Correlation between copy number variation genes (focal events) and molecular subtypes
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
04 October 2018 | None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 110 focal events and 3 molecular subtypes across 100 patients, 97 significant findings detected with P value < 0.05 and Q value < 0.25.

- amp_1p36.33 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_1q22 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_1q32.2 cnv correlated to 'METHYLATION_CNMF'.

- amp_2p23.3 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_2q11.1 cnv correlated to 'METHYLATION_CNMF'.

- amp_2q13 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_3p21.31 cnv correlated to 'METHYLATION_CNMF'.

- amp_3q26.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_3q27.1 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_4p16.3 cnv correlated to 'METHYLATION_CNMF'.

- amp_5q35.2 cnv correlated to 'METHYLATION_CNMF'.

- amp_7p13 cnv correlated to 'METHYLATION_CNMF'.

- amp_8q22.3 cnv correlated to 'MRNA_CHIERARCHICAL'.

- amp_9q34.3 cnv correlated to 'METHYLATION_CNMF'.

- amp_10q26.13 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_11p11.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_11q13.2 cnv correlated to 'METHYLATION_CNMF'.

- amp_11q13.3 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_12p13.33 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

- amp_12q13.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_13q12.11 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

- amp_14q24.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_17q12 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_17q24.1 cnv correlated to 'METHYLATION_CNMF'.

- amp_19p13.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_19p13.11 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_19q12 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_19q13.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- amp_20q13.33 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_1p36.12 cnv correlated to 'METHYLATION_CNMF'.

- del_1p13.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_3p26.3 cnv correlated to 'METHYLATION_CNMF'.

- del_3p21.1 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_4p15.31 cnv correlated to 'METHYLATION_CNMF'.

- del_4q21.21 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

- del_5q23.1 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_6q22.31 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_8p23.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_9p24.3 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

- del_9p24.1 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_10q11.22 cnv correlated to 'METHYLATION_CNMF'.

- del_11p15.5 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_11p15.3 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_11q24.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_12p13.33 cnv correlated to 'METHYLATION_CNMF'.

- del_13q12.11 cnv correlated to 'MRNA_CHIERARCHICAL' and 'METHYLATION_CNMF'.

- del_13q31.3 cnv correlated to 'METHYLATION_CNMF'.

- del_15q11.2 cnv correlated to 'METHYLATION_CNMF'.

- del_15q15.1 cnv correlated to 'MRNA_CHIERARCHICAL'.

- del_15q24.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_16p13.3 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

- del_16p11.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_16q22.1 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_16q22.2 cnv correlated to 'METHYLATION_CNMF'.

- del_17p11.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_17q21.32 cnv correlated to 'METHYLATION_CNMF'.

- del_18q22.1 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

- del_19p13.3 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_19q13.33 cnv correlated to 'METHYLATION_CNMF'.

- del_xp11.23 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

- del_xp11.23 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

- del_xp11.22 cnv correlated to 'METHYLATION_CNMF'.

- del_xq24 cnv correlated to 'METHYLATION_CNMF'.

- del_xq27.3 cnv correlated to 'METHYLATION_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 110 focal events and 3 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 97 significant findings detected.

