Correlation between copy number variation genes (focal events) and molecular subtypes
Sarcoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1B56HF6
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/C1B56HF6
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 58 focal events and 8 molecular subtypes across 150 patients, 76 significant findings detected with P value < 0.05 and Q value < 0.25.

- amp_1p32.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- amp_1q24.3 cnv correlated to 'CN_CNMF'.

- amp_5p15.33 cnv correlated to 'CN_CNMF'.

- amp_6p21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- amp_6q24.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', '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_17p11.2 cnv correlated to 'CN_CNMF'.

- amp_17q24.3 cnv correlated to 'METHLYATION_CNMF'.

- amp_19p13.2 cnv correlated to 'CN_CNMF'.

- amp_19q12 cnv correlated to 'CN_CNMF'.

- amp_21q21.1 cnv correlated to 'CN_CNMF'.

- amp_xp21.1 cnv correlated to 'CN_CNMF'.

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

- del_1q44 cnv correlated to 'CN_CNMF'.

- del_2p25.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_2q37.3 cnv correlated to 'CN_CNMF'.

- del_2q37.3 cnv correlated to 'CN_CNMF'.

- del_3p21.31 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- del_4q35.1 cnv correlated to 'CN_CNMF'.

- del_6q14.1 cnv correlated to 'CN_CNMF'.

- del_9p24.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- del_9p21.3 cnv correlated to 'CN_CNMF'.

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

- del_11p15.5 cnv correlated to 'CN_CNMF'.

- del_11q24.3 cnv correlated to 'CN_CNMF'.

- del_12p13.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- del_16q12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_17p13.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- del_17q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_19p13.3 cnv correlated to 'METHLYATION_CNMF'.

- del_22q13.31 cnv correlated to 'CN_CNMF'.

- del_xq21.1 cnv correlated to 'METHLYATION_CNMF'.

