Correlation between copy number variation genes (focal events) and molecular subtypes
Sarcoma (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C13F4NKG
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 variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13F4NKG
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 66 focal events and 8 molecular subtypes across 257 patients, 178 significant findings detected with P value < 0.05 and Q value < 0.25.

- amp_1p32.1 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_1q21.3 cnv correlated to 'CN_CNMF'.

- amp_1q24.3 cnv correlated to 'CN_CNMF'.

- amp_2p11.2 cnv correlated to 'CN_CNMF'.

- amp_3p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_4q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_5p15.33 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- amp_6p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_6q25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- amp_7q31.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- amp_12q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- amp_13q34 cnv correlated to 'CN_CNMF'.

- amp_15q26.3 cnv correlated to 'CN_CNMF'.

- amp_17p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_17p11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- amp_19p13.2 cnv correlated to 'CN_CNMF'.

- amp_19q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- amp_20q13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- amp_21q21.1 cnv correlated to 'CN_CNMF'.

- amp_xp21.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- amp_xq21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_1p36.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_1q44 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- del_2p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- del_2q37.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- del_2q37.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- del_3p21.31 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_3q29 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_4q35.1 cnv correlated to 'CN_CNMF'.

- del_6p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- del_7q36.3 cnv correlated to 'CN_CNMF'.

- del_8p23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- del_9p21.3 cnv correlated to 'MIRSEQ_MATURE_CNMF'.

- del_9q34.3 cnv correlated to 'CN_CNMF'.

- del_10p15.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_10q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_11p15.5 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_11q24.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_12p13.1 cnv correlated to 'CN_CNMF'.

- del_12q12 cnv correlated to 'CN_CNMF'.

- del_12q24.33 cnv correlated to 'CN_CNMF'.

- del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_14q24.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- del_16q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_17p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- del_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- del_17q25.3 cnv correlated to 'CN_CNMF'.

- del_18q23 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_19p13.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- del_19q13.43 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_21q11.2 cnv correlated to 'CN_CNMF'.

- del_22q13.32 cnv correlated to 'CN_CNMF'.