|  | Clinical Features | MRNA CHIERARCHICAL | METHYLATION CNMF | METHYLATION CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test
amp 1p36 33 | 24 (24%) | 76 | 0.29 (0.469) | 0.0203 (0.0985) | 0.0113 (0.0621)
amp 1q22 | 42 (42%) | 58 | 0.156 (0.329) | 1e-05 (0.00165) | 5e-05 (0.00236)
amp 2p23 3 | 27 (27%) | 73 | 0.769 (0.852) | 0.00447 (0.0321) | 0.00367 (0.0288)
amp 2q13 | 27 (27%) | 73 | 0.807 (0.873) | 0.00288 (0.0264) | 0.00238 (0.0264)
amp 3q26 2 | 20 (20%) | 80 | 0.132 (0.307) | 0.00265 (0.0264) | 0.00013 (0.00536)
amp 3q27 1 | 27 (27%) | 73 | 0.371 (0.556) | 3e-05 (0.0022) | 2e-05 (0.0022)
amp 10q26 13 | 34 (34%) | 66 | 0.486 (0.638) | 0.0329 (0.128) | 0.0453 (0.16)
amp 11p11 2 | 15 (15%) | 85 | 0.874 (0.92) | 0.00526 (0.0362) | 0.00335 (0.0278)
amp 11q13 3 | 19 (19%) | 81 | 0.646 (0.764) | 0.00019 (0.00627) | 0.00447 (0.0321)
amp 12q13 2 | 24 (24%) | 76 | 0.0708 (0.215) | 0.0275 (0.118) | 0.00587 (0.0395)
amp 14q24 2 | 15 (15%) | 85 | 0.429 (0.593) | 0.00034 (0.00935) | 0.00738 (0.046)
amp 17q12 | 21 (21%) | 79 | 0.1 (0.267) | 4e-05 (0.0022) | 0.00267 (0.0264)
amp 19p13 2 | 20 (20%) | 80 | 0.6 (0.731) | 0.00281 (0.0264) | 0.00615 (0.0406)
amp 19p13 11 | 22 (22%) | 78 | 0.236 (0.416) | 0.03 (0.122) | 0.0443 (0.159)
amp 19q12 | 18 (18%) | 82 | 0.604 (0.733) | 0.0257 (0.113) | 0.00384 (0.0293)
amp 19q13 2 | 18 (18%) | 82 | 0.962 (0.977) | 0.013 (0.0692) | 0.00346 (0.0278)
amp 20q13 33 | 28 (28%) | 72 | 0.473 (0.632) | 0.00061 (0.0144) | 0.00166 (0.0211)
del 1p13 2 | 12 (12%) | 88 | 0.329 (0.512) | 0.00066 (0.0145) | 0.00205 (0.0251)
del 3p21 1 | 13 (13%) | 87 | 0.867 (0.92) | 0.0244 (0.11) | 0.0289 (0.122)
del 5q23 1 | 13 (13%) | 87 | 0.0847 (0.237) | 0.00146 (0.0201) | 0.0469 (0.161)
del 6q22 31 | 9 (9%) | 91 | 0.128 (0.305) | 4e-05 (0.0022) | 0.00707 (0.0454)
del 8p23 2 | 11 (11%) | 89 | 0.136 (0.313) | 0.00045 (0.0114) | 0.00021 (0.0063)
del 9p24 1 | 11 (11%) | 89 | 0.138 (0.313) | 0.00099 (0.0156) | 0.00091 (0.015)
del 11p15 5 | 11 (11%) | 89 | 0.633 (0.752) | 1e-05 (0.00165) | 0.00075 (0.0145)
del 11p15 3 | 15 (15%) | 85 | 0.536 (0.691) | 0.0138 (0.0725) | 0.00251 (0.0264)
del 11q24 2 | 14 (14%) | 86 | 1 (1.00) | 0.00716 (0.0454) | 0.00084 (0.0146)
del 13q12 11 | 14 (14%) | 86 | 0.0268 (0.116) | 0.0324 (0.128) | 0.38 (0.562)
del 15q24 2 | 28 (28%) | 72 | 0.18 (0.357) | 0.0296 (0.122) | 0.0298 (0.122)
del 16p11 2 | 21 (21%) | 79 | 0.249 (0.428) | 0.00391 (0.0293) | 0.0219 (0.105)
del 16q22 1 | 11 (11%) | 89 | 0.466 (0.627) | 0.00335 (0.0278) | 0.0463 (0.161)
del 17p11 2 | 17 (17%) | 83 | 0.283 (0.465) | 0.00079 (0.0145) | 0.00077 (0.0145)
del 19p13 3 | 23 (23%) | 77 | 0.759 (0.851) | 0.00016 (0.00587) | 0.00152 (0.0201)
del xp11 23 | 36 (36%) | 64 | 0.761 (0.851) | 0.039 (0.146) | 0.00966 (0.0559)
amp 1q32 2 | 39 (39%) | 61 | 0.104 (0.271) | 0.00143 (0.0201) | 0.357 (0.545)
amp 2q11 1 | 48 (48%) | 52 | 0.583 (0.715) | 0.0342 (0.131) | 0.11 (0.282)
amp 3p21 31 | 27 (27%) | 73 | 0.437 (0.596) | 0.0096 (0.0559) | 0.0885 (0.245)
amp 4p16 3 | 10 (10%) | 90 | 0.424 (0.59) | 0.0187 (0.092) | 0.186 (0.365)
amp 5q35 2 | 10 (10%) | 90 | 0.538 (0.691) | 0.0156 (0.0794) | 0.14 (0.313)
amp 7p13 | 29 (29%) | 71 | 0.401 (0.576) | 0.00315 (0.0278) | 0.0971 (0.263)
amp 8q22 3 | 27 (27%) | 73 | 0.00773 (0.0472) | 0.314 (0.495) | 0.654 (0.768)
amp 9q34 3 | 13 (13%) | 87 | 0.404 (0.576) | 0.0255 (0.113) | 0.495 (0.648)
amp 11q13 2 | 22 (22%) | 78 | 0.92 (0.954) | 0.00982 (0.0559) | 0.0548 (0.185)
amp 12p13 33 | 37 (37%) | 63 | 0.664 (0.773) | 0.236 (0.416) | 0.0436 (0.159)
amp 13q12 11 | 14 (14%) | 86 | 0.168 (0.341) | 0.335 (0.517) | 0.00113 (0.0169)
amp 17q24 1 | 18 (18%) | 82 | 0.176 (0.353) | 0.0376 (0.143) | 0.172 (0.345)
del 1p36 12 | 16 (16%) | 84 | 0.732 (0.827) | 0.00921 (0.0553) | 0.0771 (0.224)
del 3p26 3 | 15 (15%) | 85 | 0.404 (0.576) | 0.0222 (0.105) | 0.071 (0.215)
del 4p15 31 | 13 (13%) | 87 | 0.13 (0.306) | 0.0325 (0.128) | 0.0633 (0.201)
del 4q21 21 | 24 (24%) | 76 | 0.203 (0.384) | 0.165 (0.336) | 0.0437 (0.159)
del 9p24 3 | 15 (15%) | 85 | 0.571 (0.705) | 0.141 (0.313) | 0.0046 (0.0323)
del 10q11 22 | 6 (6%) | 94 | 0.944 (0.973) | 0.0227 (0.105) | 0.369 (0.556)
del 12p13 33 | 4 (4%) | 96 | 1 (1.00) | 0.016 (0.08) | 0.189 (0.368)
del 13q31 3 | 11 (11%) | 89 | 0.82 (0.881) | 0.0233 (0.107) | 0.105 (0.273)
del 15q11 2 | 20 (20%) | 80 | 0.221 (0.402) | 0.00288 (0.0264) | 0.157 (0.329)
del 15q15 1 | 26 (26%) | 74 | 0.0106 (0.0593) | 0.211 (0.391) | 0.412 (0.578)
del 16p13 3 | 9 (9%) | 91 | 0.797 (0.868) | 0.157 (0.329) | 0.044 (0.159)
del 16q22 2 | 16 (16%) | 84 | 0.968 (0.98) | 0.0146 (0.0753) | 0.227 (0.407)
del 17q21 32 | 10 (10%) | 90 | 0.546 (0.695) | 0.00266 (0.0264) | 0.162 (0.335)
del 18q22 1 | 16 (16%) | 84 | 0.476 (0.632) | 0.0772 (0.224) | 0.0455 (0.16)
del 19q13 33 | 13 (13%) | 87 | 1 (1.00) | 0.00268 (0.0264) | 0.309 (0.491)
del xp11 23 | 47 (47%) | 53 | 0.303 (0.485) | 0.125 (0.304) | 0.0302 (0.122)
del xp11 22 | 29 (29%) | 71 | 0.666 (0.773) | 0.0127 (0.0689) | 0.0796 (0.228)
del xq24 | 32 (32%) | 68 | 0.132 (0.307) | 0.0493 (0.168) | 0.0819 (0.231)
del xq27 3 | 34 (34%) | 66 | 0.415 (0.58) | 0.00337 (0.0278) | 0.0566 (0.187)
amp 1p36 13 | 14 (14%) | 86 | 0.954 (0.973) | 0.444 (0.603) | 0.304 (0.485)
amp 6p21 32 | 44 (44%) | 56 | 0.922 (0.954) | 0.119 (0.292) | 0.184 (0.364)
amp 6q25 1 | 17 (17%) | 83 | 0.223 (0.404) | 0.374 (0.556) | 0.691 (0.797)
amp 7q11 23 | 35 (35%) | 65 | 0.405 (0.576) | 0.155 (0.329) | 0.613 (0.741)
amp 7q22 1 | 32 (32%) | 68 | 0.162 (0.335) | 0.064 (0.201) | 0.251 (0.429)
amp 9p24 3 | 38 (38%) | 62 | 0.072 (0.216) | 0.102 (0.269) | 0.463 (0.627)
amp 10q23 2 | 30 (30%) | 70 | 0.765 (0.852) | 0.8 (0.868) | 0.513 (0.669)
amp 11p15 2 | 5 (5%) | 95 | 0.237 (0.416) | 0.114 (0.288) | 0.261 (0.44)
amp 12q24 31 | 21 (21%) | 79 | 0.288 (0.468) | 0.0611 (0.198) | 0.119 (0.292)
amp 15q24 2 | 16 (16%) | 84 | 0.429 (0.593) | 0.116 (0.29) | 0.391 (0.57)
amp 15q26 3 | 35 (35%) | 65 | 0.622 (0.745) | 0.572 (0.705) | 0.623 (0.745)
amp 16p11 2 | 31 (31%) | 69 | 0.0986 (0.264) | 0.14 (0.313) | 0.0619 (0.198)
amp 16q22 2 | 19 (19%) | 81 | 0.954 (0.973) | 0.196 (0.374) | 0.359 (0.545)
amp 18p11 31 | 20 (20%) | 80 | 0.0938 (0.256) | 0.253 (0.431) | 0.406 (0.576)
amp 22q13 2 | 19 (19%) | 81 | 0.954 (0.973) | 0.219 (0.401) | 0.432 (0.594)
amp xp11 23 | 22 (22%) | 78 | 0.769 (0.852) | 0.272 (0.451) | 0.531 (0.69)
amp xp11 23 | 31 (31%) | 69 | 0.324 (0.507) | 0.56 (0.703) | 0.241 (0.416)
amp xq24 | 32 (32%) | 68 | 0.874 (0.92) | 0.783 (0.862) | 0.206 (0.385)
amp xq28 | 40 (40%) | 60 | 0.108 (0.279) | 0.469 (0.628) | 0.811 (0.875)
del 1p36 32 | 11 (11%) | 89 | 0.759 (0.851) | 0.149 (0.322) | 0.477 (0.632)
del 1q32 2 | 13 (13%) | 87 | 0.723 (0.822) | 0.559 (0.703) | 0.21 (0.391)
del 2q31 2 | 9 (9%) | 91 | 0.862 (0.92) | 0.871 (0.92) | 0.292 (0.47)
del 3p12 2 | 22 (22%) | 78 | 0.259 (0.438) | 0.485 (0.638) | 0.627 (0.747)
del 3q25 1 | 6 (6%) | 94 | 0.697 (0.8) | 0.569 (0.705) | 0.145 (0.316)
del 3q25 33 | 5 (5%) | 95 | 0.402 (0.576) | 0.0576 (0.188) | 0.164 (0.336)
del 4q13 2 | 25 (25%) | 75 | 0.0566 (0.187) | 0.0702 (0.215) | 0.0811 (0.231)
del 7p22 1 | 9 (9%) | 91 | 0.571 (0.705) | 0.317 (0.498) | 0.239 (0.416)
del 7q11 21 | 16 (16%) | 84 | 0.65 (0.767) | 0.267 (0.447) | 0.789 (0.865)
del 7q11 23 | 6 (6%) | 94 | 0.347 (0.533) | 0.875 (0.92) | 0.838 (0.898)
del 7q22 1 | 11 (11%) | 89 | 0.798 (0.868) | 0.138 (0.313) | 0.237 (0.416)
del 7q22 1 | 7 (7%) | 93 | 0.698 (0.8) | 0.396 (0.575) | 0.215 (0.397)
del 9q21 32 | 30 (30%) | 70 | 0.332 (0.515) | 0.0648 (0.202) | 0.14 (0.313)
del 10q25 3 | 13 (13%) | 87 | 0.0742 (0.219) | 0.0902 (0.248) | 0.126 (0.304)
del 11p11 12 | 17 (17%) | 83 | 0.618 (0.744) | 0.144 (0.316) | 0.546 (0.695)
del 12p11 23 | 10 (10%) | 90 | 0.538 (0.691) | 0.204 (0.384) | 0.196 (0.374)
del 12q21 32 | 18 (18%) | 82 | 0.919 (0.954) | 0.196 (0.374) | 0.373 (0.556)
del 13q12 11 | 16 (16%) | 84 | 0.41 (0.578) | 0.597 (0.73) | 0.274 (0.452)
del 14q32 31 | 20 (20%) | 80 | 0.556 (0.703) | 0.227 (0.407) | 0.126 (0.304)
del 15q26 3 | 15 (15%) | 85 | 0.286 (0.467) | 0.24 (0.416) | 0.39 (0.57)
del 16p13 3 | 24 (24%) | 76 | 0.189 (0.368) | 0.658 (0.77) | 0.155 (0.329)
del 17q24 1 | 11 (11%) | 89 | 0.901 (0.941) | 0.385 (0.567) | 0.37 (0.556)
del 19p13 2 | 17 (17%) | 83 | 0.956 (0.973) | 0.129 (0.306) | 0.725 (0.822)
del 19p12 | 29 (29%) | 71 | 0.985 (0.994) | 0.783 (0.862) | 0.548 (0.695)
del 20p13 | 9 (9%) | 91 | 0.703 (0.802) | 0.115 (0.29) | 0.0738 (0.219)
del 20q13 13 | 6 (6%) | 94 | 0.569 (0.705) | 0.686 (0.794) | 0.272 (0.451)
del 22q13 2 | 22 (22%) | 78 | 0.887 (0.93) | 0.437 (0.596) | 0.147 (0.32)