- del_xq27.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 58 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, 76 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 | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
amp 12q15 | 58 (39%) | 92 | 3.94e-17 (1.83e-14) | 8.67e-10 (3.94e-07) | 5.17e-10 (2.36e-07) | 3.47e-13 (1.6e-10) | 2.88e-10 (1.32e-07) | 1.03e-11 (4.77e-09) | 5.53e-11 (2.55e-08) | 1.03e-11 (4.77e-09)
amp 6q24 3 | 47 (31%) | 103 | 0.00291 (1.00) | 2.06e-05 (0.00883) | 0.000218 (0.0882) | 9.54e-06 (0.00413) | 2.36e-05 (0.01) | 2.74e-05 (0.0117) | 1.11e-05 (0.00481) | 0.000142 (0.058)
del 1p36 32 | 46 (31%) | 104 | 0.0281 (1.00) | 1.35e-06 (0.000597) | 2.77e-05 (0.0117) | 4.56e-06 (0.00199) | 2e-06 (0.000878) | 3.48e-09 (1.58e-06) | 6.19e-07 (0.000277) | 3.48e-09 (1.58e-06)
del 10q23 31 | 84 (56%) | 66 | 6.14e-10 (2.8e-07) | 3.5e-10 (1.6e-07) | 3.76e-09 (1.7e-06) | 3.3e-07 (0.000148) | 0.00176 (0.642) | 0.000606 (0.237) | 0.00148 (0.549) | 0.000606 (0.237)
del 2p25 3 | 52 (35%) | 98 | 0.00207 (0.738) | 2.29e-05 (0.00978) | 0.000317 (0.127) | 4.79e-06 (0.00208) | 0.00176 (0.642) | 8.81e-05 (0.0363) | 0.00283 (0.983) | 8.81e-05 (0.0363)
del 13q14 2 | 106 (71%) | 44 | 6.33e-07 (0.000282) | 7.15e-07 (0.000318) | 2.08e-05 (0.00892) | 4.37e-06 (0.0019) | 0.0138 (1.00) | 0.0141 (1.00) | 0.00805 (1.00) | 0.0141 (1.00)
del 17p13 1 | 71 (47%) | 79 | 0.00044 (0.174) | 0.000961 (0.369) | 3.34e-05 (0.0141) | 0.000263 (0.106) | 0.0684 (1.00) | 0.0518 (1.00) | 0.0303 (1.00) | 0.0518 (1.00)
del xq27 1 | 74 (49%) | 76 | 0.000611 (0.238) | 0.000303 (0.122) | 0.0403 (1.00) | 0.00051 (0.201) | 0.00607 (1.00) | 0.00115 (0.438) | 0.00553 (1.00) | 0.00115 (0.438)
amp 1p32 1 | 55 (37%) | 95 | 1.32e-06 (0.000584) | 9.87e-07 (0.000438) | 0.887 (1.00) | 0.219 (1.00) | 0.017 (1.00) | 0.00269 (0.941) | 0.0596 (1.00) | 0.00834 (1.00)
amp 6p21 1 | 36 (24%) | 114 | 4.82e-05 (0.0202) | 7.31e-05 (0.0304) | 0.0015 (0.554) | 0.00129 (0.482) | 0.0177 (1.00) | 0.0015 (0.554) | 0.00825 (1.00) | 0.00643 (1.00)
del 3p21 31 | 33 (22%) | 117 | 0.012 (1.00) | 0.00019 (0.0773) | 0.00194 (0.695) | 0.000343 (0.136) | 0.0089 (1.00) | 0.0152 (1.00) | 0.00505 (1.00) | 0.00409 (1.00)
del 9p24 3 | 58 (39%) | 92 | 0.000266 (0.107) | 0.0283 (1.00) | 0.172 (1.00) | 0.00114 (0.435) | 0.00289 (1.00) | 0.000341 (0.136) | 0.0021 (0.746) | 0.00113 (0.433)
del 12p13 1 | 52 (35%) | 98 | 5.89e-05 (0.0245) | 7.32e-05 (0.0304) | 0.281 (1.00) | 0.269 (1.00) | 0.0468 (1.00) | 0.0315 (1.00) | 0.0819 (1.00) | 0.0315 (1.00)
del 16q12 1 | 83 (55%) | 67 | 4.93e-05 (0.0206) | 0.000406 (0.161) | 0.0457 (1.00) | 0.00556 (1.00) | 0.0472 (1.00) | 0.00586 (1.00) | 0.0399 (1.00) | 0.00586 (1.00)
del 17q11 2 | 45 (30%) | 105 | 3.5e-06 (0.00153) | 0.00012 (0.0494) | 0.139 (1.00) | 0.179 (1.00) | 0.00234 (0.828) | 0.000696 (0.269) | 0.00127 (0.475) | 0.0027 (0.943)
amp 1q24 3 | 65 (43%) | 85 | 5.84e-05 (0.0243) | 0.00482 (1.00) | 0.747 (1.00) | 0.28 (1.00) | 0.268 (1.00) | 0.154 (1.00) | 0.142 (1.00) | 0.305 (1.00)
amp 5p15 33 | 67 (45%) | 83 | 0.000629 (0.245) | 0.0258 (1.00) | 0.237 (1.00) | 0.386 (1.00) | 0.273 (1.00) | 0.113 (1.00) | 0.178 (1.00) | 0.212 (1.00)
amp 17p11 2 | 60 (40%) | 90 | 1.73e-07 (7.77e-05) | 0.0174 (1.00) | 0.456 (1.00) | 0.319 (1.00) | 1 (1.00) | 1 (1.00) | 0.841 (1.00) | 1 (1.00)
amp 17q24 3 | 45 (30%) | 105 | 0.085 (1.00) | 0.000162 (0.0658) | 0.00505 (1.00) | 0.5 (1.00) | 0.0353 (1.00) | 0.00121 (0.456) | 0.0671 (1.00) | 0.00358 (1.00)
amp 19p13 2 | 60 (40%) | 90 | 4.12e-05 (0.0174) | 0.527 (1.00) | 1 (1.00) | 0.428 (1.00) | 0.659 (1.00) | 0.562 (1.00) | 0.892 (1.00) | 0.562 (1.00)
amp 19q12 | 53 (35%) | 97 | 1.09e-06 (0.000482) | 0.00143 (0.532) | 0.777 (1.00) | 0.0638 (1.00) | 0.391 (1.00) | 0.228 (1.00) | 0.539 (1.00) | 0.228 (1.00)
amp 21q21 1 | 48 (32%) | 102 | 4.36e-05 (0.0184) | 0.000889 (0.342) | 0.763 (1.00) | 0.271 (1.00) | 0.191 (1.00) | 0.268 (1.00) | 0.164 (1.00) | 0.268 (1.00)
amp xp21 1 | 52 (35%) | 98 | 2.3e-06 (0.00101) | 0.0273 (1.00) | 1 (1.00) | 0.451 (1.00) | 0.913 (1.00) | 0.788 (1.00) | 0.882 (1.00) | 1 (1.00)
del 1q44 | 47 (31%) | 103 | 1.19e-05 (0.00513) | 0.00786 (1.00) | 0.42 (1.00) | 0.0625 (1.00) | 0.077 (1.00) | 0.0658 (1.00) | 0.129 (1.00) | 0.183 (1.00)
del 2q37 3 | 63 (42%) | 87 | 2.62e-08 (1.18e-05) | 0.0278 (1.00) | 0.0664 (1.00) | 0.467 (1.00) | 0.705 (1.00) | 0.751 (1.00) | 0.639 (1.00) | 0.751 (1.00)
del 2q37 3 | 65 (43%) | 85 | 1.21e-08 (5.44e-06) | 0.0083 (1.00) | 0.0134 (1.00) | 0.216 (1.00) | 0.872 (1.00) | 1 (1.00) | 0.859 (1.00) | 1 (1.00)
del 4q35 1 | 56 (37%) | 94 | 1.3e-05 (0.00561) | 0.207 (1.00) | 0.057 (1.00) | 0.766 (1.00) | 0.729 (1.00) | 0.675 (1.00) | 0.611 (1.00) | 0.675 (1.00)