- del_xp21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_xq21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- del_xq22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 66 focal 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, 178 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
amp 12q15 | 94 (37%) | 163 | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528)
del 1p36 32 | 69 (27%) | 188 | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 0.00021 (0.0817)
del 10q23 31 | 138 (54%) | 119 | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 0.00042 (0.156) | 0.00041 (0.153)
del 10q26 3 | 132 (51%) | 125 | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 0.00014 (0.0557) | 2e-05 (0.00876) | 8e-05 (0.0331) | 0.00029 (0.11)
del 13q14 2 | 180 (70%) | 77 | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 0.00024 (0.0922) | 0.00022 (0.0851)
del 16q11 2 | 130 (51%) | 127 | 1e-05 (0.00528) | 7e-05 (0.0293) | 0.00027 (0.103) | 0.00068 (0.239) | 0.00303 (0.936) | 0.0003 (0.114) | 2e-05 (0.00876) | 4e-05 (0.0171)
del 17p13 1 | 129 (50%) | 128 | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 4e-05 (0.0171) | 3e-05 (0.013) | 4e-05 (0.0171) | 3e-05 (0.013) | 0.00077 (0.266)
amp 6q25 1 | 75 (29%) | 182 | 0.00023 (0.0885) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 0.0006 (0.213) | 0.0001 (0.0407) | 0.00396 (1.00) | 0.00812 (1.00)
del 2p25 3 | 94 (37%) | 163 | 1e-05 (0.00528) | 3e-05 (0.013) | 1e-05 (0.00528) | 0.00097 (0.328) | 0.00033 (0.125) | 1e-05 (0.00528) | 0.00021 (0.0817) | 0.00074 (0.258)
del xq21 1 | 114 (44%) | 143 | 1e-05 (0.00528) | 1e-05 (0.00528) | 0.00033 (0.125) | 0.00017 (0.067) | 0.00019 (0.0741) | 0.00049 (0.179) | 0.0255 (1.00) | 0.0303 (1.00)
del xq22 3 | 123 (48%) | 134 | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 2e-05 (0.00876) | 0.00048 (0.176) | 9e-05 (0.0371) | 0.017 (1.00) | 0.0338 (1.00)
del 3p21 31 | 65 (25%) | 192 | 0.0101 (1.00) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 0.00017 (0.067) | 0.00798 (1.00) | 0.00186 (0.601) | 1e-05 (0.00528)
del 16q23 1 | 134 (52%) | 123 | 1e-05 (0.00528) | 0.00044 (0.162) | 0.00118 (0.393) | 0.00354 (1.00) | 0.00511 (1.00) | 0.00014 (0.0557) | 1e-05 (0.00528) | 7e-05 (0.0293)
amp 3p12 1 | 69 (27%) | 188 | 0.00017 (0.067) | 0.00059 (0.211) | 7e-05 (0.0293) | 9e-05 (0.0371) | 0.506 (1.00) | 0.00339 (1.00) | 0.00121 (0.402) | 0.00237 (0.751)
amp 4q12 | 78 (30%) | 179 | 0.00036 (0.135) | 0.00012 (0.0482) | 1e-05 (0.00528) | 0.00051 (0.185) | 0.0556 (1.00) | 0.0134 (1.00) | 0.0474 (1.00) | 0.0195 (1.00)
amp 6p21 1 | 60 (23%) | 197 | 3e-05 (0.013) | 1e-05 (0.00528) | 0.00045 (0.165) | 0.00012 (0.0482) | 0.0183 (1.00) | 0.0112 (1.00) | 0.289 (1.00) | 0.0419 (1.00)
amp 7q31 2 | 77 (30%) | 180 | 0.00656 (1.00) | 9e-05 (0.0371) | 0.0001 (0.0407) | 0.00188 (0.605) | 0.00148 (0.487) | 0.0457 (1.00) | 5e-05 (0.0212) | 0.00041 (0.153)
amp 20q13 33 | 98 (38%) | 159 | 1e-05 (0.00528) | 6e-05 (0.0253) | 6e-05 (0.0253) | 0.00117 (0.391) | 0.0288 (1.00) | 0.0006 (0.213) | 0.0135 (1.00) | 0.012 (1.00)
del 1q44 | 80 (31%) | 177 | 5e-05 (0.0212) | 1e-05 (0.00528) | 3e-05 (0.013) | 6e-05 (0.0253) | 0.0163 (1.00) | 0.00703 (1.00) | 0.138 (1.00) | 0.00554 (1.00)
del 17q11 2 | 81 (32%) | 176 | 0.0001 (0.0407) | 1e-05 (0.00528) | 2e-05 (0.00876) | 0.00013 (0.052) | 0.0091 (1.00) | 0.122 (1.00) | 0.012 (1.00) | 0.0162 (1.00)
amp 1p32 1 | 94 (37%) | 163 | 0.00083 (0.284) | 1e-05 (0.00528) | 1e-05 (0.00528) | 1e-05 (0.00528) | 0.00914 (1.00) | 0.00473 (1.00) | 0.211 (1.00) | 0.00073 (0.255)
amp 17p12 | 102 (40%) | 155 | 1e-05 (0.00528) | 1e-05 (0.00528) | 0.00795 (1.00) | 0.0001 (0.0407) | 0.373 (1.00) | 0.00195 (0.622) | 0.0466 (1.00) | 0.00977 (1.00)
del 6p25 3 | 81 (32%) | 176 | 1e-05 (0.00528) | 0.00059 (0.211) | 0.00014 (0.0557) | 0.00132 (0.437) | 0.0144 (1.00) | 0.0257 (1.00) | 0.0359 (1.00) | 0.272 (1.00)
del 8p23 3 | 81 (32%) | 176 | 3e-05 (0.013) | 1e-05 (0.00528) | 0.00059 (0.211) | 0.0022 (0.7) | 0.00746 (1.00) | 0.00419 (1.00) | 0.00928 (1.00) | 0.00106 (0.356)
del 18q23 | 86 (33%) | 171 | 0.0017 (0.554) | 0.00017 (0.067) | 1e-05 (0.00528) | 0.00349 (1.00) | 0.01 (1.00) | 0.146 (1.00) | 0.133 (1.00) | 0.00035 (0.132)
amp 5p15 33 | 119 (46%) | 138 | 1e-05 (0.00528) | 0.0129 (1.00) | 0.0271 (1.00) | 0.0005 (0.182) | 0.343 (1.00) | 0.0134 (1.00) | 0.688 (1.00) | 0.747 (1.00)
amp 17p11 2 | 104 (40%) | 153 | 1e-05 (0.00528) | 1e-05 (0.00528) | 0.00526 (1.00) | 0.00441 (1.00) | 0.778 (1.00) | 0.00188 (0.605) | 0.0852 (1.00) | 0.00578 (1.00)
amp 19q12 | 93 (36%) | 164 | 1e-05 (0.00528) | 7e-05 (0.0293) | 0.0317 (1.00) | 0.00581 (1.00) | 0.693 (1.00) | 0.00931 (1.00) | 0.769 (1.00) | 0.0264 (1.00)
amp xp21 2 | 97 (38%) | 160 | 1e-05 (0.00528) | 0.00027 (0.103) | 0.116 (1.00) | 0.00688 (1.00) | 0.925 (1.00) | 0.0405 (1.00) | 0.304 (1.00) | 0.0109 (1.00)
amp xq21 1 | 46 (18%) | 211 | 0.00013 (0.052) | 0.00051 (0.185) | 0.0396 (1.00) | 0.0237 (1.00) | 0.109 (1.00) | 0.405 (1.00) | 0.589 (1.00) | 0.586 (1.00)
del 2q37 3 | 108 (42%) | 149 | 1e-05 (0.00528) | 0.006 (1.00) | 0.0183 (1.00) | 0.00039 (0.146) | 0.204 (1.00) | 0.00632 (1.00) | 0.0548 (1.00) | 0.0492 (1.00)
del 2q37 3 | 110 (43%) | 147 | 1e-05 (0.00528) | 0.00098 (0.33) | 0.00811 (1.00) | 0.0005 (0.182) | 0.631 (1.00) | 0.0246 (1.00) | 0.477 (1.00) | 0.156 (1.00)
del 3q29 | 54 (21%) | 203 | 0.00067 (0.236) | 0.00022 (0.0851) | 0.198 (1.00) | 0.0839 (1.00) | 0.301 (1.00) | 0.0384 (1.00) | 0.215 (1.00) | 0.071 (1.00)
del 10p15 3 | 128 (50%) | 129 | 1e-05 (0.00528) | 1e-05 (0.00528) | 0.364 (1.00) | 0.00901 (1.00) | 0.284 (1.00) | 0.0195 (1.00) | 0.727 (1.00) | 0.566 (1.00)
del 11p15 5 | 110 (43%) | 147 | 1e-05 (0.00528) | 0.00054 (0.194) | 0.487 (1.00) | 0.145 (1.00) | 0.477 (1.00) | 0.318 (1.00) | 0.737 (1.00) | 0.758 (1.00)
del 11q24 2 | 123 (48%) | 134 | 1e-05 (0.00528) | 1e-05 (0.00528) | 0.00243 (0.768) | 0.00134 (0.442) | 0.0545 (1.00) | 0.0407 (1.00) | 0.376 (1.00) | 0.0329 (1.00)
del 14q24 1 | 80 (31%) | 177 | 1e-05 (0.00528) | 0.00078 (0.268) | 0.235 (1.00) | 1e-05 (0.00528) | 0.108 (1.00) | 0.00446 (1.00) | 0.162 (1.00) | 0.0257 (1.00)
del 19p13 3 | 70 (27%) | 187 | 9e-05 (0.0371) | 0.00181 (0.588) | 0.0001 (0.0407) | 0.00453 (1.00) | 0.0183 (1.00) | 0.00396 (1.00) | 0.00114 (0.382) | 0.0192 (1.00)
del 19q13 43 | 106 (41%) | 151 | 1e-05 (0.00528) | 0.00038 (0.142) | 0.39 (1.00) | 0.276 (1.00) | 0.385 (1.00) | 0.0333 (1.00) | 0.435 (1.00) | 0.00767 (1.00)
del xp21 1 | 55 (21%) | 202 | 0.00043 (0.159) | 0.00061 (0.215) | 0.0101 (1.00) | 0.0249 (1.00) | 0.00858 (1.00) | 0.1 (1.00) | 0.32 (1.00) | 0.109 (1.00)
amp 1q21 3 | 104 (40%) | 153 | 1e-05 (0.00528) | 0.00799 (1.00) | 0.174 (1.00) | 0.0919 (1.00) | 0.554 (1.00) | 0.132 (1.00) | 0.0624 (1.00) | 0.248 (1.00)
amp 1q24 3 | 102 (40%) | 155 | 1e-05 (0.00528) | 0.00504 (1.00) | 0.0474 (1.00) | 0.213 (1.00) | 0.888 (1.00) | 0.135 (1.00) | 0.616 (1.00) | 0.491 (1.00)
amp 2p11 2 | 64 (25%) | 193 | 0.00054 (0.194) | 0.00876 (1.00) | 0.917 (1.00) | 0.877 (1.00) | 1 (1.00) | 0.316 (1.00) | 0.767 (1.00) | 1 (1.00)
amp 13q34 | 54 (21%) | 203 | 0.00014 (0.0557) | 0.0107 (1.00) | 0.219 (1.00) | 0.0333 (1.00) | 0.512 (1.00) | 0.141 (1.00) | 0.803 (1.00) | 0.00977 (1.00)
amp 15q26 3 | 84 (33%) | 173 | 1e-05 (0.00528) | 0.00422 (1.00) | 0.849 (1.00) | 0.278 (1.00) | 0.812 (1.00) | 0.184 (1.00) | 0.878 (1.00) | 0.697 (1.00)
amp 19p13 2 | 107 (42%) | 150 | 1e-05 (0.00528) | 0.0186 (1.00) | 0.0835 (1.00) | 0.0493 (1.00) | 0.76 (1.00) | 0.267 (1.00) | 0.946 (1.00) | 0.0811 (1.00)
amp 21q21 1 | 73 (28%) | 184 | 1e-05 (0.00528) | 0.00079 (0.271) | 0.0852 (1.00) | 0.248 (1.00) | 0.397 (1.00) | 0.141 (1.00) | 0.603 (1.00) | 0.374 (1.00)
del 4q35 1 | 94 (37%) | 163 | 1e-05 (0.00528) | 0.00194 (0.621) | 0.0897 (1.00) | 0.0444 (1.00) | 0.859 (1.00) | 0.108 (1.00) | 1 (1.00) | 0.551 (1.00)
del 7q36 3 | 71 (28%) | 186 | 2e-05 (0.00876) | 0.0622 (1.00) | 0.0174 (1.00) | 0.157 (1.00) | 0.108 (1.00) | 0.00554 (1.00) | 0.086 (1.00) | 0.514 (1.00)
del 9p21 3 | 114 (44%) | 143 | 0.0332 (1.00) | 0.111 (1.00) | 0.00074 (0.258) | 0.00582 (1.00) | 0.0251 (1.00) | 0.557 (1.00) | 7e-05 (0.0293) | 0.0016 (0.525)
del 9q34 3 | 61 (24%) | 196 | 1e-05 (0.00528) | 0.00246 (0.775) | 0.0254 (1.00) | 0.132 (1.00) | 0.00268 (0.836) | 0.00271 (0.843) | 0.105 (1.00) | 0.0408 (1.00)
del 12p13 1 | 87 (34%) | 170 | 1e-05 (0.00528) | 0.00084 (0.286) | 0.0313 (1.00) | 0.00535 (1.00) | 0.227 (1.00) | 0.0337 (1.00) | 0.33 (1.00) | 0.33 (1.00)
del 12q12 | 56 (22%) | 201 | 9e-05 (0.0371) | 0.00874 (1.00) | 0.0953 (1.00) | 0.0158 (1.00) | 0.0446 (1.00) | 0.0304 (1.00) | 0.108 (1.00) | 0.395 (1.00)
del 12q24 33 | 69 (27%) | 188 | 8e-05 (0.0331) | 0.00167 (0.546) | 0.725 (1.00) | 0.0171 (1.00) | 0.242 (1.00) | 0.125 (1.00) | 0.159 (1.00) | 0.464 (1.00)
del 17q25 3 | 67 (26%) | 190 | 1e-05 (0.00528) | 0.00742 (1.00) | 0.196 (1.00) | 0.359 (1.00) | 0.608 (1.00) | 0.00782 (1.00) | 0.207 (1.00) | 0.104 (1.00)
del 21q11 2 | 51 (20%) | 206 | 0.00044 (0.162) | 0.22 (1.00) | 0.0361 (1.00) | 0.282 (1.00) | 0.00246 (0.775) | 0.955 (1.00) | 0.0681 (1.00) | 0.288 (1.00)
del 22q13 32 | 83 (32%) | 174 | 1e-05 (0.00528) | 0.0629 (1.00) | 0.845 (1.00) | 0.0356 (1.00) | 0.287 (1.00) | 0.44 (1.00) | 0.946 (1.00) | 0.534 (1.00)
amp 8p11 22 | 81 (32%) | 176 | 0.00092 (0.313) | 0.0835 (1.00) | 0.00291 (0.902) | 0.0362 (1.00) | 0.151 (1.00) | 0.0103 (1.00) | 0.421 (1.00) | 0.164 (1.00)
amp 8q24 21 | 83 (32%) | 174 | 0.00782 (1.00) | 0.0431 (1.00) | 0.0338 (1.00) | 0.238 (1.00) | 0.539 (1.00) | 0.291 (1.00) | 0.174 (1.00) | 0.348 (1.00)
amp 11q22 2 | 36 (14%) | 221 | 0.0269 (1.00) | 0.0285 (1.00) | 0.0129 (1.00) | 0.0532 (1.00) | 0.316 (1.00) | 0.00428 (1.00) | 0.651 (1.00) | 0.0549 (1.00)
amp 17q24 3 | 79 (31%) | 178 | 0.00096 (0.325) | 0.00248 (0.776) | 0.0691 (1.00) | 0.00477 (1.00) | 0.106 (1.00) | 0.153 (1.00) | 0.066 (1.00) | 0.256 (1.00)
del 3q13 31 | 51 (20%) | 206 | 0.00665 (1.00) | 0.00183 (0.593) | 0.0115 (1.00) | 0.0109 (1.00) | 0.0177 (1.00) | 0.0186 (1.00) | 0.0216 (1.00) | 0.0306 (1.00)
del 5p15 33 | 33 (13%) | 224 | 0.243 (1.00) | 0.0868 (1.00) | 0.00077 (0.266) | 0.00075 (0.26) | 0.132 (1.00) | 0.611 (1.00) | 0.0495 (1.00) | 0.0552 (1.00)
del 6q14 1 | 78 (30%) | 179 | 0.00824 (1.00) | 0.00443 (1.00) | 0.231 (1.00) | 0.565 (1.00) | 0.453 (1.00) | 0.591 (1.00) | 0.0368 (1.00) | 0.967 (1.00)
del 9p24 3 | 100 (39%) | 157 | 0.215 (1.00) | 0.732 (1.00) | 0.0234 (1.00) | 0.438 (1.00) | 0.198 (1.00) | 0.913 (1.00) | 0.0671 (1.00) | 0.803 (1.00)
del 21q22 3 | 66 (26%) | 191 | 0.00474 (1.00) | 0.0082 (1.00) | 0.0208 (1.00) | 0.0654 (1.00) | 0.436 (1.00) | 0.0572 (1.00) | 0.431 (1.00) | 0.48 (1.00)