'amp_1p36.33' versus 'METHYLATION_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.099

Table S1. Gene #1: 'amp_1p36.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 1(1P36.33) MUTATED | 6 | 5 | 8 | 5
AMP PEAK 1(1P36.33) WILD-TYPE | 29 | 28 | 8 | 7

Figure S1. Get High-res Image Gene #1: 'amp_1p36.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_1p36.33' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.062

Table S2. Gene #1: 'amp_1p36.33' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 1(1P36.33) MUTATED | 7 | 4 | 5 | 3 | 0 | 1 | 4
AMP PEAK 1(1P36.33) WILD-TYPE | 27 | 7 | 4 | 4 | 6 | 19 | 5

Figure S2. Get High-res Image Gene #1: 'amp_1p36.33' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_1q22' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S3. Gene #3: 'amp_1q22' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 3(1Q22) MUTATED | 5 | 11 | 13 | 10
AMP PEAK 3(1Q22) WILD-TYPE | 30 | 22 | 3 | 2

Figure S3. Get High-res Image Gene #3: 'amp_1q22' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_1q22' versus 'METHYLATION_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0024

Table S4. Gene #3: 'amp_1q22' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 3(1Q22) MUTATED | 9 | 9 | 2 | 6 | 6 | 5 | 2
AMP PEAK 3(1Q22) WILD-TYPE | 25 | 2 | 7 | 1 | 0 | 15 | 7

Figure S4. Get High-res Image Gene #3: 'amp_1q22' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_1q32.2' versus 'METHYLATION_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.02

Table S5. Gene #4: 'amp_1q32.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 4(1Q32.2) MUTATED | 10 | 8 | 8 | 10
AMP PEAK 4(1Q32.2) WILD-TYPE | 25 | 25 | 8 | 2

Figure S5. Get High-res Image Gene #4: 'amp_1q32.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_2p23.3' versus 'METHYLATION_CNMF'

P value = 0.00447 (Fisher's exact test), Q value = 0.032

Table S6. Gene #5: 'amp_2p23.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 5(2P23.3) MUTATED | 5 | 7 | 10 | 3
AMP PEAK 5(2P23.3) WILD-TYPE | 30 | 26 | 6 | 9

Figure S6. Get High-res Image Gene #5: 'amp_2p23.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_2p23.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00367 (Fisher's exact test), Q value = 0.029

Table S7. Gene #5: 'amp_2p23.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 5(2P23.3) MUTATED | 7 | 7 | 2 | 5 | 0 | 3 | 1
AMP PEAK 5(2P23.3) WILD-TYPE | 27 | 4 | 7 | 2 | 6 | 17 | 8