del 6q14 1 | 43 (29%) | 107 | 0.000574 (0.226) | 0.0389 (1.00) | 0.42 (1.00) | 0.749 (1.00) | 0.23 (1.00) | 0.237 (1.00) | 0.282 (1.00) | 0.159 (1.00)
del 9p21 3 | 63 (42%) | 87 | 0.0004 (0.159) | 0.00866 (1.00) | 0.328 (1.00) | 0.00398 (1.00) | 0.0102 (1.00) | 0.00363 (1.00) | 0.00164 (0.598) | 0.00943 (1.00)
del 11p15 5 | 67 (45%) | 83 | 4.79e-05 (0.0201) | 0.00121 (0.455) | 0.298 (1.00) | 0.222 (1.00) | 0.852 (1.00) | 0.896 (1.00) | 0.771 (1.00) | 1 (1.00)
del 11q24 3 | 65 (43%) | 85 | 2.43e-06 (0.00106) | 0.00305 (1.00) | 0.359 (1.00) | 0.0129 (1.00) | 0.00346 (1.00) | 0.00532 (1.00) | 0.00719 (1.00) | 0.0144 (1.00)
del 19p13 3 | 45 (30%) | 105 | 0.00141 (0.525) | 7.93e-05 (0.0328) | 0.00736 (1.00) | 0.0216 (1.00) | 0.0213 (1.00) | 0.031 (1.00) | 0.0149 (1.00) | 0.031 (1.00)
del 22q13 31 | 53 (35%) | 97 | 0.00033 (0.132) | 0.0221 (1.00) | 0.00225 (0.795) | 0.388 (1.00) | 0.491 (1.00) | 0.324 (1.00) | 0.545 (1.00) | 0.324 (1.00)
del xq21 1 | 72 (48%) | 78 | 0.106 (1.00) | 0.00013 (0.0534) | 0.0137 (1.00) | 0.00316 (1.00) | 0.00921 (1.00) | 0.00181 (0.653) | 0.0109 (1.00) | 0.00181 (0.653)
amp 3p11 2 | 36 (24%) | 114 | 0.0104 (1.00) | 0.0983 (1.00) | 0.627 (1.00) | 1 (1.00) | 0.608 (1.00) | 0.407 (1.00) | 0.268 (1.00) | 0.692 (1.00)
amp 7q31 1 | 44 (29%) | 106 | 0.000825 (0.318) | 0.0379 (1.00) | 0.494 (1.00) | 0.0578 (1.00) | 0.0707 (1.00) | 0.0405 (1.00) | 0.0154 (1.00) | 0.115 (1.00)
amp 8q21 12 | 54 (36%) | 96 | 0.0199 (1.00) | 0.0323 (1.00) | 0.852 (1.00) | 0.577 (1.00) | 0.807 (1.00) | 0.873 (1.00) | 0.843 (1.00) | 0.873 (1.00)
amp 11q22 2 | 25 (17%) | 125 | 0.226 (1.00) | 0.098 (1.00) | 0.0485 (1.00) | 0.0499 (1.00) | 0.0578 (1.00) | 0.0649 (1.00) | 0.0762 (1.00) | 0.0649 (1.00)
amp 12p13 32 | 28 (19%) | 122 | 0.291 (1.00) | 0.594 (1.00) | 0.302 (1.00) | 0.0785 (1.00) | 0.086 (1.00) | 0.284 (1.00) | 0.122 (1.00) | 0.129 (1.00)
amp 13q34 | 28 (19%) | 122 | 0.00158 (0.581) | 0.00162 (0.593) | 0.212 (1.00) | 0.391 (1.00) | 0.736 (1.00) | 1 (1.00) | 0.843 (1.00) | 0.789 (1.00)
amp 20q13 33 | 62 (41%) | 88 | 0.00136 (0.506) | 0.0086 (1.00) | 0.253 (1.00) | 0.00877 (1.00) | 0.0103 (1.00) | 0.0736 (1.00) | 0.0112 (1.00) | 0.0302 (1.00)
amp xq21 2 | 24 (16%) | 126 | 0.00394 (1.00) | 0.0179 (1.00) | 0.191 (1.00) | 0.616 (1.00) | 0.349 (1.00) | 0.334 (1.00) | 0.382 (1.00) | 0.334 (1.00)
del 1p32 3 | 26 (17%) | 124 | 0.315 (1.00) | 0.145 (1.00) | 0.048 (1.00) | 1 (1.00) | 0.752 (1.00) | 0.04 (1.00) | 0.757 (1.00) | 0.04 (1.00)
del 3q29 | 35 (23%) | 115 | 0.00592 (1.00) | 0.00237 (0.835) | 0.0551 (1.00) | 0.161 (1.00) | 0.28 (1.00) | 0.214 (1.00) | 0.326 (1.00) | 0.214 (1.00)
del 6p25 1 | 52 (35%) | 98 | 0.376 (1.00) | 0.0448 (1.00) | 0.0421 (1.00) | 0.0106 (1.00) | 0.107 (1.00) | 0.233 (1.00) | 0.117 (1.00) | 0.233 (1.00)
del 7q36 3 | 38 (25%) | 112 | 0.00119 (0.451) | 0.209 (1.00) | 0.821 (1.00) | 0.611 (1.00) | 0.397 (1.00) | 0.43 (1.00) | 0.782 (1.00) | 0.43 (1.00)
del 8p23 3 | 44 (29%) | 106 | 0.0822 (1.00) | 0.00212 (0.751) | 0.188 (1.00) | 0.0988 (1.00) | 0.00487 (1.00) | 0.00503 (1.00) | 0.00268 (0.939) | 0.00179 (0.647)
del 9q34 3 | 42 (28%) | 108 | 0.00436 (1.00) | 0.0976 (1.00) | 0.00509 (1.00) | 0.156 (1.00) | 0.176 (1.00) | 0.101 (1.00) | 0.134 (1.00) | 0.101 (1.00)
del 10p15 3 | 76 (51%) | 74 | 0.00809 (1.00) | 0.00069 (0.268) | 0.0463 (1.00) | 0.138 (1.00) | 0.959 (1.00) | 0.62 (1.00) | 0.863 (1.00) | 0.62 (1.00)
del 12q12 | 29 (19%) | 121 | 0.0999 (1.00) | 0.0642 (1.00) | 0.203 (1.00) | 0.585 (1.00) | 0.478 (1.00) | 1 (1.00) | 0.514 (1.00) | 1 (1.00)
del 14q24 1 | 51 (34%) | 99 | 0.68 (1.00) | 0.0105 (1.00) | 0.00104 (0.398) | 0.268 (1.00) | 0.566 (1.00) | 0.156 (1.00) | 0.534 (1.00) | 0.275 (1.00)
del 15q11 2 | 30 (20%) | 120 | 0.453 (1.00) | 0.206 (1.00) | 0.0752 (1.00) | 0.135 (1.00) | 0.112 (1.00) | 0.108 (1.00) | 0.0611 (1.00) | 0.108 (1.00)
del 17q25 3 | 40 (27%) | 110 | 0.00515 (1.00) | 0.0573 (1.00) | 0.335 (1.00) | 0.078 (1.00) | 0.357 (1.00) | 0.192 (1.00) | 0.273 (1.00) | 0.317 (1.00)
del 18q23 | 50 (33%) | 100 | 0.0593 (1.00) | 0.0312 (1.00) | 0.632 (1.00) | 0.137 (1.00) | 0.0409 (1.00) | 0.291 (1.00) | 0.0514 (1.00) | 0.429 (1.00)
del 19q13 43 | 63 (42%) | 87 | 0.00601 (1.00) | 0.00443 (1.00) | 0.166 (1.00) | 0.0769 (1.00) | 0.0533 (1.00) | 0.0815 (1.00) | 0.104 (1.00) | 0.0815 (1.00)
del 21q11 2 | 28 (19%) | 122 | 0.383 (1.00) | 0.257 (1.00) | 0.565 (1.00) | 0.297 (1.00) | 0.055 (1.00) | 0.153 (1.00) | 0.137 (1.00) | 0.153 (1.00)
del 21q22 3 | 39 (26%) | 111 | 0.052 (1.00) | 0.05 (1.00) | 0.875 (1.00) | 0.269 (1.00) | 0.552 (1.00) | 0.804 (1.00) | 0.442 (1.00) | 0.804 (1.00)
del xp22 32 | 47 (31%) | 103 | 0.0979 (1.00) | 0.00196 (0.702) | 0.0171 (1.00) | 0.0219 (1.00) | 0.0594 (1.00) | 0.0254 (1.00) | 0.0312 (1.00) | 0.0254 (1.00)