'amp_1p32.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S1. Gene #1: 'amp_1p32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
AMP PEAK 1(1P32.1) MUTATED | 15 | 14 | 12 | 3 | 3 | 35 | 3
AMP PEAK 1(1P32.1) WILD-TYPE | 27 | 27 | 45 | 29 | 15 | 8 | 2

Figure S1. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1p32.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S2. Gene #1: 'amp_1p32.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
AMP PEAK 1(1P32.1) MUTATED | 25 | 16 | 45 | 8
AMP PEAK 1(1P32.1) WILD-TYPE | 43 | 60 | 18 | 38

Figure S2. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_1p32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S3. Gene #1: 'amp_1p32.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
AMP PEAK 1(1P32.1) MUTATED | 19 | 8 | 10 | 7 | 43 | 6 | 1
AMP PEAK 1(1P32.1) WILD-TYPE | 28 | 14 | 39 | 21 | 16 | 23 | 18

Figure S3. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S4. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 2(1Q21.3) MUTATED | 15 | 6 | 17 | 15 | 18 | 32 | 1
AMP PEAK 2(1Q21.3) WILD-TYPE | 11 | 52 | 26 | 36 | 16 | 12 | 0

Figure S4. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S5. Gene #3: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 3(1Q24.3) MUTATED | 13 | 11 | 20 | 12 | 14 | 31 | 1
AMP PEAK 3(1Q24.3) WILD-TYPE | 13 | 47 | 23 | 39 | 20 | 13 | 0

Figure S5. Get High-res Image Gene #3: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p11.2' versus 'CN_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.19

Table S6. Gene #4: 'amp_2p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 4(2P11.2) MUTATED | 3 | 5 | 15 | 12 | 16 | 13 | 0
AMP PEAK 4(2P11.2) WILD-TYPE | 23 | 53 | 28 | 39 | 18 | 31 | 1

Figure S6. Get High-res Image Gene #4: 'amp_2p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p12.1' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.067

Table S7. Gene #5: 'amp_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 5(3P12.1) MUTATED | 11 | 9 | 9 | 6 | 14 | 20 | 0
AMP PEAK 5(3P12.1) WILD-TYPE | 15 | 49 | 34 | 45 | 20 | 24 | 1

Figure S7. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p12.1' versus 'METHLYATION_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.21

Table S8. Gene #5: 'amp_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
AMP PEAK 5(3P12.1) MUTATED | 14 | 11 | 15 | 1 | 1 | 18 | 0
AMP PEAK 5(3P12.1) WILD-TYPE | 28 | 30 | 42 | 31 | 17 | 25 | 5

Figure S8. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3p12.1' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.029

Table S9. Gene #5: 'amp_3p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
AMP PEAK 5(3P12.1) MUTATED | 21 | 16 | 28 | 3
AMP PEAK 5(3P12.1) WILD-TYPE | 47 | 60 | 35 | 43

Figure S9. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.037

Table S10. Gene #5: 'amp_3p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
AMP PEAK 5(3P12.1) MUTATED | 18 | 7 | 12 | 2 | 25 | 4 | 0
AMP PEAK 5(3P12.1) WILD-TYPE | 29 | 15 | 37 | 26 | 34 | 25 | 19

Figure S10. Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.14

Table S11. Gene #6: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 6(4Q12) MUTATED | 8 | 7 | 12 | 13 | 16 | 22 | 0
AMP PEAK 6(4Q12) WILD-TYPE | 18 | 51 | 31 | 38 | 18 | 22 | 1

Figure S11. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.048

Table S12. Gene #6: 'amp_4q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
AMP PEAK 6(4Q12) MUTATED | 16 | 12 | 11 | 5 | 1 | 23 | 3
AMP PEAK 6(4Q12) WILD-TYPE | 26 | 29 | 46 | 27 | 17 | 20 | 2

Figure S12. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S13. Gene #6: 'amp_4q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
AMP PEAK 6(4Q12) MUTATED | 26 | 14 | 32 | 6
AMP PEAK 6(4Q12) WILD-TYPE | 42 | 62 | 31 | 40

Figure S13. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.18

Table S14. Gene #6: 'amp_4q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
AMP PEAK 6(4Q12) MUTATED | 19 | 8 | 7 | 8 | 28 | 7 | 1
AMP PEAK 6(4Q12) WILD-TYPE | 28 | 14 | 42 | 20 | 31 | 22 | 18

Figure S14. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S15. Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 7(5P15.33) MUTATED | 26 | 14 | 23 | 21 | 14 | 21 | 0
AMP PEAK 7(5P15.33) WILD-TYPE | 0 | 44 | 20 | 30 | 20 | 23 | 1

Figure S15. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.18

Table S16. Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
AMP PEAK 7(5P15.33) MUTATED | 33 | 8 | 23 | 9 | 32 | 6 | 7
AMP PEAK 7(5P15.33) WILD-TYPE | 14 | 14 | 26 | 19 | 27 | 23 | 12

Figure S16. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S17. Gene #8: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 8(6P21.1) MUTATED | 10 | 5 | 14 | 4 | 8 | 19 | 0
AMP PEAK 8(6P21.1) WILD-TYPE | 16 | 53 | 29 | 47 | 26 | 25 | 1

Figure S17. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S18. Gene #8: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
AMP PEAK 8(6P21.1) MUTATED | 20 | 5 | 5 | 5 | 0 | 17 | 3
AMP PEAK 8(6P21.1) WILD-TYPE | 22 | 36 | 52 | 27 | 18 | 26 | 2

Figure S18. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.17

Table S19. Gene #8: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
AMP PEAK 8(6P21.1) MUTATED | 25 | 7 | 19 | 9
AMP PEAK 8(6P21.1) WILD-TYPE | 43 | 69 | 44 | 37

Figure S19. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.048

Table S20. Gene #8: 'amp_6p21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
AMP PEAK 8(6P21.1) MUTATED | 21 | 3 | 3 | 6 | 20 | 4 | 3
AMP PEAK 8(6P21.1) WILD-TYPE | 26 | 19 | 46 | 22 | 39 | 25 | 16

Figure S20. Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.089

Table S21. Gene #9: 'amp_6q25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 9(6Q25.1) MUTATED | 10 | 11 | 23 | 6 | 10 | 15 | 0
AMP PEAK 9(6Q25.1) WILD-TYPE | 16 | 47 | 20 | 45 | 24 | 29 | 1

Figure S21. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S22. Gene #9: 'amp_6q25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
AMP PEAK 9(6Q25.1) MUTATED | 27 | 15 | 7 | 3 | 1 | 16 | 1
AMP PEAK 9(6Q25.1) WILD-TYPE | 15 | 26 | 50 | 29 | 17 | 27 | 4

Figure S22. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S23. Gene #9: 'amp_6q25.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
AMP PEAK 9(6Q25.1) MUTATED | 38 | 8 | 20 | 8
AMP PEAK 9(6Q25.1) WILD-TYPE | 30 | 68 | 43 | 38

Figure S23. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S24. Gene #9: 'amp_6q25.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
AMP PEAK 9(6Q25.1) MUTATED | 26 | 13 | 5 | 8 | 17 | 3 | 2
AMP PEAK 9(6Q25.1) WILD-TYPE | 21 | 9 | 44 | 20 | 42 | 26 | 17

Figure S24. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.21

Table S25. Gene #9: 'amp_6q25.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 47 | 99
AMP PEAK 9(6Q25.1) MUTATED | 43 | 16 | 16
AMP PEAK 9(6Q25.1) WILD-TYPE | 66 | 31 | 83

Figure S25. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_6q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.041

Table S26. Gene #9: 'amp_6q25.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 82 | 37 | 114 | 22
AMP PEAK 9(6Q25.1) MUTATED | 37 | 14 | 22 | 2
AMP PEAK 9(6Q25.1) WILD-TYPE | 45 | 23 | 92 | 20

Figure S26. Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.037

Table S27. Gene #10: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
AMP PEAK 10(7Q31.2) MUTATED | 21 | 13 | 8 | 6 | 1 | 17 | 3
AMP PEAK 10(7Q31.2) WILD-TYPE | 21 | 28 | 49 | 26 | 17 | 26 | 2

Figure S27. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.041

Table S28. Gene #10: 'amp_7q31.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
AMP PEAK 10(7Q31.2) MUTATED | 28 | 10 | 27 | 12
AMP PEAK 10(7Q31.2) WILD-TYPE | 40 | 66 | 36 | 34

Figure S28. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.021

Table S29. Gene #10: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 85 | 64 | 45
AMP PEAK 10(7Q31.2) MUTATED | 24 | 11 | 26
AMP PEAK 10(7Q31.2) WILD-TYPE | 61 | 53 | 19

Figure S29. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.15

Table S30. Gene #10: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 24 | 32 | 37 | 23 | 12 | 23 | 21 | 22
AMP PEAK 10(7Q31.2) MUTATED | 11 | 12 | 5 | 12 | 1 | 3 | 12 | 5
AMP PEAK 10(7Q31.2) WILD-TYPE | 13 | 20 | 32 | 11 | 11 | 20 | 9 | 17

Figure S30. Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S31. Gene #14: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 14(12Q15) MUTATED | 9 | 19 | 41 | 11 | 7 | 7 | 0
AMP PEAK 14(12Q15) WILD-TYPE | 17 | 39 | 2 | 40 | 27 | 37 | 1

Figure S31. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S32. Gene #14: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
AMP PEAK 14(12Q15) MUTATED | 27 | 25 | 1 | 13 | 2 | 14 | 2
AMP PEAK 14(12Q15) WILD-TYPE | 15 | 16 | 56 | 19 | 16 | 29 | 3

Figure S32. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S33. Gene #14: 'amp_12q15' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
AMP PEAK 14(12Q15) MUTATED | 43 | 2 | 26 | 23
AMP PEAK 14(12Q15) WILD-TYPE | 25 | 74 | 37 | 23

Figure S33. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S34. Gene #14: 'amp_12q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
AMP PEAK 14(12Q15) MUTATED | 30 | 13 | 1 | 19 | 24 | 1 | 6
AMP PEAK 14(12Q15) WILD-TYPE | 17 | 9 | 48 | 9 | 35 | 28 | 13

Figure S34. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S35. Gene #14: 'amp_12q15' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 47 | 99
AMP PEAK 14(12Q15) MUTATED | 58 | 23 | 11
AMP PEAK 14(12Q15) WILD-TYPE | 51 | 24 | 88

Figure S35. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S36. Gene #14: 'amp_12q15' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 82 | 37 | 114 | 22
AMP PEAK 14(12Q15) MUTATED | 50 | 19 | 16 | 7
AMP PEAK 14(12Q15) WILD-TYPE | 32 | 18 | 98 | 15

Figure S36. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S37. Gene #14: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 85 | 64 | 45
AMP PEAK 14(12Q15) MUTATED | 48 | 7 | 20
AMP PEAK 14(12Q15) WILD-TYPE | 37 | 57 | 25

Figure S37. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S38. Gene #14: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 24 | 32 | 37 | 23 | 12 | 23 | 21 | 22
AMP PEAK 14(12Q15) MUTATED | 8 | 27 | 0 | 10 | 1 | 10 | 10 | 9
AMP PEAK 14(12Q15) WILD-TYPE | 16 | 5 | 37 | 13 | 11 | 13 | 11 | 13

Figure S38. Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.056

Table S39. Gene #15: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 15(13Q34) MUTATED | 7 | 4 | 5 | 8 | 11 | 19 | 0
AMP PEAK 15(13Q34) WILD-TYPE | 19 | 54 | 38 | 43 | 23 | 25 | 1

Figure S39. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S40. Gene #16: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 16(15Q26.3) MUTATED | 17 | 0 | 18 | 20 | 18 | 11 | 0
AMP PEAK 16(15Q26.3) WILD-TYPE | 9 | 58 | 25 | 31 | 16 | 33 | 1

Figure S40. Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S41. Gene #17: 'amp_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 17(17P12) MUTATED | 10 | 4 | 12 | 21 | 34 | 20 | 1
AMP PEAK 17(17P12) WILD-TYPE | 16 | 54 | 31 | 30 | 0 | 24 | 0

Figure S41. Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S42. Gene #17: 'amp_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
AMP PEAK 17(17P12) MUTATED | 19 | 8 | 32 | 6 | 2 | 27 | 1
AMP PEAK 17(17P12) WILD-TYPE | 23 | 33 | 25 | 26 | 16 | 16 | 4

Figure S42. Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.041

Table S43. Gene #17: 'amp_17p12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
AMP PEAK 17(17P12) MUTATED | 24 | 2 | 26 | 10 | 27 | 11 | 1
AMP PEAK 17(17P12) WILD-TYPE | 23 | 20 | 23 | 18 | 32 | 18 | 18

Figure S43. Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S44. Gene #18: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 18(17P11.2) MUTATED | 12 | 4 | 11 | 21 | 33 | 22 | 1
AMP PEAK 18(17P11.2) WILD-TYPE | 14 | 54 | 32 | 30 | 1 | 22 | 0

Figure S44. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S45. Gene #18: 'amp_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
AMP PEAK 18(17P11.2) MUTATED | 20 | 7 | 30 | 7 | 1 | 30 | 1
AMP PEAK 18(17P11.2) WILD-TYPE | 22 | 34 | 27 | 25 | 17 | 13 | 4

Figure S45. Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S46. Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 20(19P13.2) MUTATED | 17 | 6 | 25 | 21 | 15 | 23 | 0
AMP PEAK 20(19P13.2) WILD-TYPE | 9 | 52 | 18 | 30 | 19 | 21 | 1

Figure S46. Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S47. Gene #21: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 21(19Q12) MUTATED | 17 | 2 | 20 | 7 | 21 | 26 | 0
AMP PEAK 21(19Q12) WILD-TYPE | 9 | 56 | 23 | 44 | 13 | 18 | 1

Figure S47. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.029

Table S48. Gene #21: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
AMP PEAK 21(19Q12) MUTATED | 23 | 10 | 15 | 8 | 2 | 25 | 2
AMP PEAK 21(19Q12) WILD-TYPE | 19 | 31 | 42 | 24 | 16 | 18 | 3

Figure S48. Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S49. Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 22(20Q13.33) MUTATED | 18 | 6 | 22 | 19 | 15 | 18 | 0
AMP PEAK 22(20Q13.33) WILD-TYPE | 8 | 52 | 21 | 32 | 19 | 26 | 1

Figure S49. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.025

Table S50. Gene #22: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
AMP PEAK 22(20Q13.33) MUTATED | 25 | 12 | 13 | 10 | 3 | 27 | 1
AMP PEAK 22(20Q13.33) WILD-TYPE | 17 | 29 | 44 | 22 | 15 | 16 | 4

Figure S50. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.025

Table S51. Gene #22: 'amp_20q13.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
AMP PEAK 22(20Q13.33) MUTATED | 29 | 16 | 37 | 15
AMP PEAK 22(20Q13.33) WILD-TYPE | 39 | 60 | 26 | 31

Figure S51. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.21

Table S52. Gene #22: 'amp_20q13.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 82 | 37 | 114 | 22
AMP PEAK 22(20Q13.33) MUTATED | 43 | 15 | 38 | 2
AMP PEAK 22(20Q13.33) WILD-TYPE | 39 | 22 | 76 | 20

Figure S52. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_21q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S53. Gene #23: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 23(21Q21.1) MUTATED | 19 | 7 | 12 | 5 | 16 | 14 | 0
AMP PEAK 23(21Q21.1) WILD-TYPE | 7 | 51 | 31 | 46 | 18 | 30 | 1

Figure S53. Get High-res Image Gene #23: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S54. Gene #24: 'amp_xp21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 24(XP21.2) MUTATED | 14 | 7 | 20 | 9 | 27 | 20 | 0
AMP PEAK 24(XP21.2) WILD-TYPE | 12 | 51 | 23 | 42 | 7 | 24 | 1

Figure S54. Get High-res Image Gene #24: 'amp_xp21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp21.2' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.1

Table S55. Gene #24: 'amp_xp21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
AMP PEAK 24(XP21.2) MUTATED | 26 | 10 | 23 | 7 | 2 | 19 | 3
AMP PEAK 24(XP21.2) WILD-TYPE | 16 | 31 | 34 | 25 | 16 | 24 | 2

Figure S55. Get High-res Image Gene #24: 'amp_xp21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq21.1' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.052

