Correlation between copy number variation genes and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C16D5R76
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C16D5R76
Overview
Introduction

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

Summary

Testing the association between copy number variation of 48 peak regions and 12 molecular subtypes across 269 patients, 116 significant findings detected with Q value < 0.25.

- Amp Peak 1(1q22) cnvs correlated to 'CN_CNMF'.

- Amp Peak 2(1q32.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- Amp Peak 6(7p11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- Amp Peak 7(7q32.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- Amp Peak 8(8q24.12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- Amp Peak 9(10p15.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- Amp Peak 11(12p13.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 12(12p12.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- Amp Peak 13(12q14.1) cnvs correlated to 'CN_CNMF'.

- Amp Peak 14(13q33.3) cnvs correlated to 'CN_CNMF'.

- Amp Peak 15(17q25.1) cnvs correlated to 'CN_CNMF'.

- Amp Peak 16(18q23) cnvs correlated to 'RPPA_CNMF' and 'MIRSEQ_MATURE_CNMF'.

- Amp Peak 17(19p13.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 18(19q13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- Amp Peak 19(Xp22.33) cnvs correlated to 'CN_CNMF'.

- Amp Peak 20(Xp11.22) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 1(1p36.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- Del Peak 2(1p32.3) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- Del Peak 4(2p25.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 5(2q37.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 6(2q37.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- Del Peak 7(3p21.1) cnvs correlated to 'CN_CNMF' and 'RPPA_CNMF'.

- Del Peak 8(4q35.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 9(5q35.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 11(6q24.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

- Del Peak 12(9p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- Del Peak 13(10q26.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- Del Peak 14(11p15.5) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 15(11q25) cnvs correlated to 'CN_CNMF'.

- Del Peak 16(12q12) cnvs correlated to 'CN_CNMF'.

- Del Peak 17(13q14.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 18(13q21.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 19(13q22.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 20(13q34) cnvs correlated to 'CN_CNMF'.

- Del Peak 21(14q24.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

- Del Peak 25(19q13.42) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- Del Peak 26(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 27(Xp22.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 28(Xq21.1) cnvs correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 48 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 116 significant findings detected.

