Correlation between copy number variation genes (focal events) and molecular subtypes

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 63 focal events and 10 molecular subtypes across 184 patients, 91 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q21.3 cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.
amp_2q36.2 cnv correlated to 'CN_CNMF'.
amp_3q26.2 cnv correlated to 'CN_CNMF'.
amp_7q22.1 cnv correlated to 'CN_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_12p13.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_12p11.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF'.
amp_17q12 cnv correlated to 'CN_CNMF'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q13.2 cnv correlated to 'CN_CNMF'.
amp_20p11.23 cnv correlated to 'CN_CNMF'.
amp_xq27.1 cnv correlated to 'CN_CNMF'.
del_1p36.32 cnv correlated to 'CN_CNMF'.
del_1p36.11 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_2q14.3 cnv correlated to 'CN_CNMF'.
del_3p21.31 cnv correlated to 'CN_CNMF'.
del_5q14.2 cnv correlated to 'CN_CNMF'.
del_6p25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.33 cnv correlated to 'CN_CNMF'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_12q12 cnv correlated to 'CN_CNMF'.
del_12q21.33 cnv correlated to 'CN_CNMF'.
del_12q24.33 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'CN_CNMF'.
del_17p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_22q13.32 cnv correlated to 'CN_CNMF'.
del_xp21.1 cnv correlated to 'CN_CNMF'.
del_xq11.2 cnv correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 63 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 91 significant findings detected.


		Clinical Features	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	Fisher's exact test	Fisher's exact test
del 9p21 3	116 (63%)	68	1e-05 (0.00628)	1e-05 (0.00628)	0.0156 (1.00)	0.0678 (1.00)	1e-05 (0.00628)	5e-05 (0.0284)	1e-05 (0.00628)	1e-05 (0.00628)	1e-05 (0.00628)	1e-05 (0.00628)
del 17p12	89 (48%)	95	1e-05 (0.00628)	1e-05 (0.00628)	0.0104 (1.00)	0.0108 (1.00)	1e-05 (0.00628)	4e-05 (0.0229)	1e-05 (0.00628)	5e-05 (0.0284)	2e-05 (0.0116)	2e-05 (0.0116)
del 18q21 2	126 (68%)	58	1e-05 (0.00628)	1e-05 (0.00628)	0.00329 (1.00)	0.0214 (1.00)	6e-05 (0.0338)	4e-05 (0.0229)	0.00017 (0.0942)	0.0001 (0.0557)	0.0103 (1.00)	1e-05 (0.00628)
del 6q25 3	91 (49%)	93	1e-05 (0.00628)	1e-05 (0.00628)	0.00954 (1.00)	0.0356 (1.00)	0.00061 (0.325)	0.00486 (1.00)	0.00463 (1.00)	0.00028 (0.154)	2e-05 (0.0116)	8e-05 (0.0448)
del 17q22	49 (27%)	135	1e-05 (0.00628)	1e-05 (0.00628)	0.00046 (0.247)	0.00044 (0.237)	0.00922 (1.00)	0.0141 (1.00)	0.00878 (1.00)	0.0265 (1.00)	1e-05 (0.00628)	0.0537 (1.00)
del 6p25 2	74 (40%)	110	1e-05 (0.00628)	1e-05 (0.00628)	0.00229 (1.00)	0.122 (1.00)	0.0311 (1.00)	0.0123 (1.00)	0.0879 (1.00)	0.00036 (0.197)	0.00133 (0.685)	0.00015 (0.0832)
del 19p13 2	28 (15%)	156	2e-05 (0.0116)	1e-05 (0.00628)	0.125 (1.00)	0.524 (1.00)	0.0066 (1.00)	0.00347 (1.00)	0.0526 (1.00)	0.00031 (0.17)	1e-05 (0.00628)	0.00056 (0.3)
amp 18q11 2	56 (30%)	128	1e-05 (0.00628)	6e-05 (0.0338)	0.0115 (1.00)	0.00248 (1.00)	0.0245 (1.00)	0.0761 (1.00)	0.00265 (1.00)	0.00061 (0.325)	0.00362 (1.00)	0.00026 (0.143)
del 6p22 2	70 (38%)	114	1e-05 (0.00628)	1e-05 (0.00628)	0.0174 (1.00)	0.31 (1.00)	0.0791 (1.00)	0.0225 (1.00)	0.229 (1.00)	0.00077 (0.405)	0.00261 (1.00)	0.00023 (0.127)
del 12p13 1	29 (16%)	155	3e-05 (0.0172)	2e-05 (0.0116)	0.0174 (1.00)	0.271 (1.00)	0.0103 (1.00)	0.0012 (0.623)	0.00465 (1.00)	6e-05 (0.0338)	0.021 (1.00)	0.00059 (0.314)
del 19p13 3	36 (20%)	148	1e-05 (0.00628)	1e-05 (0.00628)	0.391 (1.00)	0.44 (1.00)	0.0837 (1.00)	0.00166 (0.848)	0.167 (1.00)	0.0084 (1.00)	5e-05 (0.0284)	0.00416 (1.00)
del 21q11 2	62 (34%)	122	1e-05 (0.00628)	0.00042 (0.228)	0.073 (1.00)	0.251 (1.00)	0.00911 (1.00)	0.0587 (1.00)	0.374 (1.00)	0.0213 (1.00)	0.00037 (0.201)	0.0191 (1.00)
del 22q13 31	60 (33%)	124	1e-05 (0.00628)	0.00036 (0.197)	0.394 (1.00)	0.866 (1.00)	0.0131 (1.00)	0.0799 (1.00)	0.0413 (1.00)	0.0169 (1.00)	9e-05 (0.0503)	0.0011 (0.574)
amp 1q21 3	62 (34%)	122	0.00254 (1.00)	0.00042 (0.228)	0.133 (1.00)	0.205 (1.00)	0.0012 (0.623)	0.011 (1.00)	0.00147 (0.753)	0.0161 (1.00)	0.00036 (0.197)	0.0027 (1.00)
amp 8q24 21	74 (40%)	110	1e-05 (0.00628)	2e-05 (0.0116)	0.0689 (1.00)	0.0417 (1.00)	0.129 (1.00)	0.0611 (1.00)	0.113 (1.00)	0.0582 (1.00)	0.00297 (1.00)	0.00698 (1.00)
amp 12p13 33	39 (21%)	145	1e-05 (0.00628)	0.00032 (0.175)	0.605 (1.00)	0.434 (1.00)	0.773 (1.00)	0.553 (1.00)	0.122 (1.00)	0.197 (1.00)	0.00069 (0.365)	0.885 (1.00)
amp 12p11 21	43 (23%)	141	1e-05 (0.00628)	0.00043 (0.232)	0.364 (1.00)	0.891 (1.00)	0.244 (1.00)	0.311 (1.00)	0.0187 (1.00)	0.00748 (1.00)	0.00362 (1.00)	0.514 (1.00)
del 1p36 11	68 (37%)	116	1e-05 (0.00628)	1e-05 (0.00628)	0.081 (1.00)	0.231 (1.00)	0.00171 (0.872)	0.0179 (1.00)	0.107 (1.00)	0.0852 (1.00)	0.00815 (1.00)	0.00547 (1.00)
del 12q24 33	43 (23%)	141	2e-05 (0.0116)	0.00124 (0.641)	0.00613 (1.00)	0.00821 (1.00)	0.00116 (0.603)	0.00322 (1.00)	0.00362 (1.00)	0.00049 (0.263)	0.006 (1.00)	9e-05 (0.0503)