Table S56. Gene #25: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
AMP PEAK 25(XQ21.1) MUTATED | 10 | 3 | 16 | 5 | 5 | 7 | 0
AMP PEAK 25(XQ21.1) WILD-TYPE | 16 | 55 | 27 | 46 | 29 | 37 | 1

Figure S56. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq21.1' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.18

Table S57. Gene #25: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
AMP PEAK 25(XQ21.1) MUTATED | 15 | 4 | 4 | 6 | 1 | 11 | 3
AMP PEAK 25(XQ21.1) WILD-TYPE | 27 | 37 | 53 | 26 | 17 | 32 | 2

Figure S57. Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S58. Gene #26: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 1(1P36.32) MUTATED | 7 | 3 | 5 | 30 | 12 | 11 | 1
DEL PEAK 1(1P36.32) WILD-TYPE | 19 | 55 | 38 | 21 | 22 | 33 | 0

Figure S58. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S59. Gene #26: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 1(1P36.32) MUTATED | 8 | 1 | 36 | 8 | 6 | 5 | 3
DEL PEAK 1(1P36.32) WILD-TYPE | 34 | 40 | 21 | 24 | 12 | 38 | 2

Figure S59. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S60. Gene #26: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 1(1P36.32) MUTATED | 9 | 44 | 7 | 8
DEL PEAK 1(1P36.32) WILD-TYPE | 59 | 32 | 56 | 38

Figure S60. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S61. Gene #26: 'del_1p36.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 1(1P36.32) MUTATED | 8 | 1 | 30 | 3 | 6 | 15 | 5
DEL PEAK 1(1P36.32) WILD-TYPE | 39 | 21 | 19 | 25 | 53 | 14 | 14

Figure S61. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S62. Gene #26: 'del_1p36.32' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 47 | 99
DEL PEAK 1(1P36.32) MUTATED | 14 | 6 | 49
DEL PEAK 1(1P36.32) WILD-TYPE | 95 | 41 | 50

Figure S62. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S63. Gene #26: 'del_1p36.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 82 | 37 | 114 | 22
DEL PEAK 1(1P36.32) MUTATED | 11 | 3 | 51 | 4
DEL PEAK 1(1P36.32) WILD-TYPE | 71 | 34 | 63 | 18

Figure S63. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S64. Gene #26: 'del_1p36.32' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 85 | 64 | 45
DEL PEAK 1(1P36.32) MUTATED | 14 | 31 | 4
DEL PEAK 1(1P36.32) WILD-TYPE | 71 | 33 | 41

Figure S64. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.082

Table S65. Gene #26: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 24 | 32 | 37 | 23 | 12 | 23 | 21 | 22
DEL PEAK 1(1P36.32) MUTATED | 4 | 5 | 18 | 4 | 8 | 2 | 3 | 5
DEL PEAK 1(1P36.32) WILD-TYPE | 20 | 27 | 19 | 19 | 4 | 21 | 18 | 17

Figure S65. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.021

Table S66. Gene #27: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 2(1Q44) MUTATED | 9 | 5 | 18 | 12 | 16 | 20 | 0
DEL PEAK 2(1Q44) WILD-TYPE | 17 | 53 | 25 | 39 | 18 | 24 | 1

Figure S66. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S67. Gene #27: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 2(1Q44) MUTATED | 23 | 10 | 10 | 3 | 2 | 22 | 2
DEL PEAK 2(1Q44) WILD-TYPE | 19 | 31 | 47 | 29 | 16 | 21 | 3

Figure S67. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q44' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S68. Gene #27: 'del_1q44' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 2(1Q44) MUTATED | 32 | 13 | 27 | 8
DEL PEAK 2(1Q44) WILD-TYPE | 36 | 63 | 36 | 38

Figure S68. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.025

Table S69. Gene #27: 'del_1q44' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 2(1Q44) MUTATED | 27 | 6 | 10 | 8 | 24 | 3 | 2
DEL PEAK 2(1Q44) WILD-TYPE | 20 | 16 | 39 | 20 | 35 | 26 | 17

Figure S69. Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S70. Gene #28: 'del_2p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 3(2P25.3) MUTATED | 16 | 5 | 9 | 20 | 21 | 23 | 0
DEL PEAK 3(2P25.3) WILD-TYPE | 10 | 53 | 34 | 31 | 13 | 21 | 1

Figure S70. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p25.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S71. Gene #28: 'del_2p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 3(2P25.3) MUTATED | 18 | 7 | 33 | 3 | 6 | 15 | 3
DEL PEAK 3(2P25.3) WILD-TYPE | 24 | 34 | 24 | 29 | 12 | 28 | 2

Figure S71. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S72. Gene #28: 'del_2p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 3(2P25.3) MUTATED | 26 | 42 | 21 | 4
DEL PEAK 3(2P25.3) WILD-TYPE | 42 | 34 | 42 | 42

Figure S72. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.13

Table S73. Gene #28: 'del_2p25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 47 | 99
DEL PEAK 3(2P25.3) MUTATED | 25 | 20 | 48
DEL PEAK 3(2P25.3) WILD-TYPE | 84 | 27 | 51

Figure S73. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_2p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S74. Gene #28: 'del_2p25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 82 | 37 | 114 | 22
DEL PEAK 3(2P25.3) MUTATED | 27 | 10 | 56 | 0
DEL PEAK 3(2P25.3) WILD-TYPE | 55 | 27 | 58 | 22

Figure S74. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.082

Table S75. Gene #28: 'del_2p25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 85 | 64 | 45
DEL PEAK 3(2P25.3) MUTATED | 19 | 35 | 19
DEL PEAK 3(2P25.3) WILD-TYPE | 66 | 29 | 26

Figure S75. Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S76. Gene #29: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 4(2Q37.3) MUTATED | 16 | 8 | 12 | 10 | 22 | 39 | 1
DEL PEAK 4(2Q37.3) WILD-TYPE | 10 | 50 | 31 | 41 | 12 | 5 | 0

Figure S76. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.15

Table S77. Gene #29: 'del_2q37.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 4(2Q37.3) MUTATED | 27 | 6 | 16 | 9 | 27 | 19 | 2
DEL PEAK 4(2Q37.3) WILD-TYPE | 20 | 16 | 33 | 19 | 32 | 10 | 17

Figure S77. Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S78. Gene #30: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 5(2Q37.3) MUTATED | 16 | 7 | 14 | 11 | 22 | 39 | 1
DEL PEAK 5(2Q37.3) WILD-TYPE | 10 | 51 | 29 | 40 | 12 | 5 | 0

Figure S78. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.18

Table S79. Gene #30: 'del_2q37.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 5(2Q37.3) MUTATED | 29 | 6 | 16 | 9 | 26 | 19 | 3
DEL PEAK 5(2Q37.3) WILD-TYPE | 18 | 16 | 33 | 19 | 33 | 10 | 16

Figure S79. Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S80. Gene #31: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 6(3P21.31) MUTATED | 21 | 5 | 2 | 10 | 2 | 13 | 1
DEL PEAK 6(3P21.31) WILD-TYPE | 21 | 36 | 55 | 22 | 16 | 30 | 4

Figure S80. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S81. Gene #31: 'del_3p21.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 6(3P21.31) MUTATED | 28 | 4 | 15 | 18
DEL PEAK 6(3P21.31) WILD-TYPE | 40 | 72 | 48 | 28

Figure S81. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S82. Gene #31: 'del_3p21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 6(3P21.31) MUTATED | 23 | 5 | 2 | 9 | 13 | 3 | 10
DEL PEAK 6(3P21.31) WILD-TYPE | 24 | 17 | 47 | 19 | 46 | 26 | 9

Figure S82. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.067

Table S83. Gene #31: 'del_3p21.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 47 | 99
DEL PEAK 6(3P21.31) MUTATED | 39 | 14 | 12
DEL PEAK 6(3P21.31) WILD-TYPE | 70 | 33 | 87

Figure S83. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S84. Gene #31: 'del_3p21.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 24 | 32 | 37 | 23 | 12 | 23 | 21 | 22
DEL PEAK 6(3P21.31) MUTATED | 12 | 14 | 0 | 8 | 2 | 4 | 5 | 10
DEL PEAK 6(3P21.31) WILD-TYPE | 12 | 18 | 37 | 15 | 10 | 19 | 16 | 12

Figure S84. Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.24

Table S85. Gene #33: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 8(3Q29) MUTATED | 4 | 4 | 19 | 8 | 8 | 11 | 0
DEL PEAK 8(3Q29) WILD-TYPE | 22 | 54 | 24 | 43 | 26 | 33 | 1

Figure S85. Get High-res Image Gene #33: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.085

Table S86. Gene #33: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 8(3Q29) MUTATED | 14 | 3 | 10 | 5 | 0 | 12 | 4
DEL PEAK 8(3Q29) WILD-TYPE | 28 | 38 | 47 | 27 | 18 | 31 | 1

Figure S86. Get High-res Image Gene #33: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S87. Gene #34: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 9(4Q35.1) MUTATED | 16 | 10 | 13 | 11 | 19 | 24 | 1
DEL PEAK 9(4Q35.1) WILD-TYPE | 10 | 48 | 30 | 40 | 15 | 20 | 0