|  | Molecular subtypes | MRNA CNMF | MRNA CHIERARCHICAL | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | 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 | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test
Del Peak 1(1p36 31) | 0 (0%) | 173 | 0.000549 (0.239) | 5.86e-05 (0.0274) | 8.49e-14 (4.53e-11) | 4.92e-43 (2.7e-40) | 0.000732 (0.313) | 0.54 (1.00) | 7.9e-06 (0.00382) | 3.23e-23 (1.75e-20) | 8.86e-06 (0.00426) | 0.000303 (0.134) | 1.15e-08 (5.91e-06) | 0.000104 (0.0479)
Del Peak 2(1p32 3) | 0 (0%) | 181 | 0.0286 (1.00) | 0.000173 (0.0782) | 2.21e-17 (1.19e-14) | 2.3e-48 (1.27e-45) | 0.000477 (0.209) | 0.235 (1.00) | 2.73e-09 (1.42e-06) | 3.06e-27 (1.67e-24) | 5.78e-08 (2.93e-05) | 3.2e-05 (0.0151) | 1.54e-09 (8.09e-07) | 1.09e-06 (0.00054)
Del Peak 13(10q26 3) | 0 (0%) | 188 | 0.179 (1.00) | 0.022 (1.00) | 6.21e-19 (3.35e-16) | 1.3e-20 (7.03e-18) | 1.56e-07 (7.9e-05) | 0.000214 (0.0967) | 2.13e-08 (1.08e-05) | 2.92e-09 (1.52e-06) | 0.00461 (1.00) | 5.98e-06 (0.00292) | 4.5e-09 (2.32e-06) | 1.26e-11 (6.69e-09)
Del Peak 25(19q13 42) | 0 (0%) | 133 | 0.0353 (1.00) | 0.127 (1.00) | 1.55e-15 (8.27e-13) | 9.49e-28 (5.17e-25) | 0.00212 (0.877) | 0.6 (1.00) | 7.99e-07 (0.000399) | 9.06e-15 (4.84e-12) | 8.24e-05 (0.0382) | 0.000298 (0.132) | 2.28e-05 (0.0108) | 5.19e-08 (2.64e-05)
Amp Peak 6(7p11 2) | 0 (0%) | 196 | 0.864 (1.00) | 0.726 (1.00) | 2.06e-29 (1.12e-26) | 4.41e-16 (2.36e-13) | 0.000113 (0.052) | 0.00626 (1.00) | 1.96e-05 (0.00933) | 0.000756 (0.322) | 0.00133 (0.558) | 6.43e-06 (0.00312) | 4.5e-07 (0.000226) | 3.1e-12 (1.65e-09)
Amp Peak 18(19q13 2) | 0 (0%) | 250 | 0.369 (1.00) | 0.194 (1.00) | 7.29e-07 (0.000365) | 1.01e-05 (0.00485) | 0.0381 (1.00) | 0.34 (1.00) | 0.000122 (0.0558) | 0.00316 (1.00) | 0.00251 (1.00) | 0.00397 (1.00) | 5.25e-06 (0.00258) | 5.89e-06 (0.00288)
Del Peak 12(9p21 3) | 0 (0%) | 170 | 0.333 (1.00) | 0.0153 (1.00) | 3.04e-11 (1.61e-08) | 2.66e-08 (1.36e-05) | 8.67e-06 (0.00418) | 9.22e-05 (0.0425) | 0.0237 (1.00) | 0.00935 (1.00) | 0.177 (1.00) | 0.206 (1.00) | 0.0574 (1.00) | 0.000199 (0.0899)
Del Peak 26(22q13 31) | 0 (0%) | 229 | 0.25 (1.00) | 0.0588 (1.00) | 1.41e-09 (7.41e-07) | 2.85e-06 (0.00141) | 6.75e-05 (0.0315) | 0.0187 (1.00) | 6.92e-06 (0.00336) | 3.77e-05 (0.0178) | 0.011 (1.00) | 0.0269 (1.00) | 0.0161 (1.00) | 0.00779 (1.00)
Amp Peak 2(1q32 1) | 0 (0%) | 242 |  |  | 2.14e-07 (0.000108) | 2.28e-06 (0.00113) | 0.104 (1.00) | 0.846 (1.00) | 0.00996 (1.00) | 0.249 (1.00) | 0.618 (1.00) | 8.96e-05 (0.0415) | 0.0219 (1.00) | 2.79e-05 (0.0132)
Amp Peak 7(7q32 3) | 0 (0%) | 169 | 0.764 (1.00) | 0.755 (1.00) | 5.19e-23 (2.81e-20) | 2.11e-08 (1.08e-05) | 0.00814 (1.00) | 0.0242 (1.00) | 0.000267 (0.119) | 0.0012 (0.507) | 0.068 (1.00) | 0.00428 (1.00) | 0.00282 (1.00) | 1.02e-05 (0.00489)
Amp Peak 8(8q24 12) | 0 (0%) | 214 | 0.37 (1.00) | 0.164 (1.00) | 2.32e-12 (1.23e-09) | 5.52e-09 (2.85e-06) | 0.0287 (1.00) | 0.884 (1.00) | 0.225 (1.00) | 0.00715 (1.00) | 0.221 (1.00) | 0.18 (1.00) | 0.000257 (0.115) | 0.00178 (0.736)
Amp Peak 9(10p15 3) | 0 (0%) | 228 | 0.526 (1.00) | 0.207 (1.00) | 1e-09 (5.27e-07) | 2.97e-09 (1.54e-06) | 0.0343 (1.00) | 0.244 (1.00) | 0.352 (1.00) | 0.000605 (0.262) | 0.0993 (1.00) | 0.225 (1.00) | 0.000284 (0.126) | 0.0465 (1.00)
Amp Peak 12(12p12 1) | 0 (0%) | 241 | 1 (1.00) | 0.0138 (1.00) | 4.75e-06 (0.00234) | 0.0256 (1.00) | 0.169 (1.00) | 0.688 (1.00) | 0.000601 (0.261) | 0.000392 (0.173) | 0.00479 (1.00) | 0.023 (1.00) | 6.84e-05 (0.0318) | 0.161 (1.00)
Amp Peak 20(Xp11 22) | 0 (0%) | 231 | 0.651 (1.00) | 0.892 (1.00) | 1.84e-09 (9.65e-07) | 1.54e-06 (0.000762) | 0.0268 (1.00) | 0.143 (1.00) | 0.0835 (1.00) | 0.000355 (0.156) | 0.132 (1.00) | 0.0575 (1.00) | 0.292 (1.00) | 0.0226 (1.00)
Del Peak 6(2q37 3) | 0 (0%) | 229 | 0.18 (1.00) | 0.116 (1.00) | 6.07e-06 (0.00296) | 1.8e-07 (9.09e-05) | 0.0119 (1.00) | 0.0217 (1.00) | 0.227 (1.00) | 0.00405 (1.00) | 0.589 (1.00) | 0.155 (1.00) | 0.231 (1.00) | 0.000114 (0.0522)
Del Peak 14(11p15 5) | 0 (0%) | 212 | 0.642 (1.00) | 0.000741 (0.316) | 1.88e-09 (9.8e-07) | 2.11e-10 (1.11e-07) | 0.146 (1.00) | 0.849 (1.00) | 0.00267 (1.00) | 2.62e-05 (0.0124) | 0.229 (1.00) | 0.364 (1.00) | 0.147 (1.00) | 0.378 (1.00)
Amp Peak 11(12p13 32) | 0 (0%) | 226 | 0.864 (1.00) | 0.0486 (1.00) | 1.69e-10 (8.94e-08) | 5.16e-05 (0.0243) | 0.116 (1.00) | 0.218 (1.00) | 0.0218 (1.00) | 0.00214 (0.88) | 0.0142 (1.00) | 0.0371 (1.00) | 0.000803 (0.341) | 0.0776 (1.00)
Amp Peak 16(18q23) | 0 (0%) | 257 |  |  | 0.00133 (0.558) | 0.0268 (1.00) | 0.000132 (0.0601) | 1 (1.00) | 0.00594 (1.00) | 0.00296 (1.00) | 0.0543 (1.00) | 0.322 (1.00) | 0.00027 (0.12) | 0.083 (1.00)
Amp Peak 17(19p13 3) | 0 (0%) | 209 | 0.186 (1.00) | 0.41 (1.00) | 9.09e-05 (0.042) | 1.07e-08 (5.5e-06) | 0.867 (1.00) | 0.684 (1.00) | 0.654 (1.00) | 0.0121 (1.00) | 0.449 (1.00) | 0.238 (1.00) | 0.0396 (1.00) | 0.0125 (1.00)
Del Peak 5(2q37 1) | 0 (0%) | 236 | 0.651 (1.00) | 0.164 (1.00) | 9.7e-07 (0.000483) | 1.93e-05 (0.00922) | 0.00223 (0.915) | 0.024 (1.00) | 0.0249 (1.00) | 0.00127 (0.534) | 0.14 (1.00) | 0.0122 (1.00) | 0.0829 (1.00) | 0.00226 (0.924)
Del Peak 7(3p21 1) | 0 (0%) | 241 | 1 (1.00) | 0.00815 (1.00) | 5.04e-07 (0.000253) | 0.0121 (1.00) | 0.000478 (0.209) | 0.152 (1.00) | 0.0154 (1.00) | 0.00381 (1.00) | 0.00597 (1.00) | 0.0491 (1.00) | 0.0728 (1.00) | 0.0197 (1.00)
Del Peak 8(4q35 2) | 0 (0%) | 193 | 1 (1.00) | 0.602 (1.00) | 9.34e-09 (4.8e-06) | 9.66e-07 (0.000482) | 0.0826 (1.00) | 0.069 (1.00) | 0.00371 (1.00) | 0.00855 (1.00) | 0.195 (1.00) | 0.349 (1.00) | 0.0051 (1.00) | 0.00737 (1.00)
Del Peak 11(6q24 3) | 0 (0%) | 224 | 0.0479 (1.00) | 0.194 (1.00) | 0.000134 (0.0611) | 0.00125 (0.527) | 0.165 (1.00) | 0.273 (1.00) | 0.674 (1.00) | 0.0882 (1.00) | 0.000171 (0.0778) | 0.532 (1.00) | 0.507 (1.00) | 0.102 (1.00)
Del Peak 21(14q24 3) | 0 (0%) | 208 | 0.303 (1.00) | 0.171 (1.00) | 5.54e-05 (0.026) | 0.049 (1.00) | 0.00299 (1.00) | 0.0193 (1.00) | 0.00638 (1.00) | 0.071 (1.00) | 0.000514 (0.224) | 0.00345 (1.00) | 0.0747 (1.00) | 0.00259 (1.00)
Amp Peak 1(1q22) | 0 (0%) | 242 |  |  | 0.000254 (0.114) | 0.133 (1.00) | 0.251 (1.00) | 0.403 (1.00) | 0.169 (1.00) | 0.312 (1.00) | 0.937 (1.00) | 0.309 (1.00) | 0.134 (1.00) | 0.499 (1.00)
Amp Peak 13(12q14 1) | 0 (0%) | 250 |  |  | 1.97e-05 (0.00939) | 0.101 (1.00) | 0.0228 (1.00) | 0.881 (1.00) | 0.0291 (1.00) | 0.423 (1.00) | 0.0543 (1.00) | 0.192 (1.00) | 0.325 (1.00) | 0.011 (1.00)
Amp Peak 14(13q33 3) | 0 (0%) | 254 |  |  | 0.000431 (0.189) | 0.00549 (1.00) | 0.187 (1.00) | 0.293 (1.00) | 0.426 (1.00) | 0.0806 (1.00) | 0.861 (1.00) | 0.666 (1.00) | 0.408 (1.00) | 0.263 (1.00)
Amp Peak 15(17q25 1) | 0 (0%) | 253 | 0.0889 (1.00) | 0.0468 (1.00) | 7.64e-06 (0.0037) | 0.274 (1.00) | 0.208 (1.00) | 1 (1.00) | 0.468 (1.00) | 0.725 (1.00) | 0.0163 (1.00) | 0.389 (1.00) | 0.00944 (1.00) | 0.83 (1.00)
Amp Peak 19(Xp22 33) | 0 (0%) | 251 |  |  | 0.000241 (0.109) | 0.00225 (0.923) | 0.341 (1.00) | 0.34 (1.00) | 0.154 (1.00) | 0.0225 (1.00) | 0.779 (1.00) | 0.00885 (1.00) | 0.59 (1.00) | 0.306 (1.00)
Del Peak 4(2p25 3) | 0 (0%) | 245 | 0.369 (1.00) | 0.407 (1.00) | 1.97e-06 (0.000973) | 0.00447 (1.00) | 0.195 (1.00) | 1 (1.00) | 0.455 (1.00) | 0.0729 (1.00) | 0.453 (1.00) | 0.815 (1.00) | 0.56 (1.00) | 0.144 (1.00)
Del Peak 9(5q35 2) | 0 (0%) | 235 | 0.446 (1.00) | 0.0182 (1.00) | 4.08e-09 (2.11e-06) | 0.00166 (0.687) | 0.0994 (1.00) | 0.941 (1.00) | 0.0663 (1.00) | 0.00913 (1.00) | 0.393 (1.00) | 0.502 (1.00) | 0.00637 (1.00) | 0.261 (1.00)
Del Peak 15(11q25) | 0 (0%) | 248 |  |  | 0.000243 (0.109) | 0.00609 (1.00) | 0.406 (1.00) | 0.424 (1.00) | 0.11 (1.00) | 0.041 (1.00) | 0.442 (1.00) | 0.174 (1.00) | 0.725 (1.00) | 0.207 (1.00)
Del Peak 16(12q12) | 0 (0%) | 234 | 1 (1.00) | 0.0879 (1.00) | 5.28e-06 (0.00259) | 0.000714 (0.306) | 0.505 (1.00) | 0.882 (1.00) | 0.115 (1.00) | 0.0148 (1.00) | 0.922 (1.00) | 0.956 (1.00) | 0.471 (1.00) | 0.607 (1.00)
Del Peak 17(13q14 2) | 0 (0%) | 192 | 0.18 (1.00) | 0.000618 (0.267) | 3.93e-30 (2.16e-27) | 0.0078 (1.00) | 0.0343 (1.00) | 0.813 (1.00) | 0.339 (1.00) | 0.13 (1.00) | 0.203 (1.00) | 0.289 (1.00) | 0.308 (1.00) | 0.283 (1.00)
Del Peak 18(13q21 2) | 0 (0%) | 189 | 0.18 (1.00) | 0.000618 (0.267) | 1.52e-29 (8.31e-27) | 0.00278 (1.00) | 0.0185 (1.00) | 0.713 (1.00) | 0.145 (1.00) | 0.0611 (1.00) | 0.0754 (1.00) | 0.229 (1.00) | 0.34 (1.00) | 0.29 (1.00)
Del Peak 19(13q22 1) | 0 (0%) | 192 | 0.438 (1.00) | 0.000774 (0.329) | 2.75e-25 (1.49e-22) | 0.0163 (1.00) | 0.00899 (1.00) | 0.788 (1.00) | 0.457 (1.00) | 0.13 (1.00) | 0.138 (1.00) | 0.452 (1.00) | 0.611 (1.00) | 0.421 (1.00)
Del Peak 20(13q34) | 0 (0%) | 212 | 0.508 (1.00) | 0.106 (1.00) | 5.37e-17 (2.89e-14) | 0.263 (1.00) | 0.0856 (1.00) | 0.524 (1.00) | 0.454 (1.00) | 0.161 (1.00) | 0.0935 (1.00) | 0.239 (1.00) | 0.605 (1.00) | 0.699 (1.00)
Del Peak 27(Xp22 2) | 0 (0%) | 211 | 0.839 (1.00) | 0.131 (1.00) | 6.73e-09 (3.46e-06) | 0.128 (1.00) | 0.0439 (1.00) | 0.0294 (1.00) | 0.965 (1.00) | 0.0676 (1.00) | 0.491 (1.00) | 0.119 (1.00) | 0.81 (1.00) | 0.0436 (1.00)
Del Peak 28(Xq21 1) | 0 (0%) | 234 | 0.73 (1.00) | 0.00107 (0.453) | 5.92e-05 (0.0276) | 0.118 (1.00) | 0.0289 (1.00) | 0.0495 (1.00) | 0.523 (1.00) | 0.0143 (1.00) | 0.119 (1.00) | 0.176 (1.00) | 0.0416 (1.00) | 0.884 (1.00)
Amp Peak 3(3p24 3) | 0 (0%) | 255 |  |  | 0.0312 (1.00) | 0.933 (1.00) | 0.907 (1.00) | 0.0322 (1.00) | 0.0815 (1.00) | 0.252 (1.00) | 0.735 (1.00) | 0.643 (1.00) | 0.63 (1.00) | 0.621 (1.00)
Amp Peak 4(3q26 32) | 0 (0%) | 255 |  |  | 0.000655 (0.282) | 0.118 (1.00) | 0.0147 (1.00) | 0.68 (1.00) | 0.548 (1.00) | 0.434 (1.00) | 0.176 (1.00) | 0.643 (1.00) | 0.119 (1.00) | 0.276 (1.00)
Amp Peak 5(4q12) | 0 (0%) | 255 |  |  | 0.0014 (0.584) | 0.258 (1.00) | 0.0204 (1.00) | 0.737 (1.00) | 0.696 (1.00) | 0.372 (1.00) | 0.0996 (1.00) | 0.33 (1.00) | 0.191 (1.00) | 0.529 (1.00)
Amp Peak 10(11q23 3) | 0 (0%) | 224 | 0.225 (1.00) | 0.025 (1.00) | 0.185 (1.00) | 0.122 (1.00) | 0.101 (1.00) | 0.141 (1.00) | 0.603 (1.00) | 0.599 (1.00) | 0.579 (1.00) | 0.627 (1.00) | 0.0579 (1.00) | 0.246 (1.00)
Del Peak 3(1q43) | 0 (0%) | 254 |  |  | 0.0604 (1.00) | 0.228 (1.00) | 0.101 (1.00) | 0.567 (1.00) | 0.894 (1.00) | 0.186 (1.00) | 0.559 (1.00) | 0.666 (1.00) | 0.638 (1.00) | 0.557 (1.00)
Del Peak 10(6p25 3) | 0 (0%) | 241 |  |  | 0.0551 (1.00) | 0.359 (1.00) | 0.161 (1.00) | 0.808 (1.00) | 0.429 (1.00) | 0.24 (1.00) | 0.574 (1.00) | 0.705 (1.00) | 0.164 (1.00) | 0.109 (1.00)
Del Peak 22(17q25 3) | 0 (0%) | 252 |  |  | 0.00155 (0.645) | 0.216 (1.00) | 0.247 (1.00) | 0.161 (1.00) | 0.778 (1.00) | 0.161 (1.00) | 0.204 (1.00) | 0.153 (1.00) | 0.716 (1.00) | 0.341 (1.00)
Del Peak 23(18p11 32) | 0 (0%) | 227 | 0.321 (1.00) | 0.316 (1.00) | 0.0604 (1.00) | 0.125 (1.00) | 0.43 (1.00) | 0.0609 (1.00) | 1 (1.00) | 1 (1.00) | 0.609 (1.00) | 0.785 (1.00) | 0.682 (1.00) | 0.689 (1.00)
Del Peak 24(18q23) | 0 (0%) | 226 | 0.321 (1.00) | 0.316 (1.00) | 0.134 (1.00) | 0.0651 (1.00) | 0.46 (1.00) | 0.115 (1.00) | 0.383 (1.00) | 0.822 (1.00) | 0.672 (1.00) | 0.421 (1.00) | 0.516 (1.00) | 0.247 (1.00)