amp 2q36 2	26 (14%)	158	0.0001 (0.0557)	0.00378 (1.00)	0.106 (1.00)	0.394 (1.00)	0.0581 (1.00)	0.0206 (1.00)	0.606 (1.00)	0.00402 (1.00)	0.165 (1.00)	0.00321 (1.00)
amp 3q26 2	32 (17%)	152	4e-05 (0.0229)	0.0007 (0.37)	0.113 (1.00)	0.156 (1.00)	0.0404 (1.00)	0.0527 (1.00)	0.218 (1.00)	0.0164 (1.00)	0.00724 (1.00)	0.0864 (1.00)
amp 7q22 1	56 (30%)	128	1e-05 (0.00628)	0.199 (1.00)	0.251 (1.00)	0.73 (1.00)	0.144 (1.00)	0.312 (1.00)	0.0444 (1.00)	0.0369 (1.00)	0.00578 (1.00)	0.066 (1.00)
amp 12q15	29 (16%)	155	1e-05 (0.00628)	0.0023 (1.00)	0.338 (1.00)	0.286 (1.00)	0.804 (1.00)	0.327 (1.00)	0.0959 (1.00)	0.0769 (1.00)	0.0136 (1.00)	0.406 (1.00)
amp 17q12	31 (17%)	153	5e-05 (0.0284)	0.212 (1.00)	0.507 (1.00)	0.443 (1.00)	0.13 (1.00)	0.212 (1.00)	0.0799 (1.00)	0.0605 (1.00)	0.257 (1.00)	0.126 (1.00)
amp 19q13 2	47 (26%)	137	1e-05 (0.00628)	0.00765 (1.00)	0.566 (1.00)	0.647 (1.00)	0.951 (1.00)	0.874 (1.00)	0.573 (1.00)	0.228 (1.00)	0.388 (1.00)	0.576 (1.00)
amp 20p11 23	38 (21%)	146	1e-05 (0.00628)	0.0486 (1.00)	0.123 (1.00)	0.442 (1.00)	0.723 (1.00)	0.396 (1.00)	0.389 (1.00)	0.0248 (1.00)	0.00094 (0.493)	0.16 (1.00)
amp xq27 1	21 (11%)	163	2e-05 (0.0116)	0.664 (1.00)	0.879 (1.00)	0.309 (1.00)	0.759 (1.00)	0.194 (1.00)	0.211 (1.00)	0.454 (1.00)	0.871 (1.00)	0.651 (1.00)
del 1p36 32	52 (28%)	132	1e-05 (0.00628)	0.00134 (0.689)	0.397 (1.00)	0.251 (1.00)	0.0101 (1.00)	0.155 (1.00)	0.176 (1.00)	0.0649 (1.00)	0.015 (1.00)	0.0177 (1.00)
del 2q14 3	9 (5%)	175	4e-05 (0.0229)	0.358 (1.00)			1 (1.00)	0.478 (1.00)	0.486 (1.00)	0.721 (1.00)	0.0955 (1.00)	0.605 (1.00)
del 3p21 31	51 (28%)	133	6e-05 (0.0338)	0.114 (1.00)	0.333 (1.00)	0.58 (1.00)	0.211 (1.00)	0.789 (1.00)	0.0963 (1.00)	0.0429 (1.00)	0.0495 (1.00)	0.214 (1.00)
del 5q14 2	35 (19%)	149	1e-05 (0.00628)	0.142 (1.00)	0.0846 (1.00)	0.218 (1.00)	0.192 (1.00)	0.219 (1.00)	0.104 (1.00)	0.178 (1.00)	0.0786 (1.00)	0.0883 (1.00)
del 8p23 2	58 (32%)	126	0.00022 (0.122)	0.0219 (1.00)	0.111 (1.00)	0.091 (1.00)	0.357 (1.00)	0.315 (1.00)	0.173 (1.00)	0.151 (1.00)	0.0216 (1.00)	0.0652 (1.00)
del 10q23 33	35 (19%)	149	0.00041 (0.223)	0.321 (1.00)	0.33 (1.00)	0.485 (1.00)	0.45 (1.00)	0.179 (1.00)	0.757 (1.00)	0.54 (1.00)	0.632 (1.00)	0.0891 (1.00)
del 12q12	25 (14%)	159	1e-05 (0.00628)	0.00072 (0.379)	0.00739 (1.00)	0.0231 (1.00)	0.00412 (1.00)	0.00093 (0.488)	0.00189 (0.953)	0.0204 (1.00)	0.0018 (0.913)	0.00311 (1.00)
del 12q21 33	44 (24%)	140	1e-05 (0.00628)	0.00058 (0.31)	0.00532 (1.00)	0.00576 (1.00)	0.00737 (1.00)	0.00183 (0.926)	0.00615 (1.00)	0.00615 (1.00)	0.00364 (1.00)	0.0013 (0.671)
del 15q15 1	36 (20%)	148	1e-05 (0.00628)	0.00109 (0.57)	0.469 (1.00)	0.779 (1.00)	0.0459 (1.00)	0.00311 (1.00)	0.183 (1.00)	0.0324 (1.00)	0.125 (1.00)	0.00579 (1.00)
del 22q13 32	62 (34%)	122	1e-05 (0.00628)	0.00144 (0.739)	0.657 (1.00)	0.861 (1.00)	0.153 (1.00)	0.177 (1.00)	0.155 (1.00)	0.282 (1.00)	0.00049 (0.263)	0.0434 (1.00)
del xp21 1	29 (16%)	155	4e-05 (0.0229)	0.0714 (1.00)	0.497 (1.00)	0.702 (1.00)	0.291 (1.00)	0.454 (1.00)	0.0551 (1.00)	0.782 (1.00)	0.0144 (1.00)	0.479 (1.00)
del xq11 2	23 (12%)	161	1e-05 (0.00628)	0.0024 (1.00)	0.3 (1.00)	0.326 (1.00)	0.00927 (1.00)	0.0213 (1.00)	0.00426 (1.00)	0.0229 (1.00)	0.00468 (1.00)	0.0153 (1.00)
amp 1p34 2	13 (7%)	171	0.113 (1.00)	1 (1.00)	0.119 (1.00)	0.0902 (1.00)	0.863 (1.00)	0.266 (1.00)	0.931 (1.00)	0.917 (1.00)	0.473 (1.00)	0.426 (1.00)
amp 1p12	27 (15%)	157	0.546 (1.00)	0.953 (1.00)	0.121 (1.00)	0.263 (1.00)	0.264 (1.00)	0.444 (1.00)	0.473 (1.00)	0.264 (1.00)	0.454 (1.00)	0.0986 (1.00)