Figure S7. Get High-res Image Gene #5: 'amp_2p23.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_2q11.1' versus 'METHYLATION_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.13

Table S8. Gene #6: 'amp_2q11.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 6(2Q11.1) MUTATED | 11 | 20 | 11 | 6
AMP PEAK 6(2Q11.1) WILD-TYPE | 24 | 13 | 5 | 6

Figure S8. Get High-res Image Gene #6: 'amp_2q11.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_2q13' versus 'METHYLATION_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.026

Table S9. Gene #7: 'amp_2q13' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 7(2Q13) MUTATED | 5 | 6 | 10 | 3
AMP PEAK 7(2Q13) WILD-TYPE | 30 | 27 | 6 | 9

Figure S9. Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_2q13' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00238 (Fisher's exact test), Q value = 0.026

Table S10. Gene #7: 'amp_2q13' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 7(2Q13) MUTATED | 6 | 7 | 2 | 5 | 0 | 3 | 1
AMP PEAK 7(2Q13) WILD-TYPE | 28 | 4 | 7 | 2 | 6 | 17 | 8

Figure S10. Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_3p21.31' versus 'METHYLATION_CNMF'

P value = 0.0096 (Fisher's exact test), Q value = 0.056

Table S11. Gene #8: 'amp_3p21.31' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 8(3P21.31) MUTATED | 7 | 6 | 10 | 3
AMP PEAK 8(3P21.31) WILD-TYPE | 28 | 27 | 6 | 9

Figure S11. Get High-res Image Gene #8: 'amp_3p21.31' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_3q26.2' versus 'METHYLATION_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.026

Table S12. Gene #9: 'amp_3q26.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 9(3Q26.2) MUTATED | 2 | 6 | 8 | 1
AMP PEAK 9(3Q26.2) WILD-TYPE | 33 | 27 | 8 | 11

Figure S12. Get High-res Image Gene #9: 'amp_3q26.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_3q26.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0054

Table S13. Gene #9: 'amp_3q26.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 9(3Q26.2) MUTATED | 4 | 8 | 0 | 3 | 0 | 2 | 0
AMP PEAK 9(3Q26.2) WILD-TYPE | 30 | 3 | 9 | 4 | 6 | 18 | 9

Figure S13. Get High-res Image Gene #9: 'amp_3q26.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_3q27.1' versus 'METHYLATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0022

Table S14. Gene #10: 'amp_3q27.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 10(3Q27.1) MUTATED | 3 | 7 | 12 | 2
AMP PEAK 10(3Q27.1) WILD-TYPE | 32 | 26 | 4 | 10

Figure S14. Get High-res Image Gene #10: 'amp_3q27.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_3q27.1' versus 'METHYLATION_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0022

Table S15. Gene #10: 'amp_3q27.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 10(3Q27.1) MUTATED | 6 | 9 | 0 | 5 | 1 | 2 | 1
AMP PEAK 10(3Q27.1) WILD-TYPE | 28 | 2 | 9 | 2 | 5 | 18 | 8

Figure S15. Get High-res Image Gene #10: 'amp_3q27.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_4p16.3' versus 'METHYLATION_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.092

Table S16. Gene #11: 'amp_4p16.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 11(4P16.3) MUTATED | 3 | 1 | 5 | 0
AMP PEAK 11(4P16.3) WILD-TYPE | 32 | 32 | 11 | 12

Figure S16. Get High-res Image Gene #11: 'amp_4p16.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_5q35.2' versus 'METHYLATION_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.079

Table S17. Gene #12: 'amp_5q35.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 12(5Q35.2) MUTATED | 1 | 3 | 5 | 0
AMP PEAK 12(5Q35.2) WILD-TYPE | 34 | 30 | 11 | 12

Figure S17. Get High-res Image Gene #12: 'amp_5q35.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_7p13' versus 'METHYLATION_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.028

Table S18. Gene #15: 'amp_7p13' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 15(7P13) MUTATED | 8 | 6 | 11 | 3
AMP PEAK 15(7P13) WILD-TYPE | 27 | 27 | 5 | 9

Figure S18. Get High-res Image Gene #15: 'amp_7p13' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_8q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00773 (Fisher's exact test), Q value = 0.047

Table S19. Gene #18: 'amp_8q22.3' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 28 | 20 | 11 | 20 | 21
AMP PEAK 18(8Q22.3) MUTATED | 10 | 2 | 0 | 10 | 5
AMP PEAK 18(8Q22.3) WILD-TYPE | 18 | 18 | 11 | 10 | 16

Figure S19. Get High-res Image Gene #18: 'amp_8q22.3' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'amp_9q34.3' versus 'METHYLATION_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.11

Table S20. Gene #20: 'amp_9q34.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 20(9Q34.3) MUTATED | 4 | 3 | 6 | 0
AMP PEAK 20(9Q34.3) WILD-TYPE | 31 | 30 | 10 | 12

Figure S20. Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_10q26.13' versus 'METHYLATION_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.13

Table S21. Gene #22: 'amp_10q26.13' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 22(10Q26.13) MUTATED | 7 | 11 | 10 | 4
AMP PEAK 22(10Q26.13) WILD-TYPE | 28 | 22 | 6 | 8

Figure S21. Get High-res Image Gene #22: 'amp_10q26.13' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_10q26.13' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0453 (Fisher's exact test), Q value = 0.16

Table S22. Gene #22: 'amp_10q26.13' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 22(10Q26.13) MUTATED | 6 | 5 | 4 | 5 | 1 | 6 | 5
AMP PEAK 22(10Q26.13) WILD-TYPE | 28 | 6 | 5 | 2 | 5 | 14 | 4

Figure S22. Get High-res Image Gene #22: 'amp_10q26.13' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_11p11.2' versus 'METHYLATION_CNMF'

P value = 0.00526 (Fisher's exact test), Q value = 0.036

Table S23. Gene #24: 'amp_11p11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 24(11P11.2) MUTATED | 3 | 3 | 7 | 0
AMP PEAK 24(11P11.2) WILD-TYPE | 32 | 30 | 9 | 12

Figure S23. Get High-res Image Gene #24: 'amp_11p11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_11p11.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.028

Table S24. Gene #24: 'amp_11p11.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 24(11P11.2) MUTATED | 4 | 5 | 0 | 3 | 0 | 0 | 1
AMP PEAK 24(11P11.2) WILD-TYPE | 30 | 6 | 9 | 4 | 6 | 20 | 8

Figure S24. Get High-res Image Gene #24: 'amp_11p11.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_11q13.2' versus 'METHYLATION_CNMF'

P value = 0.00982 (Fisher's exact test), Q value = 0.056

Table S25. Gene #25: 'amp_11q13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 25(11Q13.2) MUTATED | 7 | 3 | 8 | 1
AMP PEAK 25(11Q13.2) WILD-TYPE | 28 | 30 | 8 | 11

Figure S25. Get High-res Image Gene #25: 'amp_11q13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_11q13.3' versus 'METHYLATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0063