Figure S87. Get High-res Image Gene #34: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S88. Gene #36: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 11(6P25.3) MUTATED | 4 | 6 | 10 | 27 | 18 | 16 | 0
DEL PEAK 11(6P25.3) WILD-TYPE | 22 | 52 | 33 | 24 | 16 | 28 | 1

Figure S88. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.21

Table S89. Gene #36: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 11(6P25.3) MUTATED | 10 | 7 | 31 | 6 | 4 | 17 | 2
DEL PEAK 11(6P25.3) WILD-TYPE | 32 | 34 | 26 | 26 | 14 | 26 | 3

Figure S89. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.056

Table S90. Gene #36: 'del_6p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 11(6P25.3) MUTATED | 12 | 37 | 21 | 8
DEL PEAK 11(6P25.3) WILD-TYPE | 56 | 39 | 42 | 38

Figure S90. Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0088

Table S91. Gene #38: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 13(7Q36.3) MUTATED | 9 | 5 | 11 | 11 | 9 | 26 | 0
DEL PEAK 13(7Q36.3) WILD-TYPE | 17 | 53 | 32 | 40 | 25 | 18 | 1

Figure S91. Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S92. Gene #39: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 14(8P23.3) MUTATED | 5 | 8 | 23 | 10 | 14 | 21 | 0
DEL PEAK 14(8P23.3) WILD-TYPE | 21 | 50 | 20 | 41 | 20 | 23 | 1

Figure S92. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S93. Gene #39: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 14(8P23.3) MUTATED | 22 | 6 | 6 | 10 | 2 | 23 | 3
DEL PEAK 14(8P23.3) WILD-TYPE | 20 | 35 | 51 | 22 | 16 | 20 | 2

Figure S93. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.21

Table S94. Gene #39: 'del_8p23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 14(8P23.3) MUTATED | 30 | 12 | 26 | 12
DEL PEAK 14(8P23.3) WILD-TYPE | 38 | 64 | 37 | 34

Figure S94. Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.029

Table S95. Gene #41: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 85 | 64 | 45
DEL PEAK 16(9P21.3) MUTATED | 41 | 19 | 32
DEL PEAK 16(9P21.3) WILD-TYPE | 44 | 45 | 13

Figure S95. Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S96. Gene #42: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 17(9Q34.3) MUTATED | 8 | 3 | 7 | 10 | 15 | 17 | 1
DEL PEAK 17(9Q34.3) WILD-TYPE | 18 | 55 | 36 | 41 | 19 | 27 | 0

Figure S96. Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S97. Gene #43: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 18(10P15.3) MUTATED | 14 | 10 | 20 | 34 | 25 | 25 | 0
DEL PEAK 18(10P15.3) WILD-TYPE | 12 | 48 | 23 | 17 | 9 | 19 | 1

Figure S97. Get High-res Image Gene #43: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S98. Gene #43: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 18(10P15.3) MUTATED | 28 | 9 | 38 | 14 | 4 | 23 | 3
DEL PEAK 18(10P15.3) WILD-TYPE | 14 | 32 | 19 | 18 | 14 | 20 | 2

Figure S98. Get High-res Image Gene #43: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S99. Gene #44: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 19(10Q23.31) MUTATED | 16 | 8 | 12 | 42 | 26 | 33 | 1
DEL PEAK 19(10Q23.31) WILD-TYPE | 10 | 50 | 31 | 9 | 8 | 11 | 0

Figure S99. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S100. Gene #44: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 19(10Q23.31) MUTATED | 26 | 6 | 50 | 8 | 6 | 29 | 4
DEL PEAK 19(10Q23.31) WILD-TYPE | 16 | 35 | 7 | 24 | 12 | 14 | 1

Figure S100. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S101. Gene #44: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 19(10Q23.31) MUTATED | 29 | 60 | 36 | 12
DEL PEAK 19(10Q23.31) WILD-TYPE | 39 | 16 | 27 | 34

Figure S101. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S102. Gene #44: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 19(10Q23.31) MUTATED | 25 | 7 | 46 | 7 | 33 | 15 | 4
DEL PEAK 19(10Q23.31) WILD-TYPE | 22 | 15 | 3 | 21 | 26 | 14 | 15

Figure S102. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S103. Gene #44: 'del_10q23.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 47 | 99
DEL PEAK 19(10Q23.31) MUTATED | 42 | 26 | 69
DEL PEAK 19(10Q23.31) WILD-TYPE | 67 | 21 | 30

Figure S103. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S104. Gene #44: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 82 | 37 | 114 | 22
DEL PEAK 19(10Q23.31) MUTATED | 38 | 14 | 81 | 4
DEL PEAK 19(10Q23.31) WILD-TYPE | 44 | 23 | 33 | 18

Figure S104. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.16

Table S105. Gene #44: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 85 | 64 | 45
DEL PEAK 19(10Q23.31) MUTATED | 35 | 47 | 24
DEL PEAK 19(10Q23.31) WILD-TYPE | 50 | 17 | 21

Figure S105. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.15

Table S106. Gene #44: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 24 | 32 | 37 | 23 | 12 | 23 | 21 | 22
DEL PEAK 19(10Q23.31) MUTATED | 15 | 12 | 30 | 13 | 8 | 14 | 9 | 5
DEL PEAK 19(10Q23.31) WILD-TYPE | 9 | 20 | 7 | 10 | 4 | 9 | 12 | 17

Figure S106. Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S107. Gene #45: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 20(10Q26.3) MUTATED | 14 | 8 | 11 | 42 | 24 | 32 | 1
DEL PEAK 20(10Q26.3) WILD-TYPE | 12 | 50 | 32 | 9 | 10 | 12 | 0

Figure S107. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S108. Gene #45: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 20(10Q26.3) MUTATED | 23 | 7 | 47 | 6 | 7 | 31 | 4
DEL PEAK 20(10Q26.3) WILD-TYPE | 19 | 34 | 10 | 26 | 11 | 12 | 1

Figure S108. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S109. Gene #45: 'del_10q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 20(10Q26.3) MUTATED | 24 | 56 | 39 | 11
DEL PEAK 20(10Q26.3) WILD-TYPE | 44 | 20 | 24 | 35

Figure S109. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S110. Gene #45: 'del_10q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 20(10Q26.3) MUTATED | 21 | 7 | 41 | 6 | 35 | 16 | 4
DEL PEAK 20(10Q26.3) WILD-TYPE | 26 | 15 | 8 | 22 | 24 | 13 | 15

Figure S110. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.056

Table S111. Gene #45: 'del_10q26.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 47 | 99
DEL PEAK 20(10Q26.3) MUTATED | 39 | 27 | 64
DEL PEAK 20(10Q26.3) WILD-TYPE | 70 | 20 | 35

Figure S111. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0088

Table S112. Gene #45: 'del_10q26.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 82 | 37 | 114 | 22
DEL PEAK 20(10Q26.3) MUTATED | 37 | 14 | 76 | 3
DEL PEAK 20(10Q26.3) WILD-TYPE | 45 | 23 | 38 | 19

Figure S112. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.033

Table S113. Gene #45: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 85 | 64 | 45
DEL PEAK 20(10Q26.3) MUTATED | 32 | 47 | 24
DEL PEAK 20(10Q26.3) WILD-TYPE | 53 | 17 | 21

Figure S113. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.11

Table S114. Gene #45: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 24 | 32 | 37 | 23 | 12 | 23 | 21 | 22
DEL PEAK 20(10Q26.3) MUTATED | 14 | 10 | 29 | 12 | 9 | 14 | 10 | 5
DEL PEAK 20(10Q26.3) WILD-TYPE | 10 | 22 | 8 | 11 | 3 | 9 | 11 | 17

Figure S114. Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S115. Gene #46: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 21(11P15.5) MUTATED | 14 | 3 | 27 | 21 | 20 | 25 | 0
DEL PEAK 21(11P15.5) WILD-TYPE | 12 | 55 | 16 | 30 | 14 | 19 | 1

Figure S115. Get High-res Image Gene #46: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.19

Table S116. Gene #46: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 21(11P15.5) MUTATED | 25 | 9 | 29 | 9 | 3 | 21 | 3
DEL PEAK 21(11P15.5) WILD-TYPE | 17 | 32 | 28 | 23 | 15 | 22 | 2

Figure S116. Get High-res Image Gene #46: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S117. Gene #47: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 22(11Q24.2) MUTATED | 12 | 8 | 32 | 16 | 20 | 35 | 0
DEL PEAK 22(11Q24.2) WILD-TYPE | 14 | 50 | 11 | 35 | 14 | 9 | 1

Figure S117. Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S118. Gene #47: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 22(11Q24.2) MUTATED | 35 | 12 | 23 | 10 | 2 | 27 | 4
DEL PEAK 22(11Q24.2) WILD-TYPE | 7 | 29 | 34 | 22 | 16 | 16 | 1

Figure S118. Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S119. Gene #48: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 23(12P13.1) MUTATED | 17 | 9 | 18 | 6 | 17 | 20 | 0
DEL PEAK 23(12P13.1) WILD-TYPE | 9 | 49 | 25 | 45 | 17 | 24 | 1

Figure S119. Get High-res Image Gene #48: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q12' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.037

Table S120. Gene #49: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 24(12Q12) MUTATED | 9 | 3 | 7 | 9 | 14 | 13 | 1
DEL PEAK 24(12Q12) WILD-TYPE | 17 | 55 | 36 | 42 | 20 | 31 | 0

Figure S120. Get High-res Image Gene #49: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.033

Table S121. Gene #50: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 25(12Q24.33) MUTATED | 14 | 7 | 10 | 8 | 15 | 14 | 1
DEL PEAK 25(12Q24.33) WILD-TYPE | 12 | 51 | 33 | 43 | 19 | 30 | 0

Figure S121. Get High-res Image Gene #50: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S122. Gene #51: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 26(13Q14.2) MUTATED | 21 | 13 | 27 | 47 | 31 | 40 | 1
DEL PEAK 26(13Q14.2) WILD-TYPE | 5 | 45 | 16 | 4 | 3 | 4 | 0

Figure S122. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S123. Gene #51: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 26(13Q14.2) MUTATED | 34 | 18 | 55 | 12 | 9 | 34 | 5
DEL PEAK 26(13Q14.2) WILD-TYPE | 8 | 23 | 2 | 20 | 9 | 9 | 0

Figure S123. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S124. Gene #51: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 26(13Q14.2) MUTATED | 41 | 68 | 50 | 19
DEL PEAK 26(13Q14.2) WILD-TYPE | 27 | 8 | 13 | 27

Figure S124. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S125. Gene #51: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 26(13Q14.2) MUTATED | 34 | 11 | 47 | 13 | 44 | 22 | 7
DEL PEAK 26(13Q14.2) WILD-TYPE | 13 | 11 | 2 | 15 | 15 | 7 | 12

Figure S125. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S126. Gene #51: 'del_13q14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 47 | 99
DEL PEAK 26(13Q14.2) MUTATED | 61 | 32 | 85
DEL PEAK 26(13Q14.2) WILD-TYPE | 48 | 15 | 14

Figure S126. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S127. Gene #51: 'del_13q14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 82 | 37 | 114 | 22
DEL PEAK 26(13Q14.2) MUTATED | 54 | 20 | 97 | 7
DEL PEAK 26(13Q14.2) WILD-TYPE | 28 | 17 | 17 | 15

Figure S127. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.092

Table S128. Gene #51: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 85 | 64 | 45
DEL PEAK 26(13Q14.2) MUTATED | 50 | 56 | 35
DEL PEAK 26(13Q14.2) WILD-TYPE | 35 | 8 | 10

Figure S128. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.085

Table S129. Gene #51: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 24 | 32 | 37 | 23 | 12 | 23 | 21 | 22
DEL PEAK 26(13Q14.2) MUTATED | 17 | 21 | 36 | 19 | 8 | 16 | 15 | 9
DEL PEAK 26(13Q14.2) WILD-TYPE | 7 | 11 | 1 | 4 | 4 | 7 | 6 | 13

Figure S129. Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S130. Gene #52: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 27(14Q24.1) MUTATED | 7 | 4 | 19 | 18 | 5 | 26 | 1
DEL PEAK 27(14Q24.1) WILD-TYPE | 19 | 54 | 24 | 33 | 29 | 18 | 0

Figure S130. Get High-res Image Gene #52: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S131. Gene #52: 'del_14q24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 27(14Q24.1) MUTATED | 21 | 5 | 9 | 9 | 13 | 21 | 2
DEL PEAK 27(14Q24.1) WILD-TYPE | 26 | 17 | 40 | 19 | 46 | 8 | 17

Figure S131. Get High-res Image Gene #52: 'del_14q24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S132. Gene #53: 'del_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 28(16Q11.2) MUTATED | 14 | 10 | 18 | 33 | 28 | 26 | 1
DEL PEAK 28(16Q11.2) WILD-TYPE | 12 | 48 | 25 | 18 | 6 | 18 | 0

Figure S132. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q11.2' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.029

Table S133. Gene #53: 'del_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 28(16Q11.2) MUTATED | 23 | 11 | 40 | 9 | 9 | 28 | 2
DEL PEAK 28(16Q11.2) WILD-TYPE | 19 | 30 | 17 | 23 | 9 | 15 | 3

Figure S133. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.1

Table S134. Gene #53: 'del_16q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 28(16Q11.2) MUTATED | 28 | 50 | 37 | 14
DEL PEAK 28(16Q11.2) WILD-TYPE | 40 | 26 | 26 | 32

Figure S134. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.24

Table S135. Gene #53: 'del_16q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 28(16Q11.2) MUTATED | 24 | 8 | 34 | 7 | 34 | 17 | 5
DEL PEAK 28(16Q11.2) WILD-TYPE | 23 | 14 | 15 | 21 | 25 | 12 | 14

Figure S135. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.11

Table S136. Gene #53: 'del_16q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 82 | 37 | 114 | 22
DEL PEAK 28(16Q11.2) MUTATED | 38 | 11 | 73 | 7
DEL PEAK 28(16Q11.2) WILD-TYPE | 44 | 26 | 41 | 15

Figure S136. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0088

Table S137. Gene #53: 'del_16q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 85 | 64 | 45
DEL PEAK 28(16Q11.2) MUTATED | 31 | 47 | 29
DEL PEAK 28(16Q11.2) WILD-TYPE | 54 | 17 | 16

Figure S137. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S138. Gene #53: 'del_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 24 | 32 | 37 | 23 | 12 | 23 | 21 | 22
DEL PEAK 28(16Q11.2) MUTATED | 12 | 10 | 31 | 14 | 8 | 13 | 14 | 5
DEL PEAK 28(16Q11.2) WILD-TYPE | 12 | 22 | 6 | 9 | 4 | 10 | 7 | 17

Figure S138. Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S139. Gene #54: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 29(16Q23.1) MUTATED | 14 | 11 | 19 | 33 | 27 | 29 | 1
DEL PEAK 29(16Q23.1) WILD-TYPE | 12 | 47 | 24 | 18 | 7 | 15 | 0

Figure S139. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.16

Table S140. Gene #54: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 29(16Q23.1) MUTATED | 26 | 13 | 40 | 10 | 9 | 27 | 2
DEL PEAK 29(16Q23.1) WILD-TYPE | 16 | 28 | 17 | 22 | 9 | 16 | 3

Figure S140. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.056

Table S141. Gene #54: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 82 | 37 | 114 | 22
DEL PEAK 29(16Q23.1) MUTATED | 40 | 12 | 75 | 6
DEL PEAK 29(16Q23.1) WILD-TYPE | 42 | 25 | 39 | 16

Figure S141. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S142. Gene #54: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 85 | 64 | 45
DEL PEAK 29(16Q23.1) MUTATED | 31 | 47 | 31
DEL PEAK 29(16Q23.1) WILD-TYPE | 54 | 17 | 14

Figure S142. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.029

Table S143. Gene #54: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 24 | 32 | 37 | 23 | 12 | 23 | 21 | 22
DEL PEAK 29(16Q23.1) MUTATED | 14 | 10 | 30 | 15 | 9 | 10 | 15 | 6
DEL PEAK 29(16Q23.1) WILD-TYPE | 10 | 22 | 7 | 8 | 3 | 13 | 6 | 16

Figure S143. Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S144. Gene #55: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 30(17P13.1) MUTATED | 9 | 9 | 13 | 45 | 23 | 29 | 1
DEL PEAK 30(17P13.1) WILD-TYPE | 17 | 49 | 30 | 6 | 11 | 15 | 0

Figure S144. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S145. Gene #55: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 30(17P13.1) MUTATED | 15 | 13 | 46 | 12 | 8 | 22 | 2
DEL PEAK 30(17P13.1) WILD-TYPE | 27 | 28 | 11 | 20 | 10 | 21 | 3

Figure S145. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S146. Gene #55: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 30(17P13.1) MUTATED | 23 | 54 | 35 | 15
DEL PEAK 30(17P13.1) WILD-TYPE | 45 | 22 | 28 | 31

Figure S146. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S147. Gene #55: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 30(17P13.1) MUTATED | 18 | 9 | 40 | 7 | 29 | 14 | 10
DEL PEAK 30(17P13.1) WILD-TYPE | 29 | 13 | 9 | 21 | 30 | 15 | 9

Figure S147. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S148. Gene #55: 'del_17p13.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 47 | 99
DEL PEAK 30(17P13.1) MUTATED | 37 | 26 | 64
DEL PEAK 30(17P13.1) WILD-TYPE | 72 | 21 | 35

Figure S148. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S149. Gene #55: 'del_17p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 82 | 37 | 114 | 22
DEL PEAK 30(17P13.1) MUTATED | 30 | 16 | 75 | 6
DEL PEAK 30(17P13.1) WILD-TYPE | 52 | 21 | 39 | 16

Figure S149. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S150. Gene #55: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 85 | 64 | 45
DEL PEAK 30(17P13.1) MUTATED | 27 | 44 | 29
DEL PEAK 30(17P13.1) WILD-TYPE | 58 | 20 | 16

Figure S150. Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.041

Table S151. Gene #56: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 31(17Q11.2) MUTATED | 13 | 7 | 19 | 10 | 15 | 17 | 0
DEL PEAK 31(17Q11.2) WILD-TYPE | 13 | 51 | 24 | 41 | 19 | 27 | 1

Figure S151. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S152. Gene #56: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 31(17Q11.2) MUTATED | 22 | 8 | 9 | 9 | 0 | 23 | 2
DEL PEAK 31(17Q11.2) WILD-TYPE | 20 | 33 | 48 | 23 | 18 | 20 | 3

Figure S152. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0088

Table S153. Gene #56: 'del_17q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 31(17Q11.2) MUTATED | 30 | 10 | 29 | 12
DEL PEAK 31(17Q11.2) WILD-TYPE | 38 | 66 | 34 | 34

Figure S153. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.052

Table S154. Gene #56: 'del_17q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 31(17Q11.2) MUTATED | 24 | 7 | 7 | 7 | 26 | 3 | 7
DEL PEAK 31(17Q11.2) WILD-TYPE | 23 | 15 | 42 | 21 | 33 | 26 | 12

Figure S154. Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17q25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S155. Gene #57: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 32(17Q25.3) MUTATED | 13 | 5 | 13 | 6 | 17 | 12 | 1
DEL PEAK 32(17Q25.3) WILD-TYPE | 13 | 53 | 30 | 45 | 17 | 32 | 0

Figure S155. Get High-res Image Gene #57: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.067

Table S156. Gene #58: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 33(18Q23) MUTATED | 14 | 13 | 14 | 6 | 3 | 28 | 1
DEL PEAK 33(18Q23) WILD-TYPE | 28 | 28 | 43 | 26 | 15 | 15 | 4

Figure S156. Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S157. Gene #58: 'del_18q23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 33(18Q23) MUTATED | 21 | 17 | 37 | 10
DEL PEAK 33(18Q23) WILD-TYPE | 47 | 59 | 26 | 36

Figure S157. Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.13

Table S158. Gene #58: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 24 | 32 | 37 | 23 | 12 | 23 | 21 | 22
DEL PEAK 33(18Q23) MUTATED | 6 | 8 | 9 | 11 | 2 | 14 | 15 | 5
DEL PEAK 33(18Q23) WILD-TYPE | 18 | 24 | 28 | 12 | 10 | 9 | 6 | 17

Figure S158. Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.037

Table S159. Gene #59: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 34(19P13.3) MUTATED | 9 | 5 | 8 | 16 | 17 | 14 | 1
DEL PEAK 34(19P13.3) WILD-TYPE | 17 | 53 | 35 | 35 | 17 | 30 | 0

Figure S159. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.041

Table S160. Gene #59: 'del_19p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 34(19P13.3) MUTATED | 9 | 31 | 23 | 7
DEL PEAK 34(19P13.3) WILD-TYPE | 59 | 45 | 40 | 39

Figure S160. Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S161. Gene #60: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 35(19Q13.43) MUTATED | 12 | 3 | 21 | 30 | 15 | 25 | 0
DEL PEAK 35(19Q13.43) WILD-TYPE | 14 | 55 | 22 | 21 | 19 | 19 | 1

Figure S161. Get High-res Image Gene #60: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.14

Table S162. Gene #60: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 35(19Q13.43) MUTATED | 23 | 6 | 30 | 8 | 7 | 20 | 3
DEL PEAK 35(19Q13.43) WILD-TYPE | 19 | 35 | 27 | 24 | 11 | 23 | 2

Figure S162. Get High-res Image Gene #60: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.16

Table S163. Gene #61: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 36(21Q11.2) MUTATED | 2 | 3 | 7 | 17 | 7 | 15 | 0
DEL PEAK 36(21Q11.2) WILD-TYPE | 24 | 55 | 36 | 34 | 27 | 29 | 1

Figure S163. Get High-res Image Gene #61: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S164. Gene #63: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 38(22Q13.32) MUTATED | 9 | 8 | 9 | 9 | 18 | 29 | 1
DEL PEAK 38(22Q13.32) WILD-TYPE | 17 | 50 | 34 | 42 | 16 | 15 | 0

Figure S164. Get High-res Image Gene #63: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.16

Table S165. Gene #64: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 39(XP21.1) MUTATED | 5 | 5 | 6 | 19 | 4 | 15 | 1
DEL PEAK 39(XP21.1) WILD-TYPE | 21 | 53 | 37 | 32 | 30 | 29 | 0

Figure S165. Get High-res Image Gene #64: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.22

Table S166. Gene #64: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 39(XP21.1) MUTATED | 5 | 1 | 19 | 7 | 7 | 10 | 2
DEL PEAK 39(XP21.1) WILD-TYPE | 37 | 40 | 38 | 25 | 11 | 33 | 3

Figure S166. Get High-res Image Gene #64: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S167. Gene #65: 'del_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 40(XQ21.1) MUTATED | 14 | 5 | 16 | 30 | 23 | 25 | 1
DEL PEAK 40(XQ21.1) WILD-TYPE | 12 | 53 | 27 | 21 | 11 | 19 | 0

Figure S167. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S168. Gene #65: 'del_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 40(XQ21.1) MUTATED | 20 | 7 | 41 | 11 | 8 | 15 | 2
DEL PEAK 40(XQ21.1) WILD-TYPE | 22 | 34 | 16 | 21 | 10 | 28 | 3

Figure S168. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.1' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.13

Table S169. Gene #65: 'del_xq21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 40(XQ21.1) MUTATED | 25 | 50 | 22 | 16
DEL PEAK 40(XQ21.1) WILD-TYPE | 43 | 26 | 41 | 30

Figure S169. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_xq21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.067

Table S170. Gene #65: 'del_xq21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 40(XQ21.1) MUTATED | 19 | 6 | 36 | 13 | 19 | 15 | 5
DEL PEAK 40(XQ21.1) WILD-TYPE | 28 | 16 | 13 | 15 | 40 | 14 | 14

Figure S170. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.1' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.074

Table S171. Gene #65: 'del_xq21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 47 | 99
DEL PEAK 40(XQ21.1) MUTATED | 36 | 17 | 60
DEL PEAK 40(XQ21.1) WILD-TYPE | 73 | 30 | 39

Figure S171. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_xq21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.18

Table S172. Gene #65: 'del_xq21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 82 | 37 | 114 | 22
DEL PEAK 40(XQ21.1) MUTATED | 28 | 12 | 67 | 6
DEL PEAK 40(XQ21.1) WILD-TYPE | 54 | 25 | 47 | 16

Figure S172. Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_xq22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S173. Gene #66: 'del_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 26 | 58 | 43 | 51 | 34 | 44 | 1
DEL PEAK 41(XQ22.3) MUTATED | 14 | 7 | 17 | 31 | 24 | 29 | 1
DEL PEAK 41(XQ22.3) WILD-TYPE | 12 | 51 | 26 | 20 | 10 | 15 | 0

Figure S173. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S174. Gene #66: 'del_xq22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 42 | 41 | 57 | 32 | 18 | 43 | 5
DEL PEAK 41(XQ22.3) MUTATED | 23 | 7 | 42 | 8 | 9 | 19 | 4
DEL PEAK 41(XQ22.3) WILD-TYPE | 19 | 34 | 15 | 24 | 9 | 24 | 1

Figure S174. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S175. Gene #66: 'del_xq22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 68 | 76 | 63 | 46
DEL PEAK 41(XQ22.3) MUTATED | 33 | 54 | 22 | 13
DEL PEAK 41(XQ22.3) WILD-TYPE | 35 | 22 | 41 | 33

Figure S175. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_xq22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0088

Table S176. Gene #66: 'del_xq22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 47 | 22 | 49 | 28 | 59 | 29 | 19
DEL PEAK 41(XQ22.3) MUTATED | 27 | 5 | 35 | 11 | 21 | 19 | 4
DEL PEAK 41(XQ22.3) WILD-TYPE | 20 | 17 | 14 | 17 | 38 | 10 | 15

Figure S176. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_xq22.3' versus 'MIRSEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.18

Table S177. Gene #66: 'del_xq22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 47 | 99
DEL PEAK 41(XQ22.3) MUTATED | 40 | 19 | 62
DEL PEAK 41(XQ22.3) WILD-TYPE | 69 | 28 | 37

Figure S177. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_xq22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.037

Table S178. Gene #66: 'del_xq22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 82 | 37 | 114 | 22
DEL PEAK 41(XQ22.3) MUTATED | 32 | 10 | 72 | 7
DEL PEAK 41(XQ22.3) WILD-TYPE | 50 | 27 | 42 | 15

Figure S178. Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

- Copy number data file = transformed.cor.cli.txt

- Molecular subtype file = SARC-TP.transferedmergedcluster.txt

- Number of patients = 257

- Number of significantly focal cnvs = 66

- Number of molecular subtypes = 8

- 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.

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle