Correlation between copy number variations of arm-level result and molecular subtypes

Adrenocortical Carcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

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 (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ZS2V51

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 80 arm-level events and 8 molecular subtypes across 90 patients, 54 significant findings detected with P value < 0.05 and Q value < 0.25.

2p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
4p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
4q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
5p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
5q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
7p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
7q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
9p gain cnv correlated to 'CN_CNMF'.
9q gain cnv correlated to 'CN_CNMF'.
10p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
10q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
12p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
12q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
14q gain cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
16q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
19p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
19q gain cnv correlated to 'MRNASEQ_CNMF'.
20p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
20q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
xq gain cnv correlated to 'CN_CNMF'.
2q loss cnv correlated to 'CN_CNMF'.
9p loss cnv correlated to 'MRNASEQ_CNMF'.
11q loss cnv correlated to 'CN_CNMF'.
17p loss cnv correlated to 'METHLYATION_CNMF'.
17q loss cnv correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 54 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE 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
14q gain	21 (23%)	69	0.0141 (1.00)	0.0557 (1.00)	0.00038 (0.208)	0.00082 (0.44)	2e-05 (0.0117)	0.00014 (0.0784)	2e-05 (0.0117)	2e-05 (0.0117)
20p gain	46 (51%)	44	1e-05 (0.00598)	0.236 (1.00)	9e-05 (0.0509)	0.00014 (0.0784)	0.00495 (1.00)	0.0912 (1.00)	0.00013 (0.0729)	0.00372 (1.00)
4p gain	37 (41%)	53	3e-05 (0.0174)	0.0438 (1.00)	5e-05 (0.0287)	5e-05 (0.0287)	0.295 (1.00)	0.00193 (0.998)	0.688 (1.00)	0.146 (1.00)