Table S26. Gene #26: 'amp_11q13.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 26(11Q13.3) MUTATED | 6 | 2 | 9 | 0
AMP PEAK 26(11Q13.3) WILD-TYPE | 29 | 31 | 7 | 12

Figure S26. Get High-res Image Gene #26: 'amp_11q13.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_11q13.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00447 (Fisher's exact test), Q value = 0.032

Table S27. Gene #26: 'amp_11q13.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 26(11Q13.3) MUTATED | 8 | 5 | 0 | 3 | 0 | 0 | 1
AMP PEAK 26(11Q13.3) WILD-TYPE | 26 | 6 | 9 | 4 | 6 | 20 | 8

Figure S27. Get High-res Image Gene #26: 'amp_11q13.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_12p13.33' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.16

Table S28. Gene #27: 'amp_12p13.33' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 27(12P13.33) MUTATED | 15 | 8 | 3 | 1 | 2 | 3 | 4
AMP PEAK 27(12P13.33) WILD-TYPE | 19 | 3 | 6 | 6 | 4 | 17 | 5

Figure S28. Get High-res Image Gene #27: 'amp_12p13.33' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_12q13.2' versus 'METHYLATION_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.12

Table S29. Gene #28: 'amp_12q13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 28(12Q13.2) MUTATED | 4 | 8 | 8 | 2
AMP PEAK 28(12Q13.2) WILD-TYPE | 31 | 25 | 8 | 10

Figure S29. Get High-res Image Gene #28: 'amp_12q13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_12q13.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00587 (Fisher's exact test), Q value = 0.04

Table S30. Gene #28: 'amp_12q13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 28(12Q13.2) MUTATED | 5 | 7 | 1 | 4 | 0 | 4 | 1
AMP PEAK 28(12Q13.2) WILD-TYPE | 29 | 4 | 8 | 3 | 6 | 16 | 8

Figure S30. Get High-res Image Gene #28: 'amp_12q13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_13q12.11' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00113 (Fisher's exact test), Q value = 0.017

Table S31. Gene #30: 'amp_13q12.11' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 30(13Q12.11) MUTATED | 0 | 2 | 4 | 2 | 0 | 5 | 0
AMP PEAK 30(13Q12.11) WILD-TYPE | 34 | 9 | 5 | 5 | 6 | 15 | 9

Figure S31. Get High-res Image Gene #30: 'amp_13q12.11' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_14q24.2' versus 'METHYLATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0093

Table S32. Gene #31: 'amp_14q24.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 31(14Q24.2) MUTATED | 2 | 2 | 8 | 1
AMP PEAK 31(14Q24.2) WILD-TYPE | 33 | 31 | 8 | 11

Figure S32. Get High-res Image Gene #31: 'amp_14q24.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_14q24.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00738 (Fisher's exact test), Q value = 0.046

Table S33. Gene #31: 'amp_14q24.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 31(14Q24.2) MUTATED | 4 | 3 | 0 | 4 | 1 | 0 | 1
AMP PEAK 31(14Q24.2) WILD-TYPE | 30 | 8 | 9 | 3 | 5 | 20 | 8

Figure S33. Get High-res Image Gene #31: 'amp_14q24.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_17q12' versus 'METHYLATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0022

Table S34. Gene #36: 'amp_17q12' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 36(17Q12) MUTATED | 1 | 5 | 10 | 2
AMP PEAK 36(17Q12) WILD-TYPE | 34 | 28 | 6 | 10

Figure S34. Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_17q12' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.026

Table S35. Gene #36: 'amp_17q12' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 36(17Q12) MUTATED | 3 | 5 | 1 | 5 | 1 | 2 | 1
AMP PEAK 36(17Q12) WILD-TYPE | 31 | 6 | 8 | 2 | 5 | 18 | 8

Figure S35. Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_17q24.1' versus 'METHYLATION_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.14

Table S36. Gene #37: 'amp_17q24.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 37(17Q24.1) MUTATED | 2 | 6 | 5 | 4
AMP PEAK 37(17Q24.1) WILD-TYPE | 33 | 27 | 11 | 8

Figure S36. Get High-res Image Gene #37: 'amp_17q24.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_19p13.2' versus 'METHYLATION_CNMF'

P value = 0.00281 (Fisher's exact test), Q value = 0.026

Table S37. Gene #39: 'amp_19p13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 39(19P13.2) MUTATED | 4 | 5 | 9 | 1
AMP PEAK 39(19P13.2) WILD-TYPE | 31 | 28 | 7 | 11

Figure S37. Get High-res Image Gene #39: 'amp_19p13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_19p13.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00615 (Fisher's exact test), Q value = 0.041

Table S38. Gene #39: 'amp_19p13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 39(19P13.2) MUTATED | 5 | 6 | 0 | 4 | 1 | 2 | 1
AMP PEAK 39(19P13.2) WILD-TYPE | 29 | 5 | 9 | 3 | 5 | 18 | 8

Figure S38. Get High-res Image Gene #39: 'amp_19p13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_19p13.11' versus 'METHYLATION_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.12

Table S39. Gene #40: 'amp_19p13.11' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 40(19P13.11) MUTATED | 5 | 7 | 8 | 1
AMP PEAK 40(19P13.11) WILD-TYPE | 30 | 26 | 8 | 11

Figure S39. Get High-res Image Gene #40: 'amp_19p13.11' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_19p13.11' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0443 (Fisher's exact test), Q value = 0.16

Table S40. Gene #40: 'amp_19p13.11' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 40(19P13.11) MUTATED | 7 | 6 | 0 | 3 | 0 | 4 | 1
AMP PEAK 40(19P13.11) WILD-TYPE | 27 | 5 | 9 | 4 | 6 | 16 | 8

Figure S40. Get High-res Image Gene #40: 'amp_19p13.11' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_19q12' versus 'METHYLATION_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.11

Table S41. Gene #41: 'amp_19q12' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 41(19Q12) MUTATED | 3 | 7 | 6 | 0
AMP PEAK 41(19Q12) WILD-TYPE | 32 | 26 | 10 | 12

Figure S41. Get High-res Image Gene #41: 'amp_19q12' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_19q12' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.029

Table S42. Gene #41: 'amp_19q12' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 41(19Q12) MUTATED | 3 | 7 | 0 | 1 | 0 | 4 | 1
AMP PEAK 41(19Q12) WILD-TYPE | 31 | 4 | 9 | 6 | 6 | 16 | 8

Figure S42. Get High-res Image Gene #41: 'amp_19q12' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_19q13.2' versus 'METHYLATION_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.069

Table S43. Gene #42: 'amp_19q13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 42(19Q13.2) MUTATED | 4 | 5 | 8 | 1
AMP PEAK 42(19Q13.2) WILD-TYPE | 31 | 28 | 8 | 11

Figure S43. Get High-res Image Gene #42: 'amp_19q13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_19q13.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00346 (Fisher's exact test), Q value = 0.028