amp 3p12 2	12 (7%)	172	0.00777 (1.00)	0.69 (1.00)	0.833 (1.00)	0.794 (1.00)	1 (1.00)	0.922 (1.00)	0.834 (1.00)	1 (1.00)	1 (1.00)	0.717 (1.00)
amp 4p16 3	15 (8%)	169	0.0458 (1.00)	1 (1.00)	0.592 (1.00)	0.606 (1.00)	0.0326 (1.00)	0.0192 (1.00)	0.131 (1.00)	0.0257 (1.00)	0.644 (1.00)	0.137 (1.00)
amp 6p21 31	12 (7%)	172	0.00232 (1.00)	0.24 (1.00)	0.841 (1.00)	0.929 (1.00)	0.294 (1.00)	0.855 (1.00)	0.48 (1.00)	0.715 (1.00)	0.00889 (1.00)	0.146 (1.00)
amp 8p11 22	34 (18%)	150	0.0175 (1.00)	0.178 (1.00)	0.102 (1.00)	0.0797 (1.00)	1 (1.00)	0.696 (1.00)	0.812 (1.00)	0.688 (1.00)	0.0496 (1.00)	0.506 (1.00)
amp 8p11 21	34 (18%)	150	0.00647 (1.00)	0.177 (1.00)	0.172 (1.00)	0.0888 (1.00)	0.593 (1.00)	0.698 (1.00)	0.859 (1.00)	0.213 (1.00)	0.0213 (1.00)	0.169 (1.00)
amp 9p13 3	24 (13%)	160	0.00243 (1.00)	0.686 (1.00)	0.393 (1.00)	0.0405 (1.00)	0.145 (1.00)	0.392 (1.00)	0.625 (1.00)	0.0807 (1.00)	0.74 (1.00)	0.587 (1.00)
amp 15q26 1	22 (12%)	162	0.0109 (1.00)	0.0372 (1.00)	0.0354 (1.00)	0.121 (1.00)	0.21 (1.00)	0.11 (1.00)	0.45 (1.00)	0.536 (1.00)	0.363 (1.00)	0.301 (1.00)
amp 17p11 2	15 (8%)	169	0.00213 (1.00)	0.119 (1.00)	0.511 (1.00)	0.55 (1.00)	0.182 (1.00)	0.0505 (1.00)	0.0473 (1.00)	0.11 (1.00)	0.886 (1.00)	0.312 (1.00)
amp 19p13 2	18 (10%)	166	0.00174 (0.886)	0.117 (1.00)	0.712 (1.00)	0.744 (1.00)	0.901 (1.00)	0.71 (1.00)	0.00438 (1.00)	0.111 (1.00)	0.107 (1.00)	0.267 (1.00)
amp xp22 11	11 (6%)	173	0.0151 (1.00)	0.264 (1.00)	0.498 (1.00)	0.00847 (1.00)	0.11 (1.00)	0.0769 (1.00)	0.0367 (1.00)	0.0909 (1.00)	0.842 (1.00)	0.00847 (1.00)
del 4p15 31	30 (16%)	154	0.0115 (1.00)	0.0285 (1.00)	0.218 (1.00)	0.487 (1.00)	0.0344 (1.00)	0.0266 (1.00)	0.459 (1.00)	0.00987 (1.00)	0.514 (1.00)	0.0107 (1.00)
del 4q22 1	27 (15%)	157	0.13 (1.00)	0.0331 (1.00)	0.307 (1.00)	0.434 (1.00)	0.00542 (1.00)	0.0894 (1.00)	0.133 (1.00)	0.00175 (0.889)	0.221 (1.00)	0.00546 (1.00)
del 4q34 3	35 (19%)	149	0.00434 (1.00)	0.15 (1.00)	0.146 (1.00)	0.258 (1.00)	0.187 (1.00)	0.621 (1.00)	0.713 (1.00)	0.172 (1.00)	0.615 (1.00)	0.232 (1.00)
del 7q36 1	15 (8%)	169	0.00186 (0.939)	0.256 (1.00)	0.199 (1.00)	0.0501 (1.00)	0.213 (1.00)	0.605 (1.00)	0.906 (1.00)	0.344 (1.00)	0.0567 (1.00)	0.25 (1.00)
del 9q22 33	47 (26%)	137	0.0651 (1.00)	0.909 (1.00)	0.258 (1.00)	0.302 (1.00)	0.135 (1.00)	0.43 (1.00)	0.0812 (1.00)	0.1 (1.00)	0.154 (1.00)	0.116 (1.00)
del 10p15 3	41 (22%)	143	0.00112 (0.584)	0.0478 (1.00)	0.454 (1.00)	0.586 (1.00)	0.0282 (1.00)	0.013 (1.00)	0.107 (1.00)	0.025 (1.00)	0.0591 (1.00)	0.00697 (1.00)
del 11p15 4	29 (16%)	155	0.00065 (0.344)	0.837 (1.00)	0.00349 (1.00)	0.045 (1.00)	0.927 (1.00)	0.785 (1.00)	0.464 (1.00)	0.55 (1.00)	0.171 (1.00)	1 (1.00)
del 13q14 2	20 (11%)	164	0.003 (1.00)	0.078 (1.00)	0.867 (1.00)	0.939 (1.00)	0.063 (1.00)	0.266 (1.00)	0.122 (1.00)	0.0621 (1.00)	0.00228 (1.00)	0.09 (1.00)
del 14q11 2	20 (11%)	164	0.00346 (1.00)	0.126 (1.00)	0.925 (1.00)	0.653 (1.00)	0.101 (1.00)	0.132 (1.00)	0.248 (1.00)	0.249 (1.00)	0.264 (1.00)	0.535 (1.00)
del 16q23 1	19 (10%)	165	0.0152 (1.00)	0.355 (1.00)	0.408 (1.00)	0.0206 (1.00)	0.56 (1.00)	0.0478 (1.00)	0.299 (1.00)	0.334 (1.00)	0.15 (1.00)	0.277 (1.00)
del 18p11 31	54 (29%)	130	0.349 (1.00)	0.244 (1.00)	0.644 (1.00)	0.146 (1.00)	0.612 (1.00)	0.975 (1.00)	0.19 (1.00)	0.855 (1.00)	0.592 (1.00)	0.113 (1.00)
del 19q13 33	22 (12%)	162	0.00229 (1.00)	0.108 (1.00)	0.749 (1.00)	0.939 (1.00)	0.195 (1.00)	0.227 (1.00)	0.186 (1.00)	0.0848 (1.00)	0.255 (1.00)	0.0719 (1.00)

'amp_1q21.3' versus 'METHLYATION_CNMF'

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

Table S1. Gene #3: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
AMP PEAK 3(1Q21.3) MUTATED	34	7	6
AMP PEAK 3(1Q21.3) WILD-TYPE	36	35	27

Figure S1. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S2. Gene #3: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
AMP PEAK 3(1Q21.3) MUTATED	35	13	10
AMP PEAK 3(1Q21.3) WILD-TYPE	34	54	27

Figure S2. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_2q36.2' versus 'CN_CNMF'

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

Table S3. Gene #4: 'amp_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 4(2Q36.2) MUTATED	3	19	4
AMP PEAK 4(2Q36.2) WILD-TYPE	82	56	20

Figure S3. Get High-res Image Gene #4: 'amp_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

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

Table S4. Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 6(3Q26.2) MUTATED	4	18	10
AMP PEAK 6(3Q26.2) WILD-TYPE	81	57	14

Figure S4. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S5. Gene #9: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 9(7Q22.1) MUTATED	12	28	16
AMP PEAK 9(7Q22.1) WILD-TYPE	73	47	8

Figure S5. Get High-res Image Gene #9: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S6. Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 12(8Q24.21) MUTATED	14	41	19
AMP PEAK 12(8Q24.21) WILD-TYPE	71	34	5

Figure S6. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

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

Table S7. Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
AMP PEAK 12(8Q24.21) MUTATED	41	9	5
AMP PEAK 12(8Q24.21) WILD-TYPE	29	33	28

Figure S7. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S8. Gene #14: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 14(12P13.33) MUTATED	2	15	22
AMP PEAK 14(12P13.33) WILD-TYPE	83	60	2

Figure S8. Get High-res Image Gene #14: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.18

Table S9. Gene #14: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
AMP PEAK 14(12P13.33) MUTATED	21	7	0
AMP PEAK 14(12P13.33) WILD-TYPE	49	35	33

Figure S9. Get High-res Image Gene #14: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S10. Gene #15: 'amp_12p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 15(12P11.21) MUTATED	2	21	20
AMP PEAK 15(12P11.21) WILD-TYPE	83	54	4

Figure S10. Get High-res Image Gene #15: 'amp_12p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p11.21' versus 'METHLYATION_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.23

Table S11. Gene #15: 'amp_12p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
AMP PEAK 15(12P11.21) MUTATED	24	6	1
AMP PEAK 15(12P11.21) WILD-TYPE	46	36	32

Figure S11. Get High-res Image Gene #15: 'amp_12p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S12. Gene #16: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 16(12Q15) MUTATED	2	10	17
AMP PEAK 16(12Q15) WILD-TYPE	83	65	7

Figure S12. Get High-res Image Gene #16: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S13. Gene #19: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 19(17Q12) MUTATED	4	20	7
AMP PEAK 19(17Q12) WILD-TYPE	81	55	17

Figure S13. Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S14. Gene #20: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 20(18Q11.2) MUTATED	10	36	10
AMP PEAK 20(18Q11.2) WILD-TYPE	75	39	14

Figure S14. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

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

Table S15. Gene #20: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
AMP PEAK 20(18Q11.2) MUTATED	31	6	3
AMP PEAK 20(18Q11.2) WILD-TYPE	39	36	30

Figure S15. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S16. Gene #20: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
AMP PEAK 20(18Q11.2) MUTATED	36	14	3
AMP PEAK 20(18Q11.2) WILD-TYPE	50	33	37

Figure S16. Get High-res Image Gene #20: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S17. Gene #22: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 22(19Q13.2) MUTATED	8	28	11
AMP PEAK 22(19Q13.2) WILD-TYPE	77	47	13

Figure S17. Get High-res Image Gene #22: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S18. Gene #23: 'amp_20p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 23(20P11.23) MUTATED	7	15	16
AMP PEAK 23(20P11.23) WILD-TYPE	78	60	8

Figure S18. Get High-res Image Gene #23: 'amp_20p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq27.1' versus 'CN_CNMF'

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

Table S19. Gene #25: 'amp_xq27.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
AMP PEAK 25(XQ27.1) MUTATED	2	9	10
AMP PEAK 25(XQ27.1) WILD-TYPE	83	66	14

Figure S19. Get High-res Image Gene #25: 'amp_xq27.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S20. Gene #26: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 1(1P36.32) MUTATED	12	26	14
DEL PEAK 1(1P36.32) WILD-TYPE	73	49	10

Figure S20. Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S21. Gene #27: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 2(1P36.11) MUTATED	16	36	16
DEL PEAK 2(1P36.11) WILD-TYPE	69	39	8

Figure S21. Get High-res Image Gene #27: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S22. Gene #27: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
DEL PEAK 2(1P36.11) MUTATED	38	13	2
DEL PEAK 2(1P36.11) WILD-TYPE	32	29	31

Figure S22. Get High-res Image Gene #27: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q14.3' versus 'CN_CNMF'

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

Table S23. Gene #28: 'del_2q14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 3(2Q14.3) MUTATED	0	3	6
DEL PEAK 3(2Q14.3) WILD-TYPE	85	72	18

Figure S23. Get High-res Image Gene #28: 'del_2q14.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.31' versus 'CN_CNMF'

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

Table S24. Gene #29: 'del_3p21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 4(3P21.31) MUTATED	11	26	14
DEL PEAK 4(3P21.31) WILD-TYPE	74	49	10

Figure S24. Get High-res Image Gene #29: 'del_3p21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S25. Gene #33: 'del_5q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 8(5Q14.2) MUTATED	4	24	7
DEL PEAK 8(5Q14.2) WILD-TYPE	81	51	17

Figure S25. Get High-res Image Gene #33: 'del_5q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S26. Gene #34: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 9(6P25.2) MUTATED	15	45	14
DEL PEAK 9(6P25.2) WILD-TYPE	70	30	10

Figure S26. Get High-res Image Gene #34: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S27. Gene #34: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
DEL PEAK 9(6P25.2) MUTATED	44	8	6
DEL PEAK 9(6P25.2) WILD-TYPE	26	34	27

Figure S27. Get High-res Image Gene #34: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S28. Gene #34: 'del_6p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 9(6P25.2) MUTATED	53	10	7
DEL PEAK 9(6P25.2) WILD-TYPE	49	32	26

Figure S28. Get High-res Image Gene #34: 'del_6p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.083

Table S29. Gene #34: 'del_6p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 9(6P25.2) MUTATED	46	18	6
DEL PEAK 9(6P25.2) WILD-TYPE	40	29	34

Figure S29. Get High-res Image Gene #34: 'del_6p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S30. Gene #35: 'del_6p22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 10(6P22.2) MUTATED	16	41	13
DEL PEAK 10(6P22.2) WILD-TYPE	69	34	11

Figure S30. Get High-res Image Gene #35: 'del_6p22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S31. Gene #35: 'del_6p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
DEL PEAK 10(6P22.2) MUTATED	41	8	6
DEL PEAK 10(6P22.2) WILD-TYPE	29	34	27

Figure S31. Get High-res Image Gene #35: 'del_6p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.13

Table S32. Gene #35: 'del_6p22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 10(6P22.2) MUTATED	45	15	6
DEL PEAK 10(6P22.2) WILD-TYPE	41	32	34

Figure S32. Get High-res Image Gene #35: 'del_6p22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S33. Gene #36: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 11(6Q25.3) MUTATED	21	54	16
DEL PEAK 11(6Q25.3) WILD-TYPE	64	21	8

Figure S33. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q25.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S34. Gene #36: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
DEL PEAK 11(6Q25.3) MUTATED	50	11	11
DEL PEAK 11(6Q25.3) WILD-TYPE	20	31	22

Figure S34. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q25.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S35. Gene #36: 'del_6q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 11(6Q25.3) MUTATED	63	12	11
DEL PEAK 11(6Q25.3) WILD-TYPE	39	30	22

Figure S35. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q25.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S36. Gene #36: 'del_6q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 11(6Q25.3) MUTATED	47	17	21
DEL PEAK 11(6Q25.3) WILD-TYPE	22	50	16

Figure S36. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S37. Gene #36: 'del_6q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 11(6Q25.3) MUTATED	54	22	9
DEL PEAK 11(6Q25.3) WILD-TYPE	32	25	31

Figure S37. Get High-res Image Gene #36: 'del_6q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

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

Table S38. Gene #38: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 13(8P23.2) MUTATED	14	33	11
DEL PEAK 13(8P23.2) WILD-TYPE	71	42	13

Figure S38. Get High-res Image Gene #38: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S39. Gene #39: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 14(9P21.3) MUTATED	31	69	16
DEL PEAK 14(9P21.3) WILD-TYPE	54	6	8

Figure S39. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S40. Gene #39: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
DEL PEAK 14(9P21.3) MUTATED	60	13	15
DEL PEAK 14(9P21.3) WILD-TYPE	10	29	18

Figure S40. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S41. Gene #39: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 14(9P21.3) MUTATED	68	26	15
DEL PEAK 14(9P21.3) WILD-TYPE	15	22	31

Figure S41. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S42. Gene #39: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 14(9P21.3) MUTATED	44	57	8
DEL PEAK 14(9P21.3) WILD-TYPE	30	18	20

Figure S42. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S43. Gene #39: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 14(9P21.3) MUTATED	60	20	18	11
DEL PEAK 14(9P21.3) WILD-TYPE	9	20	17	22

Figure S43. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S44. Gene #39: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 14(9P21.3) MUTATED	80	17	12
DEL PEAK 14(9P21.3) WILD-TYPE	22	25	21

Figure S44. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S45. Gene #39: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 14(9P21.3) MUTATED	60	26	22
DEL PEAK 14(9P21.3) WILD-TYPE	9	41	15

Figure S45. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S46. Gene #39: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 14(9P21.3) MUTATED	68	28	12
DEL PEAK 14(9P21.3) WILD-TYPE	18	19	28