'Amp Peak 1(1q22)' versus 'CN_CNMF'

P value = 0.000254 (Fisher's exact test), Q value = 0.11

Table S1. Gene #1: 'Amp Peak 1(1q22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 1(1Q22) CNV | 5 | 9 | 11 | 2
AMP PEAK 1(1Q22) WILD-TYPE | 47 | 48 | 43 | 104

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q22)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(1q32.1)' versus 'CN_CNMF'

P value = 2.14e-07 (Fisher's exact test), Q value = 0.00011

Table S2. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 2(1Q32.1) CNV | 2 | 15 | 9 | 1
AMP PEAK 2(1Q32.1) WILD-TYPE | 50 | 42 | 45 | 105

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(1q32.1)' versus 'METHLYATION_CNMF'

P value = 2.28e-06 (Fisher's exact test), Q value = 0.0011

Table S3. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
AMP PEAK 2(1Q32.1) CNV | 9 | 15 | 2 | 1
AMP PEAK 2(1Q32.1) WILD-TYPE | 113 | 27 | 64 | 33

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 2(1q32.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.96e-05 (Fisher's exact test), Q value = 0.041

Table S4. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 145 | 109
AMP PEAK 2(1Q32.1) CNV | 7 | 9 | 11
AMP PEAK 2(1Q32.1) WILD-TYPE | 7 | 136 | 98

Figure S4. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 2(1q32.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.013

Table S5. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
AMP PEAK 2(1Q32.1) CNV | 13 | 4 | 10
AMP PEAK 2(1Q32.1) WILD-TYPE | 29 | 101 | 111

Figure S5. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 6(7p11.2)' versus 'CN_CNMF'

P value = 2.06e-29 (Fisher's exact test), Q value = 1.1e-26

Table S6. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 6(7P11.2) CNV | 4 | 50 | 12 | 7
AMP PEAK 6(7P11.2) WILD-TYPE | 48 | 7 | 42 | 99

Figure S6. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(7p11.2)' versus 'METHLYATION_CNMF'