Table S44. Gene #42: 'amp_19q13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 42(19Q13.2) MUTATED | 4 | 6 | 0 | 3 | 1 | 1 | 3
AMP PEAK 42(19Q13.2) WILD-TYPE | 30 | 5 | 9 | 4 | 5 | 19 | 6

Figure S44. Get High-res Image Gene #42: 'amp_19q13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_20q13.33' versus 'METHYLATION_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.014

Table S45. Gene #43: 'amp_20q13.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
AMP PEAK 43(20Q13.33) MUTATED | 6 | 7 | 11 | 1
AMP PEAK 43(20Q13.33) WILD-TYPE | 29 | 26 | 5 | 11

Figure S45. Get High-res Image Gene #43: 'amp_20q13.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_20q13.33' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.021

Table S46. Gene #43: 'amp_20q13.33' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
AMP PEAK 43(20Q13.33) MUTATED | 8 | 8 | 1 | 4 | 0 | 2 | 2
AMP PEAK 43(20Q13.33) WILD-TYPE | 26 | 3 | 8 | 3 | 6 | 18 | 7

Figure S46. Get High-res Image Gene #43: 'amp_20q13.33' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_1p36.12' versus 'METHYLATION_CNMF'

P value = 0.00921 (Fisher's exact test), Q value = 0.055

Table S47. Gene #50: 'del_1p36.12' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 2(1P36.12) MUTATED | 4 | 2 | 7 | 1
DEL PEAK 2(1P36.12) WILD-TYPE | 31 | 31 | 9 | 11

Figure S47. Get High-res Image Gene #50: 'del_1p36.12' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_1p13.2' versus 'METHYLATION_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.014

Table S48. Gene #51: 'del_1p13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 3(1P13.2) MUTATED | 2 | 1 | 7 | 2
DEL PEAK 3(1P13.2) WILD-TYPE | 33 | 32 | 9 | 10

Figure S48. Get High-res Image Gene #51: 'del_1p13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_1p13.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00205 (Fisher's exact test), Q value = 0.025

Table S49. Gene #51: 'del_1p13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 3(1P13.2) MUTATED | 3 | 5 | 1 | 3 | 0 | 0 | 0
DEL PEAK 3(1P13.2) WILD-TYPE | 31 | 6 | 8 | 4 | 6 | 20 | 9

Figure S49. Get High-res Image Gene #51: 'del_1p13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_3p26.3' versus 'METHYLATION_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.1

Table S50. Gene #54: 'del_3p26.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 7(3P26.3) MUTATED | 3 | 2 | 6 | 2
DEL PEAK 7(3P26.3) WILD-TYPE | 32 | 31 | 10 | 10

Figure S50. Get High-res Image Gene #54: 'del_3p26.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_3p21.1' versus 'METHYLATION_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.11

Table S51. Gene #55: 'del_3p21.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 8(3P21.1) MUTATED | 3 | 2 | 6 | 1
DEL PEAK 8(3P21.1) WILD-TYPE | 32 | 31 | 10 | 11

Figure S51. Get High-res Image Gene #55: 'del_3p21.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_3p21.1' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.12

Table S52. Gene #55: 'del_3p21.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 8(3P21.1) MUTATED | 4 | 5 | 1 | 1 | 0 | 0 | 1
DEL PEAK 8(3P21.1) WILD-TYPE | 30 | 6 | 8 | 6 | 6 | 20 | 8

Figure S52. Get High-res Image Gene #55: 'del_3p21.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_4p15.31' versus 'METHYLATION_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.13

Table S53. Gene #59: 'del_4p15.31' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 12(4P15.31) MUTATED | 3 | 1 | 5 | 1
DEL PEAK 12(4P15.31) WILD-TYPE | 32 | 32 | 11 | 11

Figure S53. Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_4q21.21' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.16

Table S54. Gene #61: 'del_4q21.21' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 14(4Q21.21) MUTATED | 8 | 7 | 0 | 1 | 1 | 4 | 1
DEL PEAK 14(4Q21.21) WILD-TYPE | 26 | 4 | 9 | 6 | 5 | 16 | 8

Figure S54. Get High-res Image Gene #61: 'del_4q21.21' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_5q23.1' versus 'METHYLATION_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.02

Table S55. Gene #62: 'del_5q23.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 15(5Q23.1) MUTATED | 4 | 0 | 6 | 1
DEL PEAK 15(5Q23.1) WILD-TYPE | 31 | 33 | 10 | 11

Figure S55. Get High-res Image Gene #62: 'del_5q23.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_5q23.1' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.16

Table S56. Gene #62: 'del_5q23.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 15(5Q23.1) MUTATED | 4 | 4 | 2 | 1 | 0 | 0 | 0
DEL PEAK 15(5Q23.1) WILD-TYPE | 30 | 7 | 7 | 6 | 6 | 20 | 9

Figure S56. Get High-res Image Gene #62: 'del_5q23.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_6q22.31' versus 'METHYLATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0022

Table S57. Gene #63: 'del_6q22.31' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 16(6Q22.31) MUTATED | 0 | 0 | 6 | 2
DEL PEAK 16(6Q22.31) WILD-TYPE | 35 | 33 | 10 | 10

Figure S57. Get High-res Image Gene #63: 'del_6q22.31' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_6q22.31' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00707 (Fisher's exact test), Q value = 0.045

Table S58. Gene #63: 'del_6q22.31' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 16(6Q22.31) MUTATED | 1 | 4 | 2 | 1 | 0 | 0 | 0
DEL PEAK 16(6Q22.31) WILD-TYPE | 33 | 7 | 7 | 6 | 6 | 20 | 9

Figure S58. Get High-res Image Gene #63: 'del_6q22.31' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_8p23.2' versus 'METHYLATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.011

Table S59. Gene #69: 'del_8p23.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 22(8P23.2) MUTATED | 1 | 3 | 7 | 0
DEL PEAK 22(8P23.2) WILD-TYPE | 34 | 30 | 9 | 12

Figure S59. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_8p23.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0063

Table S60. Gene #69: 'del_8p23.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 22(8P23.2) MUTATED | 2 | 7 | 0 | 1 | 0 | 1 | 0
DEL PEAK 22(8P23.2) WILD-TYPE | 32 | 4 | 9 | 6 | 6 | 19 | 9

Figure S60. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_9p24.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.032

Table S61. Gene #70: 'del_9p24.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 23(9P24.3) MUTATED | 2 | 5 | 2 | 1 | 2 | 0 | 1
DEL PEAK 23(9P24.3) WILD-TYPE | 32 | 6 | 7 | 6 | 4 | 20 | 8

Figure S61. Get High-res Image Gene #70: 'del_9p24.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_9p24.1' versus 'METHYLATION_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.016

Table S62. Gene #71: 'del_9p24.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 24(9P24.1) MUTATED | 1 | 1 | 6 | 1
DEL PEAK 24(9P24.1) WILD-TYPE | 34 | 32 | 10 | 11

Figure S62. Get High-res Image Gene #71: 'del_9p24.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_9p24.1' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.015