Figure S46. Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.33' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.22

Table S47. Gene #42: 'del_10q23.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 17(10Q23.33) MUTATED	7	18	10
DEL PEAK 17(10Q23.33) WILD-TYPE	78	57	14

Figure S47. Get High-res Image Gene #42: 'del_10q23.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'CN_CNMF'

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

Table S48. Gene #44: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 19(12P13.1) MUTATED	4	23	2
DEL PEAK 19(12P13.1) WILD-TYPE	81	52	22

Figure S48. Get High-res Image Gene #44: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

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

Table S49. Gene #44: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
DEL PEAK 19(12P13.1) MUTATED	21	0	2
DEL PEAK 19(12P13.1) WILD-TYPE	49	42	31

Figure S49. Get High-res Image Gene #44: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S50. Gene #44: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 19(12P13.1) MUTATED	25	0	2
DEL PEAK 19(12P13.1) WILD-TYPE	77	42	31

Figure S50. Get High-res Image Gene #44: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S51. Gene #45: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 20(12Q12) MUTATED	1	23	1
DEL PEAK 20(12Q12) WILD-TYPE	84	52	23

Figure S51. Get High-res Image Gene #45: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S52. Gene #46: 'del_12q21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 21(12Q21.33) MUTATED	6	33	5
DEL PEAK 21(12Q21.33) WILD-TYPE	79	42	19

Figure S52. Get High-res Image Gene #46: 'del_12q21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'CN_CNMF'

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

Table S53. Gene #47: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 22(12Q24.33) MUTATED	7	30	6
DEL PEAK 22(12Q24.33) WILD-TYPE	78	45	18

Figure S53. Get High-res Image Gene #47: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.05

Table S54. Gene #47: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 22(12Q24.33) MUTATED	29	10	1
DEL PEAK 22(12Q24.33) WILD-TYPE	57	37	39

Figure S54. Get High-res Image Gene #47: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S55. Gene #50: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 25(15Q15.1) MUTATED	3	21	12
DEL PEAK 25(15Q15.1) WILD-TYPE	82	54	12

Figure S55. Get High-res Image Gene #50: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S56. Gene #52: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 27(17P12) MUTATED	12	66	11
DEL PEAK 27(17P12) WILD-TYPE	73	9	13

Figure S56. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S57. Gene #52: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
DEL PEAK 27(17P12) MUTATED	52	6	10
DEL PEAK 27(17P12) WILD-TYPE	18	36	23

Figure S57. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S58. Gene #52: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 27(17P12) MUTATED	54	24	8
DEL PEAK 27(17P12) WILD-TYPE	29	24	38

Figure S58. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S59. Gene #52: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 27(17P12) MUTATED	40	43	3
DEL PEAK 27(17P12) WILD-TYPE	34	32	25

Figure S59. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S60. Gene #52: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 27(17P12) MUTATED	50	18	11	7
DEL PEAK 27(17P12) WILD-TYPE	19	22	24	26

Figure S60. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S61. Gene #52: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 27(17P12) MUTATED	63	16	7
DEL PEAK 27(17P12) WILD-TYPE	39	26	26

Figure S61. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

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

Table S62. Gene #52: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 27(17P12) MUTATED	50	17	18
DEL PEAK 27(17P12) WILD-TYPE	19	50	19

Figure S62. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S63. Gene #52: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 27(17P12) MUTATED	54	24	7
DEL PEAK 27(17P12) WILD-TYPE	32	23	33

Figure S63. Get High-res Image Gene #52: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S64. Gene #53: 'del_17q22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 28(17Q22) MUTATED	4	40	5
DEL PEAK 28(17Q22) WILD-TYPE	81	35	19

Figure S64. Get High-res Image Gene #53: 'del_17q22' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S65. Gene #53: 'del_17q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
DEL PEAK 28(17Q22) MUTATED	33	3	4
DEL PEAK 28(17Q22) WILD-TYPE	37	39	29

Figure S65. Get High-res Image Gene #53: 'del_17q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q22' versus 'RPPA_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.25

Table S66. Gene #53: 'del_17q22' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	21	17	21	13
DEL PEAK 28(17Q22) MUTATED	18	5	2	1	5
DEL PEAK 28(17Q22) WILD-TYPE	15	16	15	20	8

Figure S66. Get High-res Image Gene #53: 'del_17q22' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_17q22' versus 'RPPA_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.24

Table S67. Gene #53: 'del_17q22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	21	30	16	18
DEL PEAK 28(17Q22) MUTATED	11	6	12	2	0
DEL PEAK 28(17Q22) WILD-TYPE	9	15	18	14	18

Figure S67. Get High-res Image Gene #53: 'del_17q22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17q22' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S68. Gene #53: 'del_17q22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 28(17Q22) MUTATED	31	7	8
DEL PEAK 28(17Q22) WILD-TYPE	38	60	29

Figure S68. Get High-res Image Gene #53: 'del_17q22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S69. Gene #55: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 30(18Q21.2) MUTATED	41	70	15
DEL PEAK 30(18Q21.2) WILD-TYPE	44	5	9

Figure S69. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S70. Gene #55: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
DEL PEAK 30(18Q21.2) MUTATED	60	17	20
DEL PEAK 30(18Q21.2) WILD-TYPE	10	25	13

Figure S70. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

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

Table S71. Gene #55: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	48	46
DEL PEAK 30(18Q21.2) MUTATED	67	34	19
DEL PEAK 30(18Q21.2) WILD-TYPE	16	14	27

Figure S71. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S72. Gene #55: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	75	28
DEL PEAK 30(18Q21.2) MUTATED	51	60	9
DEL PEAK 30(18Q21.2) WILD-TYPE	23	15	19

Figure S72. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.094

Table S73. Gene #55: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	40	35	33
DEL PEAK 30(18Q21.2) MUTATED	59	26	19	16
DEL PEAK 30(18Q21.2) WILD-TYPE	10	14	16	17

Figure S73. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S74. Gene #55: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 30(18Q21.2) MUTATED	82	25	13
DEL PEAK 30(18Q21.2) WILD-TYPE	20	17	20

Figure S74. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S75. Gene #55: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	47	40
DEL PEAK 30(18Q21.2) MUTATED	69	37	11
DEL PEAK 30(18Q21.2) WILD-TYPE	17	10	29

Figure S75. Get High-res Image Gene #55: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S76. Gene #56: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 31(19P13.3) MUTATED	4	25	7
DEL PEAK 31(19P13.3) WILD-TYPE	81	50	17

Figure S76. Get High-res Image Gene #56: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S77. Gene #56: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
DEL PEAK 31(19P13.3) MUTATED	23	0	2
DEL PEAK 31(19P13.3) WILD-TYPE	47	42	31

Figure S77. Get High-res Image Gene #56: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S78. Gene #56: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 31(19P13.3) MUTATED	25	4	6
DEL PEAK 31(19P13.3) WILD-TYPE	44	63	31

Figure S78. Get High-res Image Gene #56: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.2' versus 'CN_CNMF'

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

Table S79. Gene #57: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 32(19P13.2) MUTATED	2	19	7
DEL PEAK 32(19P13.2) WILD-TYPE	83	56	17

Figure S79. Get High-res Image Gene #57: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S80. Gene #57: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
DEL PEAK 32(19P13.2) MUTATED	19	0	1
DEL PEAK 32(19P13.2) WILD-TYPE	51	42	32

Figure S80. Get High-res Image Gene #57: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.17

Table S81. Gene #57: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	42	33
DEL PEAK 32(19P13.2) MUTATED	24	3	0
DEL PEAK 32(19P13.2) WILD-TYPE	78	39	33

Figure S81. Get High-res Image Gene #57: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S82. Gene #57: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 32(19P13.2) MUTATED	21	1	4
DEL PEAK 32(19P13.2) WILD-TYPE	48	66	33

Figure S82. Get High-res Image Gene #57: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S83. Gene #59: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 34(21Q11.2) MUTATED	12	40	10
DEL PEAK 34(21Q11.2) WILD-TYPE	73	35	14

Figure S83. Get High-res Image Gene #59: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

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

Table S84. Gene #59: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
DEL PEAK 34(21Q11.2) MUTATED	35	8	6
DEL PEAK 34(21Q11.2) WILD-TYPE	35	34	27

Figure S84. Get High-res Image Gene #59: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.2

Table S85. Gene #59: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 34(21Q11.2) MUTATED	33	11	12
DEL PEAK 34(21Q11.2) WILD-TYPE	36	56	25

Figure S85. Get High-res Image Gene #59: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S86. Gene #60: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 35(22Q13.31) MUTATED	8	40	12
DEL PEAK 35(22Q13.31) WILD-TYPE	77	35	12

Figure S86. Get High-res Image Gene #60: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

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

Table S87. Gene #60: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	42	33
DEL PEAK 35(22Q13.31) MUTATED	34	7	6
DEL PEAK 35(22Q13.31) WILD-TYPE	36	35	27

Figure S87. Get High-res Image Gene #60: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.05

Table S88. Gene #60: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	67	37
DEL PEAK 35(22Q13.31) MUTATED	29	9	18
DEL PEAK 35(22Q13.31) WILD-TYPE	40	58	19

Figure S88. Get High-res Image Gene #60: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S89. Gene #61: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 36(22Q13.32) MUTATED	9	40	13
DEL PEAK 36(22Q13.32) WILD-TYPE	76	35	11

Figure S89. Get High-res Image Gene #61: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'CN_CNMF'

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

Table S90. Gene #62: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 37(XP21.1) MUTATED	3	18	8
DEL PEAK 37(XP21.1) WILD-TYPE	82	57	16

Figure S90. Get High-res Image Gene #62: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0063

Table S91. Gene #63: 'del_xq11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	75	24
DEL PEAK 38(XQ11.2) MUTATED	0	16	7
DEL PEAK 38(XQ11.2) WILD-TYPE	85	59	17

Figure S91. Get High-res Image Gene #63: 'del_xq11.2' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = PAAD-TP.transferedmergedcluster.txt
Number of patients = 184
Number of significantly focal cnvs = 63
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

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

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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