'amp_1p32.1' versus 'CN_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00058

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
AMP PEAK 1(1P32.1) MUTATED | 15 | 33 | 7
AMP PEAK 1(1P32.1) WILD-TYPE | 26 | 22 | 47

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

'amp_1p32.1' versus 'METHLYATION_CNMF'

P value = 9.87e-07 (Chi-square test), Q value = 0.00044

Table S2. 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 | 30 | 28 | 15 | 21 | 18 | 35 | 3
AMP PEAK 1(1P32.1) MUTATED | 9 | 11 | 3 | 19 | 1 | 10 | 2
AMP PEAK 1(1P32.1) WILD-TYPE | 21 | 17 | 12 | 2 | 17 | 25 | 1

Figure S2. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q24.3' versus 'CN_CNMF'

P value = 5.84e-05 (Fisher's exact test), Q value = 0.024

Table S3. Gene #2: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
AMP PEAK 2(1Q24.3) MUTATED | 21 | 33 | 11
AMP PEAK 2(1Q24.3) WILD-TYPE | 20 | 22 | 43

Figure S3. Get High-res Image Gene #2: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 0.000629 (Fisher's exact test), Q value = 0.24

Table S4. Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
AMP PEAK 4(5P15.33) MUTATED | 23 | 31 | 13
AMP PEAK 4(5P15.33) WILD-TYPE | 18 | 24 | 41

Figure S4. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'CN_CNMF'

P value = 4.82e-05 (Fisher's exact test), Q value = 0.02

Table S5. Gene #5: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
AMP PEAK 5(6P21.1) MUTATED | 11 | 22 | 3
AMP PEAK 5(6P21.1) WILD-TYPE | 30 | 33 | 51

Figure S5. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 7.31e-05 (Chi-square test), Q value = 0.03

Table S6. Gene #5: '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 | 30 | 28 | 15 | 21 | 18 | 35 | 3
AMP PEAK 5(6P21.1) MUTATED | 5 | 12 | 5 | 10 | 0 | 2 | 2
AMP PEAK 5(6P21.1) WILD-TYPE | 25 | 16 | 10 | 11 | 18 | 33 | 1

Figure S6. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q24.3' versus 'METHLYATION_CNMF'

P value = 2.06e-05 (Chi-square test), Q value = 0.0088

Table S7. Gene #6: 'amp_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3
AMP PEAK 6(6Q24.3) MUTATED | 13 | 18 | 3 | 8 | 1 | 3 | 1
AMP PEAK 6(6Q24.3) WILD-TYPE | 17 | 10 | 12 | 13 | 17 | 32 | 2

Figure S7. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q24.3' versus 'MRNASEQ_CNMF'

P value = 0.000218 (Fisher's exact test), Q value = 0.088

Table S8. Gene #6: 'amp_6q24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 30 | 32
AMP PEAK 6(6Q24.3) MUTATED | 21 | 6 | 3
AMP PEAK 6(6Q24.3) WILD-TYPE | 20 | 24 | 29

Figure S8. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.54e-06 (Fisher's exact test), Q value = 0.0041

Table S9. Gene #6: 'amp_6q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 46 | 53 | 4
AMP PEAK 6(6Q24.3) MUTATED | 4 | 26 | 0
AMP PEAK 6(6Q24.3) WILD-TYPE | 42 | 27 | 4

Figure S9. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6q24.3' versus 'MIRSEQ_CNMF'

P value = 2.36e-05 (Fisher's exact test), Q value = 0.01

Table S10. Gene #6: 'amp_6q24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 63 | 22
AMP PEAK 6(6Q24.3) MUTATED | 8 | 27 | 12
AMP PEAK 6(6Q24.3) WILD-TYPE | 56 | 36 | 10

Figure S10. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_6q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.74e-05 (Fisher's exact test), Q value = 0.012

Table S11. Gene #6: 'amp_6q24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 82 | 2 | 65
AMP PEAK 6(6Q24.3) MUTATED | 38 | 0 | 9
AMP PEAK 6(6Q24.3) WILD-TYPE | 44 | 2 | 56

Figure S11. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_6q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0048

Table S12. Gene #6: 'amp_6q24.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 62 | 65 | 22
AMP PEAK 6(6Q24.3) MUTATED | 7 | 28 | 12
AMP PEAK 6(6Q24.3) WILD-TYPE | 55 | 37 | 10

Figure S12. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_6q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000142 (Fisher's exact test), Q value = 0.058

Table S13. Gene #6: 'amp_6q24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 2 | 65 | 82
AMP PEAK 6(6Q24.3) MUTATED | 0 | 10 | 37
AMP PEAK 6(6Q24.3) WILD-TYPE | 2 | 55 | 45

Figure S13. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 3.94e-17 (Fisher's exact test), Q value = 1.8e-14

Table S14. Gene #11: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
AMP PEAK 11(12Q15) MUTATED | 38 | 13 | 7
AMP PEAK 11(12Q15) WILD-TYPE | 3 | 42 | 47

Figure S14. Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 8.67e-10 (Chi-square test), Q value = 3.9e-07

Table S15. Gene #11: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3
AMP PEAK 11(12Q15) MUTATED | 20 | 20 | 9 | 6 | 1 | 1 | 1
AMP PEAK 11(12Q15) WILD-TYPE | 10 | 8 | 6 | 15 | 17 | 34 | 2

Figure S15. Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 5.17e-10 (Fisher's exact test), Q value = 2.4e-07

Table S16. Gene #11: 'amp_12q15' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 30 | 32
AMP PEAK 11(12Q15) MUTATED | 30 | 9 | 1
AMP PEAK 11(12Q15) WILD-TYPE | 11 | 21 | 31

Figure S16. Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.47e-13 (Fisher's exact test), Q value = 1.6e-10

Table S17. Gene #11: 'amp_12q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 46 | 53 | 4
AMP PEAK 11(12Q15) MUTATED | 2 | 38 | 0
AMP PEAK 11(12Q15) WILD-TYPE | 44 | 15 | 4

Figure S17. Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 2.88e-10 (Fisher's exact test), Q value = 1.3e-07

Table S18. Gene #11: 'amp_12q15' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 63 | 22
AMP PEAK 11(12Q15) MUTATED | 6 | 38 | 13
AMP PEAK 11(12Q15) WILD-TYPE | 58 | 25 | 9

Figure S18. Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.03e-11 (Fisher's exact test), Q value = 4.8e-09

Table S19. Gene #11: 'amp_12q15' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 82 | 2 | 65
AMP PEAK 11(12Q15) MUTATED | 51 | 0 | 6
AMP PEAK 11(12Q15) WILD-TYPE | 31 | 2 | 59

Figure S19. Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.53e-11 (Fisher's exact test), Q value = 2.5e-08

Table S20. Gene #11: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 62 | 65 | 22
AMP PEAK 11(12Q15) MUTATED | 5 | 41 | 11
AMP PEAK 11(12Q15) WILD-TYPE | 57 | 24 | 11

Figure S20. Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.03e-11 (Fisher's exact test), Q value = 4.8e-09

Table S21. Gene #11: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 2 | 65 | 82
AMP PEAK 11(12Q15) MUTATED | 0 | 6 | 51
AMP PEAK 11(12Q15) WILD-TYPE | 2 | 59 | 31

Figure S21. Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17p11.2' versus 'CN_CNMF'

P value = 1.73e-07 (Fisher's exact test), Q value = 7.8e-05

Table S22. Gene #13: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
AMP PEAK 13(17P11.2) MUTATED | 8 | 38 | 14
AMP PEAK 13(17P11.2) WILD-TYPE | 33 | 17 | 40

Figure S22. Get High-res Image Gene #13: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q24.3' versus 'METHLYATION_CNMF'

P value = 0.000162 (Chi-square test), Q value = 0.066

Table S23. Gene #14: 'amp_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3
AMP PEAK 14(17Q24.3) MUTATED | 6 | 13 | 8 | 9 | 3 | 3 | 3
AMP PEAK 14(17Q24.3) WILD-TYPE | 24 | 15 | 7 | 12 | 15 | 32 | 0

Figure S23. Get High-res Image Gene #14: 'amp_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 4.12e-05 (Fisher's exact test), Q value = 0.017

Table S24. Gene #15: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
AMP PEAK 15(19P13.2) MUTATED | 17 | 33 | 10
AMP PEAK 15(19P13.2) WILD-TYPE | 24 | 22 | 44

Figure S24. Get High-res Image Gene #15: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00048

Table S25. Gene #16: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
AMP PEAK 16(19Q12) MUTATED | 13 | 33 | 7
AMP PEAK 16(19Q12) WILD-TYPE | 28 | 22 | 47

Figure S25. Get High-res Image Gene #16: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_21q21.1' versus 'CN_CNMF'

P value = 4.36e-05 (Fisher's exact test), Q value = 0.018

Table S26. Gene #18: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
AMP PEAK 18(21Q21.1) MUTATED | 9 | 30 | 9
AMP PEAK 18(21Q21.1) WILD-TYPE | 32 | 25 | 45

Figure S26. Get High-res Image Gene #18: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp21.1' versus 'CN_CNMF'

P value = 2.3e-06 (Fisher's exact test), Q value = 0.001

Table S27. Gene #19: 'amp_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
AMP PEAK 19(XP21.1) MUTATED | 11 | 33 | 8
AMP PEAK 19(XP21.1) WILD-TYPE | 30 | 22 | 46

Figure S27. Get High-res Image Gene #19: 'amp_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1.35e-06 (Chi-square test), Q value = 6e-04

Table S28. Gene #21: '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 | 30 | 28 | 15 | 21 | 18 | 35 | 3
DEL PEAK 1(1P36.32) MUTATED | 0 | 6 | 5 | 3 | 8 | 22 | 2
DEL PEAK 1(1P36.32) WILD-TYPE | 30 | 22 | 10 | 18 | 10 | 13 | 1

Figure S28. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 2.77e-05 (Fisher's exact test), Q value = 0.012

Table S29. Gene #21: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 30 | 32
DEL PEAK 1(1P36.32) MUTATED | 5 | 15 | 19
DEL PEAK 1(1P36.32) WILD-TYPE | 36 | 15 | 13

Figure S29. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.56e-06 (Fisher's exact test), Q value = 0.002

Table S30. Gene #21: 'del_1p36.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 46 | 53 | 4
DEL PEAK 1(1P36.32) MUTATED | 29 | 10 | 0
DEL PEAK 1(1P36.32) WILD-TYPE | 17 | 43 | 4

Figure S30. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

P value = 2e-06 (Fisher's exact test), Q value = 0.00088

Table S31. Gene #21: 'del_1p36.32' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 64 | 63 | 22
DEL PEAK 1(1P36.32) MUTATED | 34 | 9 | 3
DEL PEAK 1(1P36.32) WILD-TYPE | 30 | 54 | 19

Figure S31. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.48e-09 (Fisher's exact test), Q value = 1.6e-06

Table S32. Gene #21: 'del_1p36.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 82 | 2 | 65
DEL PEAK 1(1P36.32) MUTATED | 9 | 2 | 35
DEL PEAK 1(1P36.32) WILD-TYPE | 73 | 0 | 30

Figure S32. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.19e-07 (Fisher's exact test), Q value = 0.00028

Table S33. Gene #21: 'del_1p36.32' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 62 | 65 | 22
DEL PEAK 1(1P36.32) MUTATED | 34 | 9 | 3
DEL PEAK 1(1P36.32) WILD-TYPE | 28 | 56 | 19

Figure S33. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.48e-09 (Fisher's exact test), Q value = 1.6e-06

Table S34. Gene #21: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 2 | 65 | 82
DEL PEAK 1(1P36.32) MUTATED | 2 | 35 | 9
DEL PEAK 1(1P36.32) WILD-TYPE | 0 | 30 | 73

Figure S34. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.0051

Table S35. Gene #23: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 3(1Q44) MUTATED | 15 | 27 | 5
DEL PEAK 3(1Q44) WILD-TYPE | 26 | 28 | 49

Figure S35. Get High-res Image Gene #23: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p25.3' versus 'METHLYATION_CNMF'

P value = 2.29e-05 (Chi-square test), Q value = 0.0098

Table S36. Gene #24: '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 | 30 | 28 | 15 | 21 | 18 | 35 | 3
DEL PEAK 4(2P25.3) MUTATED | 3 | 10 | 1 | 7 | 6 | 22 | 3
DEL PEAK 4(2P25.3) WILD-TYPE | 27 | 18 | 14 | 14 | 12 | 13 | 0

Figure S36. Get High-res Image Gene #24: 'del_2p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p25.3' versus 'MRNASEQ_CNMF'

P value = 0.000317 (Fisher's exact test), Q value = 0.13

Table S37. Gene #24: 'del_2p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 30 | 32
DEL PEAK 4(2P25.3) MUTATED | 6 | 10 | 19
DEL PEAK 4(2P25.3) WILD-TYPE | 35 | 20 | 13

Figure S37. Get High-res Image Gene #24: 'del_2p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.79e-06 (Fisher's exact test), Q value = 0.0021

Table S38. Gene #24: 'del_2p25.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 46 | 53 | 4
DEL PEAK 4(2P25.3) MUTATED | 27 | 8 | 0
DEL PEAK 4(2P25.3) WILD-TYPE | 19 | 45 | 4

Figure S38. Get High-res Image Gene #24: 'del_2p25.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.81e-05 (Fisher's exact test), Q value = 0.036

Table S39. Gene #24: 'del_2p25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 82 | 2 | 65
DEL PEAK 4(2P25.3) MUTATED | 17 | 0 | 34
DEL PEAK 4(2P25.3) WILD-TYPE | 65 | 2 | 31

Figure S39. Get High-res Image Gene #24: 'del_2p25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.81e-05 (Fisher's exact test), Q value = 0.036

Table S40. Gene #24: 'del_2p25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 2 | 65 | 82
DEL PEAK 4(2P25.3) MUTATED | 0 | 34 | 17
DEL PEAK 4(2P25.3) WILD-TYPE | 2 | 31 | 65

Figure S40. Get High-res Image Gene #24: 'del_2p25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 2.62e-08 (Fisher's exact test), Q value = 1.2e-05

Table S41. Gene #25: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 5(2Q37.3) MUTATED | 12 | 40 | 11
DEL PEAK 5(2Q37.3) WILD-TYPE | 29 | 15 | 43

Figure S41. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 1.21e-08 (Fisher's exact test), Q value = 5.4e-06

Table S42. Gene #26: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 6(2Q37.3) MUTATED | 13 | 41 | 11
DEL PEAK 6(2Q37.3) WILD-TYPE | 28 | 14 | 43

Figure S42. Get High-res Image Gene #26: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 0.00019 (Chi-square test), Q value = 0.077

Table S43. Gene #27: '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 | 30 | 28 | 15 | 21 | 18 | 35 | 3
DEL PEAK 7(3P21.31) MUTATED | 4 | 14 | 5 | 7 | 2 | 1 | 0
DEL PEAK 7(3P21.31) WILD-TYPE | 26 | 14 | 10 | 14 | 16 | 34 | 3

Figure S43. Get High-res Image Gene #27: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000343 (Fisher's exact test), Q value = 0.14

Table S44. Gene #27: 'del_3p21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 46 | 53 | 4
DEL PEAK 7(3P21.31) MUTATED | 3 | 20 | 0
DEL PEAK 7(3P21.31) WILD-TYPE | 43 | 33 | 4

Figure S44. Get High-res Image Gene #27: 'del_3p21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0056

Table S45. Gene #29: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 9(4Q35.1) MUTATED | 14 | 33 | 9
DEL PEAK 9(4Q35.1) WILD-TYPE | 27 | 22 | 45

Figure S45. Get High-res Image Gene #29: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.1' versus 'CN_CNMF'

P value = 0.000574 (Fisher's exact test), Q value = 0.23

Table S46. Gene #31: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 11(6Q14.1) MUTATED | 9 | 26 | 8
DEL PEAK 11(6Q14.1) WILD-TYPE | 32 | 29 | 46

Figure S46. Get High-res Image Gene #31: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p24.3' versus 'CN_CNMF'

P value = 0.000266 (Fisher's exact test), Q value = 0.11

Table S47. Gene #34: 'del_9p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 14(9P24.3) MUTATED | 25 | 22 | 11
DEL PEAK 14(9P24.3) WILD-TYPE | 16 | 33 | 43

Figure S47. Get High-res Image Gene #34: 'del_9p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000341 (Fisher's exact test), Q value = 0.14

Table S48. Gene #34: 'del_9p24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 82 | 2 | 65
DEL PEAK 14(9P24.3) MUTATED | 41 | 2 | 15
DEL PEAK 14(9P24.3) WILD-TYPE | 41 | 0 | 50

Figure S48. Get High-res Image Gene #34: 'del_9p24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.16

Table S49. Gene #35: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 15(9P21.3) MUTATED | 25 | 26 | 12
DEL PEAK 15(9P21.3) WILD-TYPE | 16 | 29 | 42

Figure S49. Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 6.14e-10 (Fisher's exact test), Q value = 2.8e-07

Table S50. Gene #38: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 18(10Q23.31) MUTATED | 7 | 45 | 32
DEL PEAK 18(10Q23.31) WILD-TYPE | 34 | 10 | 22

Figure S50. Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 3.5e-10 (Chi-square test), Q value = 1.6e-07

Table S51. Gene #38: '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 | 30 | 28 | 15 | 21 | 18 | 35 | 3
DEL PEAK 18(10Q23.31) MUTATED | 5 | 12 | 5 | 18 | 8 | 33 | 3
DEL PEAK 18(10Q23.31) WILD-TYPE | 25 | 16 | 10 | 3 | 10 | 2 | 0

Figure S51. Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 3.76e-09 (Fisher's exact test), Q value = 1.7e-06

Table S52. Gene #38: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 30 | 32
DEL PEAK 18(10Q23.31) MUTATED | 10 | 17 | 30
DEL PEAK 18(10Q23.31) WILD-TYPE | 31 | 13 | 2

Figure S52. Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.3e-07 (Fisher's exact test), Q value = 0.00015

Table S53. Gene #38: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 46 | 53 | 4
DEL PEAK 18(10Q23.31) MUTATED | 38 | 19 | 0
DEL PEAK 18(10Q23.31) WILD-TYPE | 8 | 34 | 4

Figure S53. Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000606 (Fisher's exact test), Q value = 0.24

Table S54. Gene #38: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 82 | 2 | 65
DEL PEAK 18(10Q23.31) MUTATED | 35 | 2 | 46
DEL PEAK 18(10Q23.31) WILD-TYPE | 47 | 0 | 19

Figure S54. Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000606 (Fisher's exact test), Q value = 0.24

Table S55. Gene #38: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 2 | 65 | 82
DEL PEAK 18(10Q23.31) MUTATED | 2 | 46 | 35
DEL PEAK 18(10Q23.31) WILD-TYPE | 0 | 19 | 47

Figure S55. Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 4.79e-05 (Fisher's exact test), Q value = 0.02

Table S56. Gene #39: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 19(11P15.5) MUTATED | 20 | 35 | 12
DEL PEAK 19(11P15.5) WILD-TYPE | 21 | 20 | 42

Figure S56. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.3' versus 'CN_CNMF'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.0011

Table S57. Gene #40: 'del_11q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 20(11Q24.3) MUTATED | 24 | 32 | 9
DEL PEAK 20(11Q24.3) WILD-TYPE | 17 | 23 | 45

Figure S57. Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 5.89e-05 (Fisher's exact test), Q value = 0.025

Table S58. Gene #41: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 21(12P13.1) MUTATED | 14 | 30 | 8
DEL PEAK 21(12P13.1) WILD-TYPE | 27 | 25 | 46

Figure S58. Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 7.32e-05 (Chi-square test), Q value = 0.03

Table S59. Gene #41: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3
DEL PEAK 21(12P13.1) MUTATED | 4 | 18 | 2 | 13 | 4 | 10 | 1
DEL PEAK 21(12P13.1) WILD-TYPE | 26 | 10 | 13 | 8 | 14 | 25 | 2

Figure S59. Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 6.33e-07 (Fisher's exact test), Q value = 0.00028

Table S60. Gene #43: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 23(13Q14.2) MUTATED | 21 | 52 | 33
DEL PEAK 23(13Q14.2) WILD-TYPE | 20 | 3 | 21

Figure S60. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 7.15e-07 (Chi-square test), Q value = 0.00032

Table S61. Gene #43: '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 | 30 | 28 | 15 | 21 | 18 | 35 | 3
DEL PEAK 23(13Q14.2) MUTATED | 11 | 21 | 7 | 19 | 11 | 34 | 3
DEL PEAK 23(13Q14.2) WILD-TYPE | 19 | 7 | 8 | 2 | 7 | 1 | 0

Figure S61. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 2.08e-05 (Fisher's exact test), Q value = 0.0089

Table S62. Gene #43: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 30 | 32
DEL PEAK 23(13Q14.2) MUTATED | 19 | 24 | 30
DEL PEAK 23(13Q14.2) WILD-TYPE | 22 | 6 | 2

Figure S62. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.37e-06 (Fisher's exact test), Q value = 0.0019

Table S63. Gene #43: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 46 | 53 | 4
DEL PEAK 23(13Q14.2) MUTATED | 42 | 31 | 0
DEL PEAK 23(13Q14.2) WILD-TYPE | 4 | 22 | 4

Figure S63. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q12.1' versus 'CN_CNMF'

P value = 4.93e-05 (Fisher's exact test), Q value = 0.021

Table S64. Gene #46: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 26(16Q12.1) MUTATED | 13 | 42 | 28
DEL PEAK 26(16Q12.1) WILD-TYPE | 28 | 13 | 26

Figure S64. Get High-res Image Gene #46: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q12.1' versus 'METHLYATION_CNMF'

P value = 0.000406 (Chi-square test), Q value = 0.16

Table S65. Gene #46: 'del_16q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3
DEL PEAK 26(16Q12.1) MUTATED | 6 | 17 | 6 | 15 | 11 | 26 | 2
DEL PEAK 26(16Q12.1) WILD-TYPE | 24 | 11 | 9 | 6 | 7 | 9 | 1

Figure S65. Get High-res Image Gene #46: 'del_16q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.17

Table S66. Gene #47: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 27(17P13.1) MUTATED | 9 | 33 | 29
DEL PEAK 27(17P13.1) WILD-TYPE | 32 | 22 | 25

Figure S66. Get High-res Image Gene #47: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.014

Table S67. Gene #47: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 30 | 32
DEL PEAK 27(17P13.1) MUTATED | 8 | 13 | 23
DEL PEAK 27(17P13.1) WILD-TYPE | 33 | 17 | 9

Figure S67. Get High-res Image Gene #47: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000263 (Fisher's exact test), Q value = 0.11

Table S68. Gene #47: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 46 | 53 | 4
DEL PEAK 27(17P13.1) MUTATED | 29 | 15 | 0
DEL PEAK 27(17P13.1) WILD-TYPE | 17 | 38 | 4

Figure S68. Get High-res Image Gene #47: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 3.5e-06 (Fisher's exact test), Q value = 0.0015

Table S69. Gene #48: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 28(17Q11.2) MUTATED | 14 | 27 | 4
DEL PEAK 28(17Q11.2) WILD-TYPE | 27 | 28 | 50

Figure S69. Get High-res Image Gene #48: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00012 (Chi-square test), Q value = 0.049

Table S70. Gene #48: '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 | 30 | 28 | 15 | 21 | 18 | 35 | 3
DEL PEAK 28(17Q11.2) MUTATED | 5 | 15 | 7 | 11 | 0 | 6 | 1
DEL PEAK 28(17Q11.2) WILD-TYPE | 25 | 13 | 8 | 10 | 18 | 29 | 2

Figure S70. Get High-res Image Gene #48: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 7.93e-05 (Chi-square test), Q value = 0.033

Table S71. Gene #51: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3
DEL PEAK 31(19P13.3) MUTATED | 1 | 4 | 5 | 11 | 6 | 15 | 3
DEL PEAK 31(19P13.3) WILD-TYPE | 29 | 24 | 10 | 10 | 12 | 20 | 0

Figure S71. Get High-res Image Gene #51: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'CN_CNMF'

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

Table S72. Gene #55: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 35(22Q13.31) MUTATED | 15 | 29 | 9
DEL PEAK 35(22Q13.31) WILD-TYPE | 26 | 26 | 45

Figure S72. Get High-res Image Gene #55: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.1' versus 'METHLYATION_CNMF'

P value = 0.00013 (Chi-square test), Q value = 0.053

Table S73. Gene #57: '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 | 30 | 28 | 15 | 21 | 18 | 35 | 3
DEL PEAK 37(XQ21.1) MUTATED | 5 | 15 | 6 | 10 | 9 | 27 | 0
DEL PEAK 37(XQ21.1) WILD-TYPE | 25 | 13 | 9 | 11 | 9 | 8 | 3

Figure S73. Get High-res Image Gene #57: 'del_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq27.1' versus 'CN_CNMF'

P value = 0.000611 (Fisher's exact test), Q value = 0.24

Table S74. Gene #58: 'del_xq27.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 55 | 54
DEL PEAK 38(XQ27.1) MUTATED | 13 | 38 | 23
DEL PEAK 38(XQ27.1) WILD-TYPE | 28 | 17 | 31

Figure S74. Get High-res Image Gene #58: 'del_xq27.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq27.1' versus 'METHLYATION_CNMF'

P value = 0.000303 (Chi-square test), Q value = 0.12

Table S75. Gene #58: 'del_xq27.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3
DEL PEAK 38(XQ27.1) MUTATED | 7 | 13 | 4 | 11 | 9 | 27 | 3
DEL PEAK 38(XQ27.1) WILD-TYPE | 23 | 15 | 11 | 10 | 9 | 8 | 0

Figure S75. Get High-res Image Gene #58: 'del_xq27.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq27.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.2

Table S76. Gene #58: 'del_xq27.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 46 | 53 | 4
DEL PEAK 38(XQ27.1) MUTATED | 33 | 22 | 0
DEL PEAK 38(XQ27.1) WILD-TYPE | 13 | 31 | 4

Figure S76. Get High-res Image Gene #58: 'del_xq27.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

- Number of patients = 150

- Number of significantly focal cnvs = 58

- 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

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)
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