P value = 4.41e-16 (Fisher's exact test), Q value = 2.4e-13

Table S7. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
AMP PEAK 6(7P11.2) CNV | 22 | 35 | 8 | 6
AMP PEAK 6(7P11.2) WILD-TYPE | 100 | 7 | 58 | 28

Figure S7. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 6(7p11.2)' versus 'RPPA_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.052

Table S8. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
AMP PEAK 6(7P11.2) CNV | 13 | 30 | 12 | 12
AMP PEAK 6(7P11.2) WILD-TYPE | 39 | 32 | 56 | 62

Figure S8. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 6(7p11.2)' versus 'MRNASEQ_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.0093

Table S9. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
AMP PEAK 6(7P11.2) CNV | 42 | 15 | 16
AMP PEAK 6(7P11.2) WILD-TYPE | 52 | 63 | 81

Figure S9. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 6(7p11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.43e-06 (Fisher's exact test), Q value = 0.0031

Table S10. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 145 | 109
AMP PEAK 6(7P11.2) CNV | 11 | 43 | 18
AMP PEAK 6(7P11.2) WILD-TYPE | 3 | 102 | 91

Figure S10. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(7p11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.5e-07 (Chi-square test), Q value = 0.00023

Table S11. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
AMP PEAK 6(7P11.2) CNV | 7 | 28 | 11 | 11 | 2 | 11 | 2 | 0
AMP PEAK 6(7P11.2) WILD-TYPE | 37 | 20 | 24 | 60 | 25 | 20 | 2 | 8

Figure S11. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 6(7p11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.1e-12 (Fisher's exact test), Q value = 1.6e-09

Table S12. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
AMP PEAK 6(7P11.2) CNV | 31 | 24 | 17
AMP PEAK 6(7P11.2) WILD-TYPE | 11 | 81 | 104

Figure S12. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 7(7q32.3)' versus 'CN_CNMF'

P value = 5.19e-23 (Fisher's exact test), Q value = 2.8e-20

Table S13. Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 7(7Q32.3) CNV | 13 | 53 | 17 | 17
AMP PEAK 7(7Q32.3) WILD-TYPE | 39 | 4 | 37 | 89

Figure S13. Get High-res Image Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(7q32.3)' versus 'METHLYATION_CNMF'

P value = 2.11e-08 (Fisher's exact test), Q value = 1.1e-05

Table S14. Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
AMP PEAK 7(7Q32.3) CNV | 45 | 32 | 15 | 6
AMP PEAK 7(7Q32.3) WILD-TYPE | 77 | 10 | 51 | 28

Figure S14. Get High-res Image Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 7(7q32.3)' versus 'MRNASEQ_CNMF'

P value = 0.000267 (Fisher's exact test), Q value = 0.12

Table S15. Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
AMP PEAK 7(7Q32.3) CNV | 50 | 25 | 25
AMP PEAK 7(7Q32.3) WILD-TYPE | 44 | 53 | 72

Figure S15. Get High-res Image Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 7(7q32.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.0049

Table S16. Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
AMP PEAK 7(7Q32.3) CNV | 29 | 37 | 33
AMP PEAK 7(7Q32.3) WILD-TYPE | 13 | 68 | 88

Figure S16. Get High-res Image Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 8(8q24.12)' versus 'CN_CNMF'

P value = 2.32e-12 (Fisher's exact test), Q value = 1.2e-09

Table S17. Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 8(8Q24.12) CNV | 17 | 11 | 25 | 2
AMP PEAK 8(8Q24.12) WILD-TYPE | 35 | 46 | 29 | 104

Figure S17. Get High-res Image Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 8(8q24.12)' versus 'METHLYATION_CNMF'

P value = 5.52e-09 (Fisher's exact test), Q value = 2.8e-06

Table S18. Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
AMP PEAK 8(8Q24.12) CNV | 46 | 4 | 3 | 2
AMP PEAK 8(8Q24.12) WILD-TYPE | 76 | 38 | 63 | 32

Figure S18. Get High-res Image Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 8(8q24.12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000257 (Chi-square test), Q value = 0.12

Table S19. Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
AMP PEAK 8(8Q24.12) CNV | 17 | 6 | 10 | 9 | 1 | 8 | 3 | 1
AMP PEAK 8(8Q24.12) WILD-TYPE | 27 | 42 | 25 | 62 | 26 | 23 | 1 | 7

Figure S19. Get High-res Image Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 9(10p15.3)' versus 'CN_CNMF'

P value = 1e-09 (Fisher's exact test), Q value = 5.3e-07

Table S20. Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 9(10P15.3) CNV | 19 | 5 | 15 | 2
AMP PEAK 9(10P15.3) WILD-TYPE | 33 | 52 | 39 | 104

Figure S20. Get High-res Image Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(10p15.3)' versus 'METHLYATION_CNMF'

P value = 2.97e-09 (Fisher's exact test), Q value = 1.5e-06

Table S21. Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
AMP PEAK 9(10P15.3) CNV | 36 | 1 | 0 | 4
AMP PEAK 9(10P15.3) WILD-TYPE | 86 | 41 | 66 | 30

Figure S21. Get High-res Image Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 9(10p15.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000284 (Chi-square test), Q value = 0.13

Table S22. Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
AMP PEAK 9(10P15.3) CNV | 12 | 3 | 10 | 7 | 2 | 3 | 3 | 1
AMP PEAK 9(10P15.3) WILD-TYPE | 32 | 45 | 25 | 64 | 25 | 28 | 1 | 7

Figure S22. Get High-res Image Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 11(12p13.32)' versus 'CN_CNMF'

P value = 1.69e-10 (Fisher's exact test), Q value = 8.9e-08

Table S23. Gene #11: 'Amp Peak 11(12p13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 11(12P13.32) CNV | 20 | 8 | 14 | 1
AMP PEAK 11(12P13.32) WILD-TYPE | 32 | 49 | 40 | 105

Figure S23. Get High-res Image Gene #11: 'Amp Peak 11(12p13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(12p13.32)' versus 'METHLYATION_CNMF'

P value = 5.16e-05 (Fisher's exact test), Q value = 0.024

Table S24. Gene #11: 'Amp Peak 11(12p13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
AMP PEAK 11(12P13.32) CNV | 33 | 5 | 2 | 3
AMP PEAK 11(12P13.32) WILD-TYPE | 89 | 37 | 64 | 31

Figure S24. Get High-res Image Gene #11: 'Amp Peak 11(12p13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 12(12p12.1)' versus 'CN_CNMF'

P value = 4.75e-06 (Fisher's exact test), Q value = 0.0023

Table S25. Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 12(12P12.1) CNV | 12 | 5 | 10 | 1
AMP PEAK 12(12P12.1) WILD-TYPE | 40 | 52 | 44 | 105

Figure S25. Get High-res Image Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(12p12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000392 (Fisher's exact test), Q value = 0.17

Table S26. Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
AMP PEAK 12(12P12.1) CNV | 2 | 24 | 2
AMP PEAK 12(12P12.1) WILD-TYPE | 34 | 117 | 90

Figure S26. Get High-res Image Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(12p12.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.84e-05 (Chi-square test), Q value = 0.032

Table S27. Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
AMP PEAK 12(12P12.1) CNV | 7 | 6 | 7 | 1 | 2 | 2 | 3 | 0
AMP PEAK 12(12P12.1) WILD-TYPE | 37 | 42 | 28 | 70 | 25 | 29 | 1 | 8

Figure S27. Get High-res Image Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 13(12q14.1)' versus 'CN_CNMF'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.0094

Table S28. Gene #13: 'Amp Peak 13(12q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 13(12Q14.1) CNV | 1 | 6 | 11 | 1
AMP PEAK 13(12Q14.1) WILD-TYPE | 51 | 51 | 43 | 105

Figure S28. Get High-res Image Gene #13: 'Amp Peak 13(12q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 14(13q33.3)' versus 'CN_CNMF'

P value = 0.000431 (Fisher's exact test), Q value = 0.19

Table S29. Gene #14: 'Amp Peak 14(13q33.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 14(13Q33.3) CNV | 5 | 3 | 7 | 0
AMP PEAK 14(13Q33.3) WILD-TYPE | 47 | 54 | 47 | 106

Figure S29. Get High-res Image Gene #14: 'Amp Peak 14(13q33.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(17q25.1)' versus 'CN_CNMF'

P value = 7.64e-06 (Fisher's exact test), Q value = 0.0037

Table S30. Gene #15: 'Amp Peak 15(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 15(17Q25.1) CNV | 1 | 1 | 12 | 2
AMP PEAK 15(17Q25.1) WILD-TYPE | 51 | 56 | 42 | 104

Figure S30. Get High-res Image Gene #15: 'Amp Peak 15(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(18q23)' versus 'RPPA_CNMF'

P value = 0.000132 (Fisher's exact test), Q value = 0.06

Table S31. Gene #16: 'Amp Peak 16(18q23)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
AMP PEAK 16(18Q23) CNV | 3 | 8 | 0 | 0
AMP PEAK 16(18Q23) WILD-TYPE | 49 | 54 | 68 | 74

Figure S31. Get High-res Image Gene #16: 'Amp Peak 16(18q23)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 16(18q23)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Chi-square test), Q value = 0.12

Table S32. Gene #16: 'Amp Peak 16(18q23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
AMP PEAK 16(18Q23) CNV | 1 | 3 | 4 | 1 | 0 | 1 | 2 | 0
AMP PEAK 16(18Q23) WILD-TYPE | 43 | 45 | 31 | 70 | 27 | 30 | 2 | 8

Figure S32. Get High-res Image Gene #16: 'Amp Peak 16(18q23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 17(19p13.3)' versus 'CN_CNMF'

P value = 9.09e-05 (Fisher's exact test), Q value = 0.042

Table S33. Gene #17: 'Amp Peak 17(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 17(19P13.3) CNV | 2 | 17 | 8 | 33
AMP PEAK 17(19P13.3) WILD-TYPE | 50 | 40 | 46 | 73

Figure S33. Get High-res Image Gene #17: 'Amp Peak 17(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 17(19p13.3)' versus 'METHLYATION_CNMF'

P value = 1.07e-08 (Fisher's exact test), Q value = 5.5e-06

Table S34. Gene #17: 'Amp Peak 17(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
AMP PEAK 17(19P13.3) CNV | 10 | 14 | 29 | 3
AMP PEAK 17(19P13.3) WILD-TYPE | 112 | 28 | 37 | 31

Figure S34. Get High-res Image Gene #17: 'Amp Peak 17(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 18(19q13.2)' versus 'CN_CNMF'

P value = 7.29e-07 (Fisher's exact test), Q value = 0.00037

Table S35. Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 18(19Q13.2) CNV | 0 | 14 | 3 | 2
AMP PEAK 18(19Q13.2) WILD-TYPE | 52 | 43 | 51 | 104

Figure S35. Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 18(19q13.2)' versus 'METHLYATION_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0048

Table S36. Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
AMP PEAK 18(19Q13.2) CNV | 6 | 11 | 0 | 1
AMP PEAK 18(19Q13.2) WILD-TYPE | 116 | 31 | 66 | 33

Figure S36. Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 18(19q13.2)' versus 'MRNASEQ_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.056

Table S37. Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
AMP PEAK 18(19Q13.2) CNV | 15 | 3 | 1
AMP PEAK 18(19Q13.2) WILD-TYPE | 79 | 75 | 96

Figure S37. Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 18(19q13.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.25e-06 (Chi-square test), Q value = 0.0026

Table S38. Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
AMP PEAK 18(19Q13.2) CNV | 2 | 13 | 1 | 3 | 0 | 0 | 0 | 0
AMP PEAK 18(19Q13.2) WILD-TYPE | 42 | 35 | 34 | 68 | 27 | 31 | 4 | 8

Figure S38. Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 18(19q13.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.89e-06 (Fisher's exact test), Q value = 0.0029

Table S39. Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
AMP PEAK 18(19Q13.2) CNV | 11 | 6 | 2
AMP PEAK 18(19Q13.2) WILD-TYPE | 31 | 99 | 119

Figure S39. Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 19(Xp22.33)' versus 'CN_CNMF'

P value = 0.000241 (Fisher's exact test), Q value = 0.11

Table S40. Gene #19: 'Amp Peak 19(Xp22.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 19(XP22.33) CNV | 7 | 6 | 5 | 0
AMP PEAK 19(XP22.33) WILD-TYPE | 45 | 51 | 49 | 106

Figure S40. Get High-res Image Gene #19: 'Amp Peak 19(Xp22.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(Xp11.22)' versus 'CN_CNMF'

P value = 1.84e-09 (Fisher's exact test), Q value = 9.6e-07

Table S41. Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
AMP PEAK 20(XP11.22) CNV | 19 | 4 | 13 | 2
AMP PEAK 20(XP11.22) WILD-TYPE | 33 | 53 | 41 | 104

Figure S41. Get High-res Image Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(Xp11.22)' versus 'METHLYATION_CNMF'

P value = 1.54e-06 (Fisher's exact test), Q value = 0.00076

Table S42. Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
AMP PEAK 20(XP11.22) CNV | 32 | 4 | 1 | 1
AMP PEAK 20(XP11.22) WILD-TYPE | 90 | 38 | 65 | 33

Figure S42. Get High-res Image Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 20(Xp11.22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000355 (Fisher's exact test), Q value = 0.16

Table S43. Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
AMP PEAK 20(XP11.22) CNV | 1 | 31 | 6
AMP PEAK 20(XP11.22) WILD-TYPE | 35 | 110 | 86

Figure S43. Get High-res Image Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'MRNA_CNMF'

P value = 0.000549 (Fisher's exact test), Q value = 0.24

Table S44. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 9 | 10 | 8
DEL PEAK 1(1P36.31) CNV | 0 | 8 | 2
DEL PEAK 1(1P36.31) WILD-TYPE | 9 | 2 | 6

Figure S44. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.31)' versus 'MRNA_CHIERARCHICAL'

P value = 5.86e-05 (Fisher's exact test), Q value = 0.027

Table S45. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 7 | 6 | 10 | 4
DEL PEAK 1(1P36.31) CNV | 7 | 2 | 0 | 1
DEL PEAK 1(1P36.31) WILD-TYPE | 0 | 4 | 10 | 3

Figure S45. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'CN_CNMF'

P value = 8.49e-14 (Fisher's exact test), Q value = 4.5e-11

Table S46. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 1(1P36.31) CNV | 5 | 9 | 15 | 67
DEL PEAK 1(1P36.31) WILD-TYPE | 47 | 48 | 39 | 39

Figure S46. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.31)' versus 'METHLYATION_CNMF'

P value = 4.92e-43 (Fisher's exact test), Q value = 2.7e-40

Table S47. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
DEL PEAK 1(1P36.31) CNV | 8 | 9 | 66 | 9
DEL PEAK 1(1P36.31) WILD-TYPE | 114 | 33 | 0 | 25

Figure S47. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.31)' versus 'MRNASEQ_CNMF'

P value = 7.9e-06 (Fisher's exact test), Q value = 0.0038

Table S48. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
DEL PEAK 1(1P36.31) CNV | 16 | 34 | 46
DEL PEAK 1(1P36.31) WILD-TYPE | 78 | 44 | 51

Figure S48. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.23e-23 (Fisher's exact test), Q value = 1.8e-20

Table S49. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
DEL PEAK 1(1P36.31) CNV | 36 | 21 | 39
DEL PEAK 1(1P36.31) WILD-TYPE | 0 | 120 | 53

Figure S49. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_CNMF'

P value = 8.86e-06 (Chi-square test), Q value = 0.0043

Table S50. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 62 | 48 | 89 | 16 | 53
DEL PEAK 1(1P36.31) CNV | 11 | 10 | 40 | 12 | 23
DEL PEAK 1(1P36.31) WILD-TYPE | 51 | 38 | 49 | 4 | 30

Figure S50. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000303 (Fisher's exact test), Q value = 0.13

Table S51. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 145 | 109
DEL PEAK 1(1P36.31) CNV | 2 | 40 | 54
DEL PEAK 1(1P36.31) WILD-TYPE | 12 | 105 | 55

Figure S51. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.15e-08 (Chi-square test), Q value = 5.9e-06