4q gain	33 (37%)	57	7e-05 (0.0399)	0.0363 (1.00)	3e-05 (0.0174)	1e-05 (0.00598)	0.559 (1.00)	0.00082 (0.44)	0.588 (1.00)	0.0892 (1.00)
7q gain	48 (53%)	42	2e-05 (0.0117)	0.116 (1.00)	1e-05 (0.00598)	0.0001 (0.0565)	0.915 (1.00)	0.331 (1.00)	1 (1.00)	0.18 (1.00)
12p gain	64 (71%)	26	2e-05 (0.0117)	0.209 (1.00)	0.00022 (0.122)	5e-05 (0.0287)	0.246 (1.00)	0.209 (1.00)	0.0698 (1.00)	0.12 (1.00)
16p gain	49 (54%)	41	1e-05 (0.00598)	0.0107 (1.00)	1e-05 (0.00598)	1e-05 (0.00598)	0.0466 (1.00)	0.0262 (1.00)	0.0122 (1.00)	0.169 (1.00)
16q gain	47 (52%)	43	1e-05 (0.00598)	0.00825 (1.00)	0.00012 (0.0676)	1e-05 (0.00598)	0.024 (1.00)	0.0131 (1.00)	0.0118 (1.00)	0.144 (1.00)
20q gain	49 (54%)	41	2e-05 (0.0117)	0.0649 (1.00)	7e-05 (0.0399)	0.00025 (0.138)	0.0194 (1.00)	0.275 (1.00)	0.00098 (0.522)	0.0334 (1.00)
2p gain	13 (14%)	77	0.00026 (0.143)	0.00112 (0.594)	0.0118 (1.00)	0.00014 (0.0784)	0.373 (1.00)	0.0185 (1.00)	0.0799 (1.00)	0.0468 (1.00)
5p gain	57 (63%)	33	1e-05 (0.00598)	0.0365 (1.00)	0.00058 (0.314)	1e-05 (0.00598)	0.251 (1.00)	0.227 (1.00)	0.0674 (1.00)	0.342 (1.00)
5q gain	53 (59%)	37	3e-05 (0.0174)	0.00886 (1.00)	0.00071 (0.383)	3e-05 (0.0174)	0.334 (1.00)	0.135 (1.00)	0.37 (1.00)	0.388 (1.00)
7p gain	48 (53%)	42	0.00042 (0.23)	0.118 (1.00)	0.00012 (0.0676)	0.00133 (0.698)	0.914 (1.00)	0.55 (1.00)	0.874 (1.00)	0.314 (1.00)
10p gain	25 (28%)	65	0.00079 (0.424)	0.0588 (1.00)	3e-05 (0.0174)	0.00019 (0.106)	0.0337 (1.00)	0.511 (1.00)	0.104 (1.00)	0.667 (1.00)
10q gain	26 (29%)	64	0.00057 (0.309)	0.0712 (1.00)	4e-05 (0.023)	0.00045 (0.246)	0.0203 (1.00)	0.34 (1.00)	0.0698 (1.00)	0.651 (1.00)
12q gain	64 (71%)	26	1e-05 (0.00598)	0.311 (1.00)	0.00068 (0.367)	0.00014 (0.0784)	0.236 (1.00)	0.455 (1.00)	0.0425 (1.00)	0.207 (1.00)
9p gain	20 (22%)	70	7e-05 (0.0399)	0.0023 (1.00)	0.00932 (1.00)	0.0112 (1.00)	0.385 (1.00)	0.55 (1.00)	0.237 (1.00)	0.63 (1.00)
9q gain	29 (32%)	61	0.00019 (0.106)	0.00121 (0.639)	0.023 (1.00)	0.00169 (0.879)	0.0342 (1.00)	0.354 (1.00)	0.0172 (1.00)	0.36 (1.00)
19p gain	56 (62%)	34	0.00757 (1.00)	0.0549 (1.00)	0.00133 (0.698)	0.00045 (0.246)	0.466 (1.00)	0.471 (1.00)	0.37 (1.00)	0.626 (1.00)
19q gain	52 (58%)	38	0.00051 (0.277)	0.0498 (1.00)	0.00036 (0.198)	0.00114 (0.603)	0.143 (1.00)	0.11 (1.00)	0.101 (1.00)	0.192 (1.00)
xq gain	40 (44%)	50	1e-05 (0.00598)	0.169 (1.00)	0.00166 (0.865)	0.0085 (1.00)	0.797 (1.00)	0.151 (1.00)	0.611 (1.00)	0.0617 (1.00)
2q loss	15 (17%)	75	0.0001 (0.0565)	0.00106 (0.564)	0.113 (1.00)	0.0535 (1.00)	0.0313 (1.00)	0.729 (1.00)	0.115 (1.00)	0.835 (1.00)
9p loss	20 (22%)	70	0.00127 (0.668)	0.0479 (1.00)	6e-05 (0.0343)	0.00125 (0.659)	0.0092 (1.00)	0.137 (1.00)	0.0587 (1.00)	0.204 (1.00)
11q loss	23 (26%)	67	8e-05 (0.0454)	0.00271 (1.00)	0.133 (1.00)	0.128 (1.00)	0.104 (1.00)	0.824 (1.00)	0.217 (1.00)	0.899 (1.00)
17p loss	32 (36%)	58	0.00109 (0.579)	0.00019 (0.106)	0.0117 (1.00)	0.0135 (1.00)	0.0812 (1.00)	0.00286 (1.00)	0.0508 (1.00)	0.0141 (1.00)
17q loss	24 (27%)	66	0.00028 (0.154)	0.00541 (1.00)	0.12 (1.00)	0.0334 (1.00)	0.0666 (1.00)	0.0199 (1.00)	0.0759 (1.00)	0.182 (1.00)
1p gain	4 (4%)	86	0.119 (1.00)
1q gain	8 (9%)	82	0.12 (1.00)	0.654 (1.00)	0.0467 (1.00)	0.0776 (1.00)	0.0647 (1.00)	0.242 (1.00)	0.298 (1.00)	0.23 (1.00)
2q gain	12 (13%)	78	0.0037 (1.00)	0.00225 (1.00)	0.018 (1.00)	0.00263 (1.00)	0.0556 (1.00)	0.00431 (1.00)	0.0196 (1.00)	0.00352 (1.00)
3p gain	13 (14%)	77	0.0925 (1.00)	0.0687 (1.00)	0.329 (1.00)	0.362 (1.00)	0.409 (1.00)	0.107 (1.00)	0.31 (1.00)	0.601 (1.00)
3q gain	15 (17%)	75	0.0599 (1.00)	0.0518 (1.00)	0.0521 (1.00)	0.793 (1.00)	0.652 (1.00)	0.246 (1.00)	0.56 (1.00)	0.856 (1.00)
6p gain	18 (20%)	72	0.0617 (1.00)	0.683 (1.00)	0.0671 (1.00)	0.472 (1.00)	0.162 (1.00)	0.0549 (1.00)	0.209 (1.00)	0.0253 (1.00)
6q gain	16 (18%)	74	0.00232 (1.00)	0.458 (1.00)	0.199 (1.00)	0.294 (1.00)	0.298 (1.00)	0.196 (1.00)	0.26 (1.00)	0.161 (1.00)
8p gain	32 (36%)	58	0.00177 (0.917)	0.139 (1.00)	0.167 (1.00)	0.145 (1.00)	0.113 (1.00)	0.174 (1.00)	0.0261 (1.00)	0.0605 (1.00)
8q gain	38 (42%)	52	0.0187 (1.00)	0.291 (1.00)	0.416 (1.00)	0.231 (1.00)	0.496 (1.00)	0.261 (1.00)	0.0963 (1.00)	0.121 (1.00)
11p gain	5 (6%)	85	0.111 (1.00)
11q gain	6 (7%)	84	0.174 (1.00)	0.176 (1.00)	0.0443 (1.00)	0.0787 (1.00)	0.187 (1.00)	0.371 (1.00)	0.445 (1.00)	0.16 (1.00)
13q gain	6 (7%)	84	1 (1.00)	0.464 (1.00)	0.0385 (1.00)	0.639 (1.00)	0.14 (1.00)	0.913 (1.00)	0.3 (1.00)	0.394 (1.00)
15q gain	11 (12%)	79	0.215 (1.00)	0.0454 (1.00)	0.0105 (1.00)	0.00482 (1.00)	0.361 (1.00)	0.00073 (0.393)	0.248 (1.00)	0.00583 (1.00)
17p gain	5 (6%)	85	0.0883 (1.00)	0.337 (1.00)	0.685 (1.00)	0.144 (1.00)	0.205 (1.00)	0.794 (1.00)	0.141 (1.00)	0.929 (1.00)
17q gain	7 (8%)	83	0.0145 (1.00)	0.338 (1.00)	0.689 (1.00)	0.144 (1.00)	0.211 (1.00)	0.793 (1.00)	0.14 (1.00)	0.928 (1.00)
18p gain	6 (7%)	84	0.493 (1.00)
18q gain	5 (6%)	85	0.66 (1.00)
21q gain	31 (34%)	59	0.0371 (1.00)	0.00888 (1.00)	0.0195 (1.00)	0.00091 (0.486)	0.0131 (1.00)	0.0205 (1.00)	0.0259 (1.00)	0.154 (1.00)
22q gain	3 (3%)	87	0.375 (1.00)
1p loss	29 (32%)	61	0.202 (1.00)	0.141 (1.00)	0.438 (1.00)	0.065 (1.00)	0.469 (1.00)	0.41 (1.00)	0.784 (1.00)	0.406 (1.00)
1q loss	20 (22%)	70	0.584 (1.00)	0.0891 (1.00)	0.962 (1.00)	0.601 (1.00)	0.367 (1.00)	0.841 (1.00)	0.594 (1.00)	0.609 (1.00)
2p loss	17 (19%)	73	0.00056 (0.304)	0.0272 (1.00)	0.612 (1.00)	0.267 (1.00)	0.0377 (1.00)	0.769 (1.00)	0.127 (1.00)	0.76 (1.00)
3p loss	20 (22%)	70	0.0597 (1.00)	0.143 (1.00)	0.112 (1.00)	0.135 (1.00)	0.523 (1.00)	0.391 (1.00)	0.195 (1.00)	0.306 (1.00)
3q loss	20 (22%)	70	0.0164 (1.00)	0.166 (1.00)	0.0222 (1.00)	0.0292 (1.00)	0.193 (1.00)	0.338 (1.00)	0.0403 (1.00)	0.185 (1.00)
4p loss	10 (11%)	80	0.0168 (1.00)	0.234 (1.00)	0.0234 (1.00)	0.081 (1.00)	0.308 (1.00)	0.931 (1.00)	0.424 (1.00)	0.903 (1.00)
4q loss	11 (12%)	79	0.0469 (1.00)	0.0975 (1.00)	0.0075 (1.00)	0.0277 (1.00)	0.252 (1.00)	0.81 (1.00)	0.383 (1.00)	0.761 (1.00)
5p loss	8 (9%)	82	0.275 (1.00)	0.05 (1.00)	0.23 (1.00)	0.0104 (1.00)	0.774 (1.00)	0.298 (1.00)	0.455 (1.00)	0.962 (1.00)
5q loss	7 (8%)	83	0.863 (1.00)	0.656 (1.00)	0.278 (1.00)	0.136 (1.00)	0.659 (1.00)	0.128 (1.00)	0.863 (1.00)	0.333 (1.00)
6p loss	19 (21%)	71	0.0303 (1.00)	0.85 (1.00)	0.622 (1.00)	0.692 (1.00)	0.624 (1.00)	0.0993 (1.00)	0.815 (1.00)	0.162 (1.00)
6q loss	22 (24%)	68	0.00738 (1.00)	0.862 (1.00)	0.634 (1.00)	0.692 (1.00)	0.729 (1.00)	0.177 (1.00)	0.74 (1.00)	0.0687 (1.00)
7p loss	5 (6%)	85	0.275 (1.00)	0.585 (1.00)	0.91 (1.00)	0.891 (1.00)	0.816 (1.00)	0.416 (1.00)	0.684 (1.00)	0.13 (1.00)
7q loss	6 (7%)	84	0.192 (1.00)	0.304 (1.00)	0.62 (1.00)	0.658 (1.00)	1 (1.00)	0.233 (1.00)	0.596 (1.00)	0.0712 (1.00)
8p loss	16 (18%)	74	0.00308 (1.00)	0.224 (1.00)	0.181 (1.00)	0.141 (1.00)	0.181 (1.00)	0.0226 (1.00)	0.0171 (1.00)	0.00696 (1.00)
8q loss	12 (13%)	78	0.00147 (0.769)	0.0869 (1.00)	0.0319 (1.00)	0.124 (1.00)	0.0782 (1.00)	0.0352 (1.00)	0.0332 (1.00)	0.116 (1.00)
9q loss	11 (12%)	79	0.142 (1.00)	0.934 (1.00)	0.0821 (1.00)	0.322 (1.00)	0.557 (1.00)	0.495 (1.00)	0.83 (1.00)	0.282 (1.00)
10p loss	12 (13%)	78	0.736 (1.00)	0.428 (1.00)	0.264 (1.00)	1 (1.00)	0.683 (1.00)	0.71 (1.00)	0.618 (1.00)	0.749 (1.00)
10q loss	10 (11%)	80	0.39 (1.00)	0.624 (1.00)	0.534 (1.00)	1 (1.00)	1 (1.00)	0.709 (1.00)	0.892 (1.00)	0.824 (1.00)
11p loss	24 (27%)	66	0.00173 (0.898)	0.0174 (1.00)	0.221 (1.00)	0.187 (1.00)	0.28 (1.00)	0.891 (1.00)	0.447 (1.00)	0.925 (1.00)
12p loss	5 (6%)	85	0.229 (1.00)	0.255 (1.00)	0.62 (1.00)	0.0386 (1.00)	0.104 (1.00)	0.517 (1.00)	0.0108 (1.00)	0.0171 (1.00)
12q loss	4 (4%)	86	0.248 (1.00)	0.0495 (1.00)	0.441 (1.00)	0.0097 (1.00)	0.33 (1.00)	0.237 (1.00)	0.0422 (1.00)	0.00337 (1.00)
13q loss	39 (43%)	51	0.01 (1.00)	0.0795 (1.00)	0.625 (1.00)	0.884 (1.00)	0.753 (1.00)	0.302 (1.00)	0.91 (1.00)	0.285 (1.00)
14q loss	18 (20%)	72	0.0275 (1.00)	0.444 (1.00)	0.0181 (1.00)	0.047 (1.00)	0.413 (1.00)	0.53 (1.00)	0.272 (1.00)	0.9 (1.00)
15q loss	21 (23%)	69	0.0182 (1.00)	0.414 (1.00)	0.11 (1.00)	0.231 (1.00)	0.607 (1.00)	0.0404 (1.00)	0.373 (1.00)	0.162 (1.00)
16p loss	6 (7%)	84	0.173 (1.00)	0.0506 (1.00)	0.00209 (1.00)	0.00412 (1.00)	0.0133 (1.00)	0.443 (1.00)	0.0311 (1.00)	0.537 (1.00)
16q loss	5 (6%)	85	0.318 (1.00)	0.0771 (1.00)	0.0582 (1.00)	0.0856 (1.00)	0.167 (1.00)	0.303 (1.00)	0.361 (1.00)	0.894 (1.00)
18p loss	37 (41%)	53	0.0261 (1.00)	0.259 (1.00)	0.776 (1.00)	0.646 (1.00)	0.692 (1.00)	0.693 (1.00)	0.875 (1.00)	0.284 (1.00)
18q loss	35 (39%)	55	0.0456 (1.00)	0.426 (1.00)	0.824 (1.00)	0.935 (1.00)	0.496 (1.00)	0.914 (1.00)	0.76 (1.00)	0.0993 (1.00)
19p loss	5 (6%)	85	0.112 (1.00)	0.443 (1.00)	0.157 (1.00)	0.0132 (1.00)	0.139 (1.00)	0.715 (1.00)	0.214 (1.00)	0.0321 (1.00)
19q loss	4 (4%)	86	0.247 (1.00)	0.705 (1.00)	0.773 (1.00)	0.119 (1.00)	0.783 (1.00)	0.205 (1.00)	0.216 (1.00)	0.0321 (1.00)
20p loss	9 (10%)	81	0.0103 (1.00)	0.303 (1.00)	0.215 (1.00)	0.127 (1.00)	0.0681 (1.00)	0.443 (1.00)	0.17 (1.00)	0.764 (1.00)
20q loss	3 (3%)	87	0.456 (1.00)
21q loss	15 (17%)	75	0.00871 (1.00)	0.337 (1.00)	0.256 (1.00)	0.252 (1.00)	0.223 (1.00)	0.51 (1.00)	0.233 (1.00)	0.815 (1.00)
22q loss	48 (53%)	42	0.0777 (1.00)	0.081 (1.00)	0.62 (1.00)	0.282 (1.00)	0.874 (1.00)	0.828 (1.00)	0.8 (1.00)	0.729 (1.00)
xq loss	17 (19%)	73	0.00153 (0.799)	0.246 (1.00)	0.0337 (1.00)	0.0448 (1.00)	0.652 (1.00)	0.172 (1.00)	0.139 (1.00)	0.45 (1.00)

'2p gain' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.14

Table S1. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
2P GAIN MUTATED	12	0	1	0	0
2P GAIN WILD-TYPE	20	24	14	10	9

Figure S1. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.078

Table S2. Gene #3: '2p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
2P GAIN MUTATED	8	0	1	0
2P GAIN WILD-TYPE	15	23	6	24

Figure S2. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S3. Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
4P GAIN MUTATED	3	13	10	4	7
4P GAIN WILD-TYPE	29	11	5	6	2

Figure S3. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S4. Gene #7: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
4P GAIN MUTATED	1	8	11	10
4P GAIN WILD-TYPE	23	5	6	13

Figure S4. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S5. Gene #7: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
4P GAIN MUTATED	2	15	0	13
4P GAIN WILD-TYPE	21	8	7	11

Figure S5. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.04

Table S6. Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
4Q GAIN MUTATED	2	12	9	4	6
4Q GAIN WILD-TYPE	30	12	6	6	3

Figure S6. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S7. Gene #8: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
4Q GAIN MUTATED	0	8	9	10
4Q GAIN WILD-TYPE	24	5	8	13

Figure S7. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S8. Gene #8: '4q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
4Q GAIN MUTATED	1	15	0	11
4Q GAIN WILD-TYPE	22	8	7	13

Figure S8. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S9. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
5P GAIN MUTATED	10	22	13	4	8
5P GAIN WILD-TYPE	22	2	2	6	1

Figure S9. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S10. Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
5P GAIN MUTATED	6	18	3	22
5P GAIN WILD-TYPE	17	5	4	2

Figure S10. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S11. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
5Q GAIN MUTATED	9	19	13	4	8
5Q GAIN WILD-TYPE	23	5	2	6	1

Figure S11. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S12. Gene #10: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
5Q GAIN MUTATED	5	19	3	20
5Q GAIN WILD-TYPE	18	4	4	4

Figure S12. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.23

Table S13. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
7P GAIN MUTATED	9	18	12	3	6
7P GAIN WILD-TYPE	23	6	3	7	3

Figure S13. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.068

Table S14. Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
7P GAIN MUTATED	6	12	13	11
7P GAIN WILD-TYPE	18	1	4	12

Figure S14. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S15. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
7Q GAIN MUTATED	8	18	13	3	6
7Q GAIN WILD-TYPE	24	6	2	7	3

Figure S15. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S16. Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
7Q GAIN MUTATED	5	13	13	11
7Q GAIN WILD-TYPE	19	0	4	12

Figure S16. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.056

Table S17. Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
7Q GAIN MUTATED	6	20	2	14
7Q GAIN WILD-TYPE	17	3	5	10

Figure S17. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.04

Table S18. Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
9P GAIN MUTATED	2	3	10	1	4
9P GAIN WILD-TYPE	30	21	5	9	5

Figure S18. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.11

Table S19. Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
9Q GAIN MUTATED	7	3	12	3	4
9Q GAIN WILD-TYPE	25	21	3	7	5

Figure S19. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S20. Gene #19: '10p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
10P GAIN MUTATED	6	11	4	2
10P GAIN WILD-TYPE	18	2	13	21

Figure S20. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.11

Table S21. Gene #19: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
10P GAIN MUTATED	7	14	1	1
10P GAIN WILD-TYPE	16	9	6	23

Figure S21. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S22. Gene #20: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
10Q GAIN MUTATED	7	11	3	2
10Q GAIN WILD-TYPE	17	2	14	21

Figure S22. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.25

Table S23. Gene #20: '10q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
10Q GAIN MUTATED	8	13	1	1
10Q GAIN WILD-TYPE	15	10	6	23

Figure S23. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S24. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
12P GAIN MUTATED	14	24	14	5	7
12P GAIN WILD-TYPE	18	0	1	5	2

Figure S24. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.12

Table S25. Gene #23: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
12P GAIN MUTATED	9	13	14	18
12P GAIN WILD-TYPE	15	0	3	5

Figure S25. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S26. Gene #23: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
12P GAIN MUTATED	10	20	2	22
12P GAIN WILD-TYPE	13	3	5	2

Figure S26. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S27. Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
12Q GAIN MUTATED	14	24	15	4	7
12Q GAIN WILD-TYPE	18	0	0	6	2

Figure S27. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.078

Table S28. Gene #24: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
12Q GAIN MUTATED	11	20	2	22
12Q GAIN WILD-TYPE	12	3	5	2

Figure S28. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.21

Table S29. Gene #26: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
14Q GAIN MUTATED	2	6	8	1
14Q GAIN WILD-TYPE	22	7	9	22

Figure S29. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S30. Gene #26: '14q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	16	26
14Q GAIN MUTATED	17	0	1
14Q GAIN WILD-TYPE	19	16	25

Figure S30. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.078

Table S31. Gene #26: '14q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	16	27	11	20	4
14Q GAIN MUTATED	7	0	3	5	3
14Q GAIN WILD-TYPE	9	27	8	15	1

