.00)	0.108 (1.00)
4q loss	25 (14%)	152	0.741 (1.00)	0.95 (1.00)	1 (1.00)	0.0343 (1.00)	0.0998 (1.00)	0.857 (1.00)	1 (1.00)	0.232 (1.00)	0.147 (1.00)	0.238 (1.00)	0.416 (1.00)
5p loss	8 (5%)	169	0.68 (1.00)	0.646 (1.00)	0.482 (1.00)	0.345 (1.00)	0.844 (1.00)	0.0423 (1.00)	0.579 (1.00)	0.242 (1.00)	1 (1.00)	1 (1.00)	0.815 (1.00)
5q loss	17 (10%)	160	0.324 (1.00)	0.248 (1.00)	0.0677 (1.00)	0.0305 (1.00)	0.105 (1.00)	0.809 (1.00)	0.295 (1.00)	0.205 (1.00)	0.4 (1.00)	0.384 (1.00)	0.884 (1.00)
6p loss	10 (6%)	167	0.701 (1.00)	0.13 (1.00)	1 (1.00)	0.0497 (1.00)	0.309 (1.00)	0.0221 (1.00)	0.819 (1.00)	0.128 (1.00)	1 (1.00)	0.907 (1.00)	0.612 (1.00)
6q loss	15 (8%)	162	0.897 (1.00)	0.327 (1.00)	0.41 (1.00)	0.312 (1.00)	0.361 (1.00)	0.134 (1.00)	0.563 (1.00)	0.00931 (1.00)	1 (1.00)	0.764 (1.00)	0.81 (1.00)
7p loss	3 (2%)	174	0.224 (1.00)	0.236 (1.00)	0.279 (1.00)	0.663 (1.00)	0.0936 (1.00)	0.0847 (1.00)	1 (1.00)	0.366 (1.00)	1 (1.00)	1 (1.00)
7q loss	6 (3%)	171	0.217 (1.00)	0.253 (1.00)	0.0825 (1.00)	0.278 (1.00)	0.291 (1.00)	0.237 (1.00)	0.454 (1.00)	1 (1.00)	1 (1.00)	0.804 (1.00)	0.395 (1.00)
8p loss	15 (8%)	162	0.799 (1.00)	0.128 (1.00)	0.166 (1.00)	0.0897 (1.00)	0.346 (1.00)	0.366 (1.00)	0.158 (1.00)	0.682 (1.00)	1 (1.00)	1 (1.00)	0.00621 (1.00)
8q loss	3 (2%)	174		0.412 (1.00)	1 (1.00)	0.00187 (1.00)			1 (1.00)		1 (1.00)	0.17 (1.00)
9p loss	30 (17%)	147	0.189 (1.00)	0.629 (1.00)	0.307 (1.00)	0.449 (1.00)	0.0543 (1.00)	0.706 (1.00)	0.675 (1.00)	0.928 (1.00)	1 (1.00)	0.86 (1.00)	0.285 (1.00)
9q loss	13 (7%)	164	0.847 (1.00)	0.163 (1.00)	0.251 (1.00)	0.615 (1.00)	0.248 (1.00)	0.346 (1.00)	0.0678 (1.00)	0.653 (1.00)	0.32 (1.00)	0.649 (1.00)	0.214 (1.00)
10p loss	12 (7%)	165	0.211 (1.00)	0.376 (1.00)	0.128 (1.00)	0.0417 (1.00)	0.203 (1.00)	0.814 (1.00)	0.7 (1.00)	0.521 (1.00)	0.0377 (1.00)	0.642 (1.00)	0.619 (1.00)
10q loss	10 (6%)	167	0.264 (1.00)	0.426 (1.00)	0.742 (1.00)	0.0113 (1.00)	0.19 (1.00)	0.965 (1.00)	0.528 (1.00)	0.307 (1.00)	0.255 (1.00)	1 (1.00)	0.834 (1.00)
11p loss	13 (7%)	164	0.0844 (1.00)	0.299 (1.00)	0.769 (1.00)	0.367 (1.00)	0.129 (1.00)	0.644 (1.00)	0.053 (1.00)	0.555 (1.00)	1 (1.00)	0.0102 (1.00)	0.327 (1.00)
11q loss	11 (6%)	166	0.0607 (1.00)	0.594 (1.00)	0.204 (1.00)	0.599 (1.00)	0.259 (1.00)	0.67 (1.00)	0.451 (1.00)	0.91 (1.00)	1 (1.00)	0.17 (1.00)	0.353 (1.00)
12p loss	12 (7%)	165	0.158 (1.00)	0.953 (1.00)	0.369 (1.00)	0.179 (1.00)	0.0587 (1.00)	0.000932 (0.737)	0.7 (1.00)	0.00831 (1.00)	1 (1.00)	0.518 (1.00)	0.769 (1.00)
12q loss	8 (5%)	169	0.36 (1.00)	0.467 (1.00)	0.149 (1.00)	0.448 (1.00)	0.147 (1.00)	0.0372 (1.00)	0.579 (1.00)	0.231 (1.00)	1 (1.00)	0.832 (1.00)	0.863 (1.00)
13q loss	5 (3%)	172	0.699 (1.00)	0.647 (1.00)	1 (1.00)	0.546 (1.00)	0.606 (1.00)	0.588 (1.00)	0.211 (1.00)	0.457 (1.00)	0.135 (1.00)	0.0778 (1.00)	0.542 (1.00)
14q loss	14 (8%)	163	0.679 (1.00)	0.147 (1.00)	1 (1.00)	0.944 (1.00)	0.924 (1.00)	0.291 (1.00)	0.268 (1.00)	0.613 (1.00)	1 (1.00)	0.931 (1.00)	0.459 (1.00)
15q loss	12 (7%)	165	0.823 (1.00)	0.488 (1.00)	1 (1.00)	0.0295 (1.00)	0.106 (1.00)	0.343 (1.00)	1 (1.00)	0.309 (1.00)	0.0377 (1.00)	0.642 (1.00)	0.501 (1.00)
16p loss	11 (6%)	166	0.605 (1.00)	0.211 (1.00)	0.204 (1.00)	0.252 (1.00)	0.239 (1.00)	0.801 (1.00)	1 (1.00)	0.867 (1.00)	0.277 (1.00)	0.0914 (1.00)	0.399 (1.00)
16q loss	15 (8%)	162	0.532 (1.00)	0.583 (1.00)	0.41 (1.00)	0.572 (1.00)	0.234 (1.00)	0.545 (1.00)	1 (1.00)	0.955 (1.00)	0.361 (1.00)	0.179 (1.00)	0.194 (1.00)
17p loss	32 (18%)	145	0.904 (1.00)	0.81 (1.00)	0.324 (1.00)	0.00783 (1.00)	0.0765 (1.00)	0.657 (1.00)	0.638 (1.00)	0.257 (1.00)	0.0418 (1.00)	0.15 (1.00)	0.314 (1.00)
17q loss	11 (6%)	166	0.49 (1.00)	0.837 (1.00)	0.755 (1.00)	0.0564 (1.00)	1 (1.00)	0.753 (1.00)	0.116 (1.00)	0.685 (1.00)	0.277 (1.00)	0.407 (1.00)	0.0775 (1.00)
18p loss	14 (8%)	163	0.424 (1.00)	0.818 (1.00)	1 (1.00)	0.984 (1.00)	0.464 (1.00)	0.515 (1.00)	0.742 (1.00)	0.129 (1.00)	1 (1.00)	0.169 (1.00)	0.374 (1.00)
18q loss	27 (15%)	150	0.26 (1.00)	0.431 (1.00)	0.527 (1.00)	0.917 (1.00)	0.408 (1.00)	0.503 (1.00)	0.293 (1.00)	0.254 (1.00)	1 (1.00)	0.0141 (1.00)	0.256 (1.00)
19p loss	18 (10%)	159	0.83 (1.00)	0.721 (1.00)	0.133 (1.00)	0.324 (1.00)	0.577 (1.00)	0.342 (1.00)	1 (1.00)	0.672 (1.00)	1 (1.00)	0.485 (1.00)	0.322 (1.00)
19q loss	13 (7%)	164	0.844 (1.00)	0.11 (1.00)	0.251 (1.00)	0.269 (1.00)	0.319 (1.00)	0.252 (1.00)	0.721 (1.00)	0.209 (1.00)	1 (1.00)	0.485 (1.00)	0.43 (1.00)
20p loss	5 (3%)	172	0.295 (1.00)	0.79 (1.00)	0.0806 (1.00)	0.747 (1.00)	0.217 (1.00)	0.272 (1.00)	0.124 (1.00)	0.0571 (1.00)	0.135 (1.00)	0.00548 (1.00)	0.528 (1.00)
21q loss	30 (17%)	147	0.495 (1.00)	0.225 (1.00)	1 (1.00)	0.84 (1.00)	0.547 (1.00)	0.701 (1.00)	0.794 (1.00)	0.569 (1.00)	1 (1.00)	0.129 (1.00)	0.266 (1.00)
22q loss	25 (14%)	152	0.299 (1.00)	0.925 (1.00)	0.826 (1.00)	0.175 (1.00)	0.592 (1.00)	0.815 (1.00)	0.146 (1.00)	0.708 (1.00)	0.537 (1.00)	0.382 (1.00)	0.359 (1.00)
Xq loss	6 (3%)	171	0.141 (1.00)	0.388 (1.00)	1 (1.00)	0.796 (1.00)	0.195 (1.00)	0.272 (1.00)	1 (1.00)	0.225 (1.00)	0.16 (1.00)	0.0117 (1.00)	0.749 (1.00)

'2p gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.37e-05 (t-test), Q value = 0.027

Table S1. Gene #3: '2p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	133	4.0 (5.7)
2P GAIN MUTATED	7	0.7 (1.3)
2P GAIN WILD-TYPE	126	4.2 (5.8)

Figure S1. Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'2q gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.85e-07 (t-test), Q value = 0.00031

Table S2. Gene #4: '2q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	133	4.0 (5.7)
2Q GAIN MUTATED	9	0.6 (1.1)
2Q GAIN WILD-TYPE	124	4.3 (5.8)

Figure S2. Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'20p gain mutation analysis' versus 'GENDER'

P value = 7.09e-05 (Fisher's exact test), Q value = 0.056

Table S3. Gene #34: '20p gain mutation analysis' versus Clinical Feature #3: 'GENDER'

nPatients	FEMALE	MALE
ALL	70	107
20P GAIN MUTATED	14	53
20P GAIN WILD-TYPE	56	54

Figure S3. Get High-res Image Gene #34: '20p gain mutation analysis' versus Clinical Feature #3: 'GENDER'

'20q gain mutation analysis' versus 'GENDER'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S4. Gene #35: '20q gain mutation analysis' versus Clinical Feature #3: 'GENDER'

nPatients	FEMALE	MALE
ALL	70	107
20Q GAIN MUTATED	19	62
20Q GAIN WILD-TYPE	51	45

Figure S4. Get High-res Image Gene #35: '20q gain mutation analysis' versus Clinical Feature #3: 'GENDER'

'3q loss mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000145 (t-test), Q value = 0.12

Table S5. Gene #41: '3q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	133	4.0 (5.7)
3Q LOSS MUTATED	7	1.1 (1.2)
3Q LOSS WILD-TYPE	126	4.2 (5.8)

Figure S5. Get High-res Image Gene #41: '3q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

Methods & Data

Input

Mutation data file = broad_values_by_arm.mutsig.cluster.txt
Clinical data file = STAD-TP.clin.merged.picked.txt
Number of patients = 177
Number of significantly arm-level cnvs = 74
Number of selected clinical features = 11
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

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

[5] 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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