Table S52. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
DEL PEAK 1(1P36.31) CNV | 2 | 14 | 8 | 33 | 21 | 14 | 0 | 4
DEL PEAK 1(1P36.31) WILD-TYPE | 42 | 34 | 27 | 38 | 6 | 17 | 4 | 4

Figure S52. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000104 (Fisher's exact test), Q value = 0.048

Table S53. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
DEL PEAK 1(1P36.31) CNV | 9 | 27 | 60
DEL PEAK 1(1P36.31) WILD-TYPE | 33 | 78 | 61

Figure S53. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000173 (Fisher's exact test), Q value = 0.078

Table S54. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 7 | 6 | 10 | 4
DEL PEAK 2(1P32.3) CNV | 7 | 2 | 1 | 0
DEL PEAK 2(1P32.3) WILD-TYPE | 0 | 4 | 9 | 4

Figure S54. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'CN_CNMF'

P value = 2.21e-17 (Fisher's exact test), Q value = 1.2e-14

Table S55. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 2(1P32.3) CNV | 4 | 5 | 12 | 67
DEL PEAK 2(1P32.3) WILD-TYPE | 48 | 52 | 42 | 39

Figure S55. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p32.3)' versus 'METHLYATION_CNMF'

P value = 2.3e-48 (Fisher's exact test), Q value = 1.3e-45

Table S56. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
DEL PEAK 2(1P32.3) CNV | 4 | 6 | 66 | 9
DEL PEAK 2(1P32.3) WILD-TYPE | 118 | 36 | 0 | 25

Figure S56. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 2(1p32.3)' versus 'RPPA_CNMF'

P value = 0.000477 (Fisher's exact test), Q value = 0.21

Table S57. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
DEL PEAK 2(1P32.3) CNV | 8 | 16 | 28 | 35
DEL PEAK 2(1P32.3) WILD-TYPE | 44 | 46 | 40 | 39

Figure S57. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 2(1p32.3)' versus 'MRNASEQ_CNMF'

P value = 2.73e-09 (Fisher's exact test), Q value = 1.4e-06

Table S58. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
DEL PEAK 2(1P32.3) CNV | 9 | 34 | 45
DEL PEAK 2(1P32.3) WILD-TYPE | 85 | 44 | 52

Figure S58. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 2(1p32.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.06e-27 (Fisher's exact test), Q value = 1.7e-24

Table S59. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
DEL PEAK 2(1P32.3) CNV | 36 | 14 | 38
DEL PEAK 2(1P32.3) WILD-TYPE | 0 | 127 | 54

Figure S59. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_CNMF'

P value = 5.78e-08 (Chi-square test), Q value = 2.9e-05

Table S60. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 62 | 48 | 89 | 16 | 53
DEL PEAK 2(1P32.3) CNV | 11 | 4 | 40 | 12 | 21
DEL PEAK 2(1P32.3) WILD-TYPE | 51 | 44 | 49 | 4 | 32

Figure S60. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.2e-05 (Fisher's exact test), Q value = 0.015

Table S61. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 145 | 109
DEL PEAK 2(1P32.3) CNV | 1 | 35 | 52
DEL PEAK 2(1P32.3) WILD-TYPE | 13 | 110 | 57

Figure S61. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.54e-09 (Chi-square test), Q value = 8.1e-07

Table S62. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
DEL PEAK 2(1P32.3) CNV | 2 | 9 | 8 | 32 | 21 | 12 | 0 | 4
DEL PEAK 2(1P32.3) WILD-TYPE | 42 | 39 | 27 | 39 | 6 | 19 | 4 | 4

Figure S62. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00054

Table S63. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
DEL PEAK 2(1P32.3) CNV | 5 | 24 | 59
DEL PEAK 2(1P32.3) WILD-TYPE | 37 | 81 | 62

Figure S63. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 4(2p25.3)' versus 'CN_CNMF'

P value = 1.97e-06 (Fisher's exact test), Q value = 0.00097

Table S64. Gene #24: 'Del Peak 4(2p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 4(2P25.3) CNV | 9 | 2 | 12 | 1
DEL PEAK 4(2P25.3) WILD-TYPE | 43 | 55 | 42 | 105

Figure S64. Get High-res Image Gene #24: 'Del Peak 4(2p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(2q37.1)' versus 'CN_CNMF'

P value = 9.7e-07 (Fisher's exact test), Q value = 0.00048

Table S65. Gene #25: 'Del Peak 5(2q37.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 5(2Q37.1) CNV | 14 | 9 | 9 | 1
DEL PEAK 5(2Q37.1) WILD-TYPE | 38 | 48 | 45 | 105

Figure S65. Get High-res Image Gene #25: 'Del Peak 5(2q37.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(2q37.1)' versus 'METHLYATION_CNMF'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.0092

Table S66. Gene #25: 'Del Peak 5(2q37.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
DEL PEAK 5(2Q37.1) CNV | 28 | 2 | 1 | 2
DEL PEAK 5(2Q37.1) WILD-TYPE | 94 | 40 | 65 | 32

Figure S66. Get High-res Image Gene #25: 'Del Peak 5(2q37.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 6(2q37.3)' versus 'CN_CNMF'

P value = 6.07e-06 (Fisher's exact test), Q value = 0.003

Table S67. Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 6(2Q37.3) CNV | 15 | 10 | 12 | 3
DEL PEAK 6(2Q37.3) WILD-TYPE | 37 | 47 | 42 | 103

Figure S67. Get High-res Image Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(2q37.3)' versus 'METHLYATION_CNMF'

P value = 1.8e-07 (Fisher's exact test), Q value = 9.1e-05

Table S68. Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
DEL PEAK 6(2Q37.3) CNV | 35 | 1 | 2 | 2
DEL PEAK 6(2Q37.3) WILD-TYPE | 87 | 41 | 64 | 32

Figure S68. Get High-res Image Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 6(2q37.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000114 (Fisher's exact test), Q value = 0.052

Table S69. Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
DEL PEAK 6(2Q37.3) CNV | 3 | 28 | 9
DEL PEAK 6(2Q37.3) WILD-TYPE | 39 | 77 | 112

Figure S69. Get High-res Image Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 7(3p21.1)' versus 'CN_CNMF'

P value = 5.04e-07 (Fisher's exact test), Q value = 0.00025

Table S70. Gene #27: 'Del Peak 7(3p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 7(3P21.1) CNV | 8 | 4 | 15 | 1
DEL PEAK 7(3P21.1) WILD-TYPE | 44 | 53 | 39 | 105

Figure S70. Get High-res Image Gene #27: 'Del Peak 7(3p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(3p21.1)' versus 'RPPA_CNMF'

P value = 0.000478 (Fisher's exact test), Q value = 0.21

Table S71. Gene #27: 'Del Peak 7(3p21.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
DEL PEAK 7(3P21.1) CNV | 4 | 16 | 3 | 4
DEL PEAK 7(3P21.1) WILD-TYPE | 48 | 46 | 65 | 70

Figure S71. Get High-res Image Gene #27: 'Del Peak 7(3p21.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 8(4q35.2)' versus 'CN_CNMF'

P value = 9.34e-09 (Fisher's exact test), Q value = 4.8e-06

Table S72. Gene #28: 'Del Peak 8(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 8(4Q35.2) CNV | 16 | 4 | 32 | 24
DEL PEAK 8(4Q35.2) WILD-TYPE | 36 | 53 | 22 | 82

Figure S72. Get High-res Image Gene #28: 'Del Peak 8(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(4q35.2)' versus 'METHLYATION_CNMF'

P value = 9.66e-07 (Fisher's exact test), Q value = 0.00048

Table S73. Gene #28: 'Del Peak 8(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
DEL PEAK 8(4Q35.2) CNV | 43 | 2 | 28 | 3
DEL PEAK 8(4Q35.2) WILD-TYPE | 79 | 40 | 38 | 31

Figure S73. Get High-res Image Gene #28: 'Del Peak 8(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 9(5q35.2)' versus 'CN_CNMF'