Figure S31. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S32. Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	18	23
14Q GAIN MUTATED	17	1	0
14Q GAIN WILD-TYPE	20	17	23

Figure S32. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S33. Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	8	25	8	18	9	10
14Q GAIN MUTATED	5	0	4	5	4	0
14Q GAIN WILD-TYPE	3	25	4	13	5	10

Figure S33. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S34. Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
16P GAIN MUTATED	6	24	10	4	5
16P GAIN WILD-TYPE	26	0	5	6	4

Figure S34. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S35. Gene #28: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
16P GAIN MUTATED	3	10	13	16
16P GAIN WILD-TYPE	21	3	4	7

Figure S35. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S36. Gene #28: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
16P GAIN MUTATED	4	20	0	18
16P GAIN WILD-TYPE	19	3	7	6

Figure S36. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S37. Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
16Q GAIN MUTATED	6	23	10	3	5
16Q GAIN WILD-TYPE	26	1	5	7	4

Figure S37. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.068

Table S38. Gene #29: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
16Q GAIN MUTATED	4	9	13	16
16Q GAIN WILD-TYPE	20	4	4	7

Figure S38. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S39. Gene #29: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
16Q GAIN MUTATED	4	19	1	18
16Q GAIN WILD-TYPE	19	4	6	6

Figure S39. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.25

Table S40. Gene #34: '19p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
19P GAIN MUTATED	14	21	1	12
19P GAIN WILD-TYPE	9	2	6	12

Figure S40. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.2

Table S41. Gene #35: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
19Q GAIN MUTATED	10	13	12	9
19Q GAIN WILD-TYPE	14	0	5	14

Figure S41. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S42. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
20P GAIN MUTATED	7	22	9	2	6
20P GAIN WILD-TYPE	25	2	6	8	3

Figure S42. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.051

Table S43. Gene #36: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
20P GAIN MUTATED	4	9	8	18
20P GAIN WILD-TYPE	20	4	9	5

Figure S43. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.078

Table S44. Gene #36: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
20P GAIN MUTATED	6	12	1	20
20P GAIN WILD-TYPE	17	11	6	4

Figure S44. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.073

Table S45. Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	18	23
20P GAIN MUTATED	13	7	20
20P GAIN WILD-TYPE	24	11	3

Figure S45. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S46. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
20Q GAIN MUTATED	9	21	11	2	6
20Q GAIN WILD-TYPE	23	3	4	8	3

Figure S46. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.04

Table S47. Gene #37: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
20Q GAIN MUTATED	5	11	8	18
20Q GAIN WILD-TYPE	19	2	9	5

Figure S47. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.14

Table S48. Gene #37: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	23	7	24
20Q GAIN MUTATED	6	14	2	20
20Q GAIN WILD-TYPE	17	9	5	4

Figure S48. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S49. Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
XQ GAIN MUTATED	6	20	9	2	3
XQ GAIN WILD-TYPE	26	4	6	8	6

Figure S49. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.056

Table S50. Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
2Q LOSS MUTATED	1	2	2	6	4
2Q LOSS WILD-TYPE	31	22	13	4	5

Figure S50. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S51. Gene #57: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	13	17	23
9P LOSS MUTATED	14	1	3	1
9P LOSS WILD-TYPE	10	12	14	22

Figure S51. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.045

Table S52. Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
11Q LOSS MUTATED	4	3	3	8	5
11Q LOSS WILD-TYPE	28	21	12	2	4

Figure S52. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.11

Table S53. Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	18	11	20	18	11
17P LOSS MUTATED	11	0	12	4	1
17P LOSS WILD-TYPE	7	11	8	14	10

Figure S53. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.15

Table S54. Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	24	15	10	9
17Q LOSS MUTATED	7	3	6	8	0
17Q LOSS WILD-TYPE	25	21	9	2	9

Figure S54. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = ACC-TP.transferedmergedcluster.txt
Number of patients = 90
Number of significantly arm-level cnvs = 80
Number of molecular subtypes = 8
Exclude genes that fewer than K tumors have mutations, 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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)

Made with Nozzle