Table S63. Gene #71: 'del_9p24.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 24(9P24.1) MUTATED | 1 | 5 | 1 | 2 | 0 | 0 | 0
DEL PEAK 24(9P24.1) WILD-TYPE | 33 | 6 | 8 | 5 | 6 | 20 | 9

Figure S63. Get High-res Image Gene #71: 'del_9p24.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_10q11.22' versus 'METHYLATION_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.11

Table S64. Gene #73: 'del_10q11.22' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 26(10Q11.22) MUTATED | 1 | 0 | 3 | 0
DEL PEAK 26(10Q11.22) WILD-TYPE | 34 | 33 | 13 | 12

Figure S64. Get High-res Image Gene #73: 'del_10q11.22' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_11p15.5' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S65. Gene #75: 'del_11p15.5' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 28(11P15.5) MUTATED | 0 | 1 | 7 | 1
DEL PEAK 28(11P15.5) WILD-TYPE | 35 | 32 | 9 | 11

Figure S65. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_11p15.5' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.014

Table S66. Gene #75: 'del_11p15.5' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 28(11P15.5) MUTATED | 1 | 5 | 1 | 2 | 0 | 0 | 0
DEL PEAK 28(11P15.5) WILD-TYPE | 33 | 6 | 8 | 5 | 6 | 20 | 9

Figure S66. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_11p15.3' versus 'METHYLATION_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.072

Table S67. Gene #76: 'del_11p15.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 29(11P15.3) MUTATED | 2 | 4 | 6 | 0
DEL PEAK 29(11P15.3) WILD-TYPE | 33 | 29 | 10 | 12

Figure S67. Get High-res Image Gene #76: 'del_11p15.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_11p15.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00251 (Fisher's exact test), Q value = 0.026

Table S68. Gene #76: 'del_11p15.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 29(11P15.3) MUTATED | 2 | 6 | 0 | 2 | 0 | 1 | 1
DEL PEAK 29(11P15.3) WILD-TYPE | 32 | 5 | 9 | 5 | 6 | 19 | 8

Figure S68. Get High-res Image Gene #76: 'del_11p15.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_11q24.2' versus 'METHYLATION_CNMF'

P value = 0.00716 (Fisher's exact test), Q value = 0.045

Table S69. Gene #78: 'del_11q24.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 31(11Q24.2) MUTATED | 4 | 3 | 7 | 0
DEL PEAK 31(11Q24.2) WILD-TYPE | 31 | 30 | 9 | 12

Figure S69. Get High-res Image Gene #78: 'del_11q24.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_11q24.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.015

Table S70. Gene #78: 'del_11q24.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 31(11Q24.2) MUTATED | 4 | 6 | 0 | 3 | 0 | 0 | 1
DEL PEAK 31(11Q24.2) WILD-TYPE | 30 | 5 | 9 | 4 | 6 | 20 | 8

Figure S70. Get High-res Image Gene #78: 'del_11q24.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_12p13.33' versus 'METHYLATION_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.08

Table S71. Gene #79: 'del_12p13.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 32(12P13.33) MUTATED | 0 | 1 | 3 | 0
DEL PEAK 32(12P13.33) WILD-TYPE | 35 | 32 | 13 | 12

Figure S71. Get High-res Image Gene #79: 'del_12p13.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_13q12.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.12

Table S72. Gene #83: 'del_13q12.11' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 28 | 20 | 11 | 20 | 21
DEL PEAK 36(13Q12.11) MUTATED | 4 | 0 | 1 | 7 | 2
DEL PEAK 36(13Q12.11) WILD-TYPE | 24 | 20 | 10 | 13 | 19

Figure S72. Get High-res Image Gene #83: 'del_13q12.11' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'del_13q12.11' versus 'METHYLATION_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.13

Table S73. Gene #83: 'del_13q12.11' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 36(13Q12.11) MUTATED | 6 | 1 | 5 | 1
DEL PEAK 36(13Q12.11) WILD-TYPE | 29 | 32 | 11 | 11

Figure S73. Get High-res Image Gene #83: 'del_13q12.11' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_13q31.3' versus 'METHYLATION_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.11

Table S74. Gene #84: 'del_13q31.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 37(13Q31.3) MUTATED | 4 | 0 | 4 | 1
DEL PEAK 37(13Q31.3) WILD-TYPE | 31 | 33 | 12 | 11

Figure S74. Get High-res Image Gene #84: 'del_13q31.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_15q11.2' versus 'METHYLATION_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.026

Table S75. Gene #86: 'del_15q11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 39(15Q11.2) MUTATED | 6 | 2 | 8 | 1
DEL PEAK 39(15Q11.2) WILD-TYPE | 29 | 31 | 8 | 11

Figure S75. Get High-res Image Gene #86: 'del_15q11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_15q15.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.059

Table S76. Gene #87: 'del_15q15.1' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 28 | 20 | 11 | 20 | 21
DEL PEAK 40(15Q15.1) MUTATED | 11 | 6 | 2 | 0 | 7
DEL PEAK 40(15Q15.1) WILD-TYPE | 17 | 14 | 9 | 20 | 14

Figure S76. Get High-res Image Gene #87: 'del_15q15.1' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'del_15q24.2' versus 'METHYLATION_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.12

Table S77. Gene #88: 'del_15q24.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 41(15Q24.2) MUTATED | 11 | 4 | 8 | 2
DEL PEAK 41(15Q24.2) WILD-TYPE | 24 | 29 | 8 | 10

Figure S77. Get High-res Image Gene #88: 'del_15q24.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_15q24.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.12

Table S78. Gene #88: 'del_15q24.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 41(15Q24.2) MUTATED | 10 | 4 | 4 | 4 | 0 | 1 | 2
DEL PEAK 41(15Q24.2) WILD-TYPE | 24 | 7 | 5 | 3 | 6 | 19 | 7

Figure S78. Get High-res Image Gene #88: 'del_15q24.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_16p13.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.16

Table S79. Gene #91: 'del_16p13.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 44(16P13.3) MUTATED | 1 | 4 | 0 | 0 | 0 | 2 | 0
DEL PEAK 44(16P13.3) WILD-TYPE | 33 | 7 | 9 | 7 | 6 | 18 | 9

Figure S79. Get High-res Image Gene #91: 'del_16p13.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_16p11.2' versus 'METHYLATION_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.029

Table S80. Gene #92: 'del_16p11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 45(16P11.2) MUTATED | 14 | 2 | 3 | 1
DEL PEAK 45(16P11.2) WILD-TYPE | 21 | 31 | 13 | 11

Figure S80. Get High-res Image Gene #92: 'del_16p11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_16p11.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.1

Table S81. Gene #92: 'del_16p11.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 45(16P11.2) MUTATED | 14 | 2 | 1 | 1 | 1 | 1 | 0
DEL PEAK 45(16P11.2) WILD-TYPE | 20 | 9 | 8 | 6 | 5 | 19 | 9

Figure S81. Get High-res Image Gene #92: 'del_16p11.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_16q22.1' versus 'METHYLATION_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.028

Table S82. Gene #93: 'del_16q22.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 46(16Q22.1) MUTATED | 3 | 1 | 6 | 0
DEL PEAK 46(16Q22.1) WILD-TYPE | 32 | 32 | 10 | 12

Figure S82. Get High-res Image Gene #93: 'del_16q22.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_16q22.1' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0463 (Fisher's exact test), Q value = 0.16

Table S83. Gene #93: 'del_16q22.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 46(16Q22.1) MUTATED | 3 | 3 | 0 | 3 | 0 | 1 | 0
DEL PEAK 46(16Q22.1) WILD-TYPE | 31 | 8 | 9 | 4 | 6 | 19 | 9

Figure S83. Get High-res Image Gene #93: 'del_16q22.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_16q22.2' versus 'METHYLATION_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.075

Table S84. Gene #94: 'del_16q22.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 47(16Q22.2) MUTATED | 6 | 2 | 6 | 0
DEL PEAK 47(16Q22.2) WILD-TYPE | 29 | 31 | 10 | 12

Figure S84. Get High-res Image Gene #94: 'del_16q22.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_17p11.2' versus 'METHYLATION_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.014

Table S85. Gene #95: 'del_17p11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 48(17P11.2) MUTATED | 2 | 6 | 8 | 0
DEL PEAK 48(17P11.2) WILD-TYPE | 33 | 27 | 8 | 12

Figure S85. Get High-res Image Gene #95: 'del_17p11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_17p11.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.014

Table S86. Gene #95: 'del_17p11.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 48(17P11.2) MUTATED | 3 | 7 | 0 | 3 | 0 | 2 | 1
DEL PEAK 48(17P11.2) WILD-TYPE | 31 | 4 | 9 | 4 | 6 | 18 | 8

Figure S86. Get High-res Image Gene #95: 'del_17p11.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_17q21.32' versus 'METHYLATION_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.026

Table S87. Gene #96: 'del_17q21.32' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 49(17Q21.32) MUTATED | 3 | 0 | 5 | 0
DEL PEAK 49(17Q21.32) WILD-TYPE | 32 | 33 | 11 | 12

Figure S87. Get High-res Image Gene #96: 'del_17q21.32' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_18q22.1' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.16

Table S88. Gene #98: 'del_18q22.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 51(18Q22.1) MUTATED | 5 | 5 | 2 | 2 | 0 | 1 | 0
DEL PEAK 51(18Q22.1) WILD-TYPE | 29 | 6 | 7 | 5 | 6 | 19 | 9

Figure S88. Get High-res Image Gene #98: 'del_18q22.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_19p13.3' versus 'METHYLATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0059

Table S89. Gene #99: 'del_19p13.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 52(19P13.3) MUTATED | 3 | 8 | 10 | 0
DEL PEAK 52(19P13.3) WILD-TYPE | 32 | 25 | 6 | 12

Figure S89. Get High-res Image Gene #99: 'del_19p13.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_19p13.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00152 (Fisher's exact test), Q value = 0.02

Table S90. Gene #99: 'del_19p13.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 52(19P13.3) MUTATED | 4 | 7 | 0 | 4 | 0 | 4 | 2
DEL PEAK 52(19P13.3) WILD-TYPE | 30 | 4 | 9 | 3 | 6 | 16 | 7

Figure S90. Get High-res Image Gene #99: 'del_19p13.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_19q13.33' versus 'METHYLATION_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.026

Table S91. Gene #102: 'del_19q13.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 55(19Q13.33) MUTATED | 3 | 2 | 7 | 0
DEL PEAK 55(19Q13.33) WILD-TYPE | 32 | 31 | 9 | 12

Figure S91. Get High-res Image Gene #102: 'del_19q13.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_xp11.23' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.12

Table S92. Gene #106: 'del_xp11.23' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 59(XP11.23) MUTATED | 19 | 9 | 3 | 5 | 1 | 6 | 3
DEL PEAK 59(XP11.23) WILD-TYPE | 15 | 2 | 6 | 2 | 5 | 14 | 6

Figure S92. Get High-res Image Gene #106: 'del_xp11.23' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_xp11.23' versus 'METHYLATION_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.15

Table S93. Gene #107: 'del_xp11.23' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 60(XP11.23) MUTATED | 9 | 15 | 8 | 1
DEL PEAK 60(XP11.23) WILD-TYPE | 26 | 18 | 8 | 11

Figure S93. Get High-res Image Gene #107: 'del_xp11.23' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_xp11.23' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00966 (Fisher's exact test), Q value = 0.056

Table S94. Gene #107: 'del_xp11.23' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 34 | 11 | 9 | 7 | 6 | 20 | 9
DEL PEAK 60(XP11.23) MUTATED | 10 | 9 | 1 | 3 | 0 | 7 | 3
DEL PEAK 60(XP11.23) WILD-TYPE | 24 | 2 | 8 | 4 | 6 | 13 | 6

Figure S94. Get High-res Image Gene #107: 'del_xp11.23' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_xp11.22' versus 'METHYLATION_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.069

Table S95. Gene #108: 'del_xp11.22' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 61(XP11.22) MUTATED | 16 | 5 | 6 | 1
DEL PEAK 61(XP11.22) WILD-TYPE | 19 | 28 | 10 | 11

Figure S95. Get High-res Image Gene #108: 'del_xp11.22' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_xq24' versus 'METHYLATION_CNMF'

P value = 0.0493 (Fisher's exact test), Q value = 0.17

Table S96. Gene #109: 'del_xq24' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 62(XQ24) MUTATED | 9 | 10 | 9 | 1
DEL PEAK 62(XQ24) WILD-TYPE | 26 | 23 | 7 | 11

Figure S96. Get High-res Image Gene #109: 'del_xq24' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_xq27.3' versus 'METHYLATION_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.028

Table S97. Gene #110: 'del_xq27.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 35 | 33 | 16 | 12
DEL PEAK 63(XQ27.3) MUTATED | 10 | 8 | 11 | 1
DEL PEAK 63(XQ27.3) WILD-TYPE | 25 | 25 | 5 | 11

Figure S97. Get High-res Image Gene #110: 'del_xq27.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

Methods & Data
Input

- Copy number data file = all_lesions.txt from GISTIC pipeline

- Processed Copy number data file = /cromwell_root/fc-8b2df640-93e1-40a2-b735-5b7a14ef6398/b8d03c5a-e1ed-4426-8834-af3b0ae152b6/correlate_genomic_events_all/b3a721d9-347a-4708-9fd3-f2507378733d/call-preprocess_genomic_event/transformed.cor.cli.txt

- Molecular subtype file = /cromwell_root/fc-8b2df640-93e1-40a2-b735-5b7a14ef6398/10d02b45-07ea-40cc-ac82-013e5f89ebb2/aggregate_clusters_workflow/b0f8dcb2-0993-4424-ad42-552c0bd1a2d5/call-aggregate_clusters/CPTAC3-UCEC-TP.transposedmergedcluster.txt

- Number of patients = 100

- Number of significantly focal cnvs = 110

- Number of molecular subtypes = 3

- Exclude genes 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.

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)
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