P value = 4.08e-09 (Fisher's exact test), Q value = 2.1e-06

Table S74. Gene #29: 'Del Peak 9(5q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 9(5Q35.2) CNV | 13 | 1 | 17 | 3
DEL PEAK 9(5Q35.2) WILD-TYPE | 39 | 56 | 37 | 103

Figure S74. Get High-res Image Gene #29: 'Del Peak 9(5q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(6q24.3)' versus 'CN_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.061

Table S75. Gene #31: 'Del Peak 11(6q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 11(6Q24.3) CNV | 6 | 12 | 19 | 8
DEL PEAK 11(6Q24.3) WILD-TYPE | 46 | 45 | 35 | 98

Figure S75. Get High-res Image Gene #31: 'Del Peak 11(6q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(6q24.3)' versus 'MIRSEQ_CNMF'

P value = 0.000171 (Chi-square test), Q value = 0.078

Table S76. Gene #31: 'Del Peak 11(6q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 62 | 48 | 89 | 16 | 53
DEL PEAK 11(6Q24.3) CNV | 22 | 7 | 12 | 1 | 3
DEL PEAK 11(6Q24.3) WILD-TYPE | 40 | 41 | 77 | 15 | 50

Figure S76. Get High-res Image Gene #31: 'Del Peak 11(6q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(9p21.3)' versus 'CN_CNMF'

P value = 3.04e-11 (Fisher's exact test), Q value = 1.6e-08

Table S77. Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 12(9P21.3) CNV | 13 | 38 | 30 | 18
DEL PEAK 12(9P21.3) WILD-TYPE | 39 | 19 | 24 | 88

Figure S77. Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(9p21.3)' versus 'METHLYATION_CNMF'

P value = 2.66e-08 (Fisher's exact test), Q value = 1.4e-05

Table S78. Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
DEL PEAK 12(9P21.3) CNV | 49 | 30 | 13 | 5
DEL PEAK 12(9P21.3) WILD-TYPE | 73 | 12 | 53 | 29

Figure S78. Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(9p21.3)' versus 'RPPA_CNMF'

P value = 8.67e-06 (Fisher's exact test), Q value = 0.0042

Table S79. Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
DEL PEAK 12(9P21.3) CNV | 11 | 38 | 26 | 18
DEL PEAK 12(9P21.3) WILD-TYPE | 41 | 24 | 42 | 56

Figure S79. Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 12(9p21.3)' versus 'RPPA_CHIERARCHICAL'

P value = 9.22e-05 (Fisher's exact test), Q value = 0.043

Table S80. Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 8 | 129 | 119
DEL PEAK 12(9P21.3) CNV | 2 | 63 | 28
DEL PEAK 12(9P21.3) WILD-TYPE | 6 | 66 | 91

Figure S80. Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 12(9p21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000199 (Fisher's exact test), Q value = 0.09

Table S81. Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
DEL PEAK 12(9P21.3) CNV | 27 | 38 | 34
DEL PEAK 12(9P21.3) WILD-TYPE | 15 | 67 | 87

Figure S81. Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(10q26.3)' versus 'CN_CNMF'

P value = 6.21e-19 (Fisher's exact test), Q value = 3.3e-16

Table S82. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 13(10Q26.3) CNV | 14 | 38 | 25 | 4
DEL PEAK 13(10Q26.3) WILD-TYPE | 38 | 19 | 29 | 102

Figure S82. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(10q26.3)' versus 'METHLYATION_CNMF'

P value = 1.3e-20 (Fisher's exact test), Q value = 7e-18

Table S83. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
DEL PEAK 13(10Q26.3) CNV | 36 | 37 | 3 | 4
DEL PEAK 13(10Q26.3) WILD-TYPE | 86 | 5 | 63 | 30

Figure S83. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 13(10q26.3)' versus 'RPPA_CNMF'

P value = 1.56e-07 (Fisher's exact test), Q value = 7.9e-05

Table S84. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
DEL PEAK 13(10Q26.3) CNV | 13 | 36 | 13 | 11
DEL PEAK 13(10Q26.3) WILD-TYPE | 39 | 26 | 55 | 63

Figure S84. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 13(10q26.3)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000214 (Fisher's exact test), Q value = 0.097

Table S85. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 8 | 129 | 119
DEL PEAK 13(10Q26.3) CNV | 2 | 51 | 20
DEL PEAK 13(10Q26.3) WILD-TYPE | 6 | 78 | 99

Figure S85. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 13(10q26.3)' versus 'MRNASEQ_CNMF'

P value = 2.13e-08 (Fisher's exact test), Q value = 1.1e-05

Table S86. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
DEL PEAK 13(10Q26.3) CNV | 50 | 14 | 17
DEL PEAK 13(10Q26.3) WILD-TYPE | 44 | 64 | 80

Figure S86. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(10q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.92e-09 (Fisher's exact test), Q value = 1.5e-06

Table S87. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
DEL PEAK 13(10Q26.3) CNV | 1 | 64 | 16
DEL PEAK 13(10Q26.3) WILD-TYPE | 35 | 77 | 76

Figure S87. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(10q26.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.98e-06 (Fisher's exact test), Q value = 0.0029

Table S88. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 145 | 109
DEL PEAK 13(10Q26.3) CNV | 10 | 53 | 18
DEL PEAK 13(10Q26.3) WILD-TYPE | 4 | 92 | 91

Figure S88. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(10q26.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.5e-09 (Chi-square test), Q value = 2.3e-06

Table S89. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
DEL PEAK 13(10Q26.3) CNV | 9 | 33 | 5 | 13 | 5 | 12 | 3 | 1
DEL PEAK 13(10Q26.3) WILD-TYPE | 35 | 15 | 30 | 58 | 22 | 19 | 1 | 7

Figure S89. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 13(10q26.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.26e-11 (Fisher's exact test), Q value = 6.7e-09

Table S90. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
DEL PEAK 13(10Q26.3) CNV | 32 | 29 | 20
DEL PEAK 13(10Q26.3) WILD-TYPE | 10 | 76 | 101

Figure S90. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 14(11p15.5)' versus 'CN_CNMF'

P value = 1.88e-09 (Fisher's exact test), Q value = 9.8e-07

Table S91. Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 14(11P15.5) CNV | 23 | 8 | 20 | 6
DEL PEAK 14(11P15.5) WILD-TYPE | 29 | 49 | 34 | 100

Figure S91. Get High-res Image Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(11p15.5)' versus 'METHLYATION_CNMF'

P value = 2.11e-10 (Fisher's exact test), Q value = 1.1e-07

Table S92. Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
DEL PEAK 14(11P15.5) CNV | 46 | 6 | 0 | 5
DEL PEAK 14(11P15.5) WILD-TYPE | 76 | 36 | 66 | 29

Figure S92. Get High-res Image Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(11p15.5)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.62e-05 (Fisher's exact test), Q value = 0.012

Table S93. Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
DEL PEAK 14(11P15.5) CNV | 0 | 42 | 15
DEL PEAK 14(11P15.5) WILD-TYPE | 36 | 99 | 77

Figure S93. Get High-res Image Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(11q25)' versus 'CN_CNMF'

P value = 0.000243 (Fisher's exact test), Q value = 0.11

Table S94. Gene #35: 'Del Peak 15(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 15(11Q25) CNV | 6 | 4 | 10 | 1
DEL PEAK 15(11Q25) WILD-TYPE | 46 | 53 | 44 | 105

Figure S94. Get High-res Image Gene #35: 'Del Peak 15(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(12q12)' versus 'CN_CNMF'

P value = 5.28e-06 (Fisher's exact test), Q value = 0.0026

Table S95. Gene #36: 'Del Peak 16(12q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 16(12Q12) CNV | 18 | 4 | 8 | 5
DEL PEAK 16(12Q12) WILD-TYPE | 34 | 53 | 46 | 101

Figure S95. Get High-res Image Gene #36: 'Del Peak 16(12q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(13q14.2)' versus 'CN_CNMF'

P value = 3.93e-30 (Fisher's exact test), Q value = 2.2e-27

Table S96. Gene #37: 'Del Peak 17(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 17(13Q14.2) CNV | 19 | 8 | 47 | 3
DEL PEAK 17(13Q14.2) WILD-TYPE | 33 | 49 | 7 | 103

Figure S96. Get High-res Image Gene #37: 'Del Peak 17(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(13q21.2)' versus 'CN_CNMF'

P value = 1.52e-29 (Fisher's exact test), Q value = 8.3e-27

Table S97. Gene #38: 'Del Peak 18(13q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 18(13Q21.2) CNV | 20 | 10 | 47 | 3
DEL PEAK 18(13Q21.2) WILD-TYPE | 32 | 47 | 7 | 103

Figure S97. Get High-res Image Gene #38: 'Del Peak 18(13q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(13q22.1)' versus 'CN_CNMF'

P value = 2.75e-25 (Fisher's exact test), Q value = 1.5e-22

Table S98. Gene #39: 'Del Peak 19(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 19(13Q22.1) CNV | 18 | 9 | 45 | 5
DEL PEAK 19(13Q22.1) WILD-TYPE | 34 | 48 | 9 | 101

Figure S98. Get High-res Image Gene #39: 'Del Peak 19(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 20(13q34)' versus 'CN_CNMF'

P value = 5.37e-17 (Fisher's exact test), Q value = 2.9e-14

Table S99. Gene #40: 'Del Peak 20(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 20(13Q34) CNV | 15 | 6 | 33 | 3
DEL PEAK 20(13Q34) WILD-TYPE | 37 | 51 | 21 | 103

Figure S99. Get High-res Image Gene #40: 'Del Peak 20(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(14q24.3)' versus 'CN_CNMF'

P value = 5.54e-05 (Fisher's exact test), Q value = 0.026

Table S100. Gene #41: 'Del Peak 21(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 21(14Q24.3) CNV | 7 | 14 | 25 | 15
DEL PEAK 21(14Q24.3) WILD-TYPE | 45 | 43 | 29 | 91

Figure S100. Get High-res Image Gene #41: 'Del Peak 21(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(14q24.3)' versus 'MIRSEQ_CNMF'

P value = 0.000514 (Chi-square test), Q value = 0.22

Table S101. Gene #41: 'Del Peak 21(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 62 | 48 | 89 | 16 | 53
DEL PEAK 21(14Q24.3) CNV | 27 | 8 | 15 | 3 | 8
DEL PEAK 21(14Q24.3) WILD-TYPE | 35 | 40 | 74 | 13 | 45

Figure S101. Get High-res Image Gene #41: 'Del Peak 21(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(19q13.42)' versus 'CN_CNMF'

P value = 1.55e-15 (Fisher's exact test), Q value = 8.3e-13

Table S102. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 25(19Q13.42) CNV | 13 | 9 | 39 | 75
DEL PEAK 25(19Q13.42) WILD-TYPE | 39 | 48 | 15 | 31

Figure S102. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(19q13.42)' versus 'METHLYATION_CNMF'

P value = 9.49e-28 (Fisher's exact test), Q value = 5.2e-25

Table S103. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
DEL PEAK 25(19Q13.42) CNV | 53 | 4 | 66 | 10
DEL PEAK 25(19Q13.42) WILD-TYPE | 69 | 38 | 0 | 24

Figure S103. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(19q13.42)' versus 'MRNASEQ_CNMF'

P value = 7.99e-07 (Fisher's exact test), Q value = 4e-04

Table S104. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
DEL PEAK 25(19Q13.42) CNV | 27 | 50 | 59
DEL PEAK 25(19Q13.42) WILD-TYPE | 67 | 28 | 38

Figure S104. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 25(19q13.42)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.06e-15 (Fisher's exact test), Q value = 4.8e-12

Table S105. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
DEL PEAK 25(19Q13.42) CNV | 36 | 47 | 53
DEL PEAK 25(19Q13.42) WILD-TYPE | 0 | 94 | 39

Figure S105. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_CNMF'

P value = 8.24e-05 (Chi-square test), Q value = 0.038

Table S106. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 62 | 48 | 89 | 16 | 53
DEL PEAK 25(19Q13.42) CNV | 27 | 14 | 51 | 15 | 29
DEL PEAK 25(19Q13.42) WILD-TYPE | 35 | 34 | 38 | 1 | 24

Figure S106. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000298 (Fisher's exact test), Q value = 0.13

Table S107. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 145 | 109
DEL PEAK 25(19Q13.42) CNV | 1 | 69 | 66
DEL PEAK 25(19Q13.42) WILD-TYPE | 13 | 76 | 43

Figure S107. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.28e-05 (Chi-square test), Q value = 0.011

Table S108. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 44 | 48 | 35 | 71 | 27 | 31 | 4 | 8
DEL PEAK 25(19Q13.42) CNV | 16 | 13 | 20 | 41 | 24 | 17 | 1 | 4
DEL PEAK 25(19Q13.42) WILD-TYPE | 28 | 35 | 15 | 30 | 3 | 14 | 3 | 4

Figure S108. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.19e-08 (Fisher's exact test), Q value = 2.6e-05

Table S109. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 105 | 121
DEL PEAK 25(19Q13.42) CNV | 5 | 57 | 74
DEL PEAK 25(19Q13.42) WILD-TYPE | 37 | 48 | 47

Figure S109. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 26(22q13.31)' versus 'CN_CNMF'

P value = 1.41e-09 (Fisher's exact test), Q value = 7.4e-07

Table S110. Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 26(22Q13.31) CNV | 11 | 14 | 15 | 0
DEL PEAK 26(22Q13.31) WILD-TYPE | 41 | 43 | 39 | 106

Figure S110. Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(22q13.31)' versus 'METHLYATION_CNMF'

P value = 2.85e-06 (Fisher's exact test), Q value = 0.0014

Table S111. Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 122 | 42 | 66 | 34
DEL PEAK 26(22Q13.31) CNV | 23 | 13 | 0 | 3
DEL PEAK 26(22Q13.31) WILD-TYPE | 99 | 29 | 66 | 31

Figure S111. Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 26(22q13.31)' versus 'RPPA_CNMF'

P value = 6.75e-05 (Fisher's exact test), Q value = 0.031

Table S112. Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 62 | 68 | 74
DEL PEAK 26(22Q13.31) CNV | 4 | 22 | 8 | 6
DEL PEAK 26(22Q13.31) WILD-TYPE | 48 | 40 | 60 | 68

Figure S112. Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 26(22q13.31)' versus 'MRNASEQ_CNMF'

P value = 6.92e-06 (Fisher's exact test), Q value = 0.0034

Table S113. Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 78 | 97
DEL PEAK 26(22Q13.31) CNV | 28 | 5 | 7
DEL PEAK 26(22Q13.31) WILD-TYPE | 66 | 73 | 90

Figure S113. Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 26(22q13.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.77e-05 (Fisher's exact test), Q value = 0.018

Table S114. Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 141 | 92
DEL PEAK 26(22Q13.31) CNV | 0 | 33 | 7
DEL PEAK 26(22Q13.31) WILD-TYPE | 36 | 108 | 85

Figure S114. Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(Xp22.2)' versus 'CN_CNMF'

P value = 6.73e-09 (Fisher's exact test), Q value = 3.5e-06

Table S115. Gene #47: 'Del Peak 27(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 27(XP22.2) CNV | 14 | 5 | 28 | 11
DEL PEAK 27(XP22.2) WILD-TYPE | 38 | 52 | 26 | 95

Figure S115. Get High-res Image Gene #47: 'Del Peak 27(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(Xq21.1)' versus 'CN_CNMF'

P value = 5.92e-05 (Fisher's exact test), Q value = 0.028

Table S116. Gene #48: 'Del Peak 28(Xq21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 52 | 57 | 54 | 106
DEL PEAK 28(XQ21.1) CNV | 6 | 3 | 18 | 8
DEL PEAK 28(XQ21.1) WILD-TYPE | 46 | 54 | 36 | 98

Figure S116. Get High-res Image Gene #48: 'Del Peak 28(Xq21.1)' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

- Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

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

- Number of patients = 269

- Number of copy number variation regions = 48

- Number of molecular subtypes = 12

- Exclude regions 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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)
[4] GISTIC_version2
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle