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

Sarcoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

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/C13777HP

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 61 focal events and 8 molecular subtypes across 169 patients, 94 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_1q24.3 cnv correlated to 'CN_CNMF'.
amp_5p15.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_6q24.3 cnv correlated to 'CN_CNMF', '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' and 'METHLYATION_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_20q13.33 cnv correlated to 'CN_CNMF'.
amp_21q21.1 cnv correlated to 'CN_CNMF'.
amp_xp21.2 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' and 'METHLYATION_CNMF'.
del_2p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_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', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3q29 cnv correlated to 'METHLYATION_CNMF'.
del_4q35.1 cnv correlated to 'CN_CNMF'.
del_6q14.1 cnv correlated to 'CN_CNMF'.
del_7q36.3 cnv correlated to 'CN_CNMF'.
del_8p23.3 cnv correlated to 'METHLYATION_CNMF'.
del_9q34.3 cnv correlated to 'CN_CNMF'.
del_10p15.3 cnv correlated to 'METHLYATION_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF'.
del_11q24.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_12p13.1 cnv correlated to 'METHLYATION_CNMF'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_14q24.1 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_15q11.2 cnv correlated to 'MRNASEQ_CNMF'.
del_16q12.1 cnv correlated to 'CN_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF'.
del_17p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_17q25.3 cnv correlated to 'CN_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_19q13.43 cnv correlated to 'CN_CNMF'.
del_22q13.31 cnv correlated to 'CN_CNMF'.
del_xq27.1 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 61 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, 94 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 6q24 3	53 (31%)	116	0.00011 (0.0464)	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)	6e-05 (0.0259)	1e-05 (0.00488)	1e-05 (0.00488)	0.00021 (0.0865)
amp 12q15	64 (38%)	105	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)
del 10q23 31	95 (56%)	74	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)	0.00026 (0.106)	5e-05 (0.0217)	2e-05 (0.00894)	0.00051 (0.203)
del 1p36 32	51 (30%)	118	0.00844 (1.00)	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)	1e-05 (0.00488)
del 17p13 1	82 (49%)	87	3e-05 (0.0132)	0.0001 (0.0424)	0.00013 (0.0546)	0.00057 (0.226)	0.0161 (1.00)	0.00268 (0.93)	0.00338 (1.00)	0.00021 (0.0865)
amp 1p32 1	62 (37%)	107	1e-05 (0.00488)	1e-05 (0.00488)	6e-05 (0.0259)	3e-05 (0.0132)	0.00544 (1.00)	0.00338 (1.00)	0.0156 (1.00)	0.00358 (1.00)
amp 6p21 1	40 (24%)	129	3e-05 (0.0132)	1e-05 (0.00488)	0.00061 (0.242)	0.00081 (0.312)	0.00316 (1.00)	0.00013 (0.0546)	0.00091 (0.344)	0.00099 (0.373)
del 2p25 3	56 (33%)	113	0.00017 (0.0707)	0.00018 (0.0745)	3e-05 (0.0132)	0.0003 (0.121)	0.00409 (1.00)	0.00086 (0.328)	0.0057 (1.00)	0.00088 (0.334)
del 13q14 2	121 (72%)	48	1e-05 (0.00488)	1e-05 (0.00488)	0.0001 (0.0424)	1e-05 (0.00488)	0.00264 (0.921)	0.0019 (0.684)	0.0022 (0.779)	0.00481 (1.00)
del 3p21 31	37 (22%)	132	0.03 (1.00)	1e-05 (0.00488)	0.00013 (0.0546)	0.00303 (1.00)	0.00671 (1.00)	0.00017 (0.0707)	0.0231 (1.00)	0.00623 (1.00)
del 17q11 2	51 (30%)	118	2e-05 (0.00894)	1e-05 (0.00488)	0.00064 (0.252)	0.00328 (1.00)	0.00107 (0.401)	0.00114 (0.426)	0.00044 (0.176)	0.00104 (0.391)
amp 5p15 2	73 (43%)	96	9e-05 (0.0382)	0.0066 (1.00)	0.0148 (1.00)	0.00026 (0.106)	0.868 (1.00)	0.0536 (1.00)	0.713 (1.00)	0.808 (1.00)
amp 17p11 2	69 (41%)	100	1e-05 (0.00488)	7e-05 (0.03)	0.155 (1.00)	0.0112 (1.00)	0.516 (1.00)	0.117 (1.00)	0.305 (1.00)	0.659 (1.00)
del 1q44	53 (31%)	116	1e-05 (0.00488)	7e-05 (0.03)	0.03 (1.00)	0.0342 (1.00)	0.0685 (1.00)	0.0231 (1.00)	0.0771 (1.00)	0.134 (1.00)
del 11q24 3	75 (44%)	94	1e-05 (0.00488)	2e-05 (0.00894)	0.0226 (1.00)	0.0139 (1.00)	0.00761 (1.00)	0.0081 (1.00)	0.00196 (0.704)	0.0568 (1.00)
del 19p13 3	50 (30%)	119	2e-05 (0.00894)	0.00012 (0.0505)	0.0054 (1.00)	0.019 (1.00)	0.0107 (1.00)	0.00186 (0.671)	0.00207 (0.737)	0.00082 (0.314)
amp 1q24 3	71 (42%)	98	2e-05 (0.00894)	0.0017 (0.619)	0.108 (1.00)	0.0197 (1.00)	0.312 (1.00)	0.199 (1.00)	0.224 (1.00)	0.273 (1.00)
amp 17q24 3	48 (28%)	121	0.00907 (1.00)	0.00014 (0.0584)	0.00508 (1.00)	0.00422 (1.00)	0.0557 (1.00)	0.029 (1.00)	0.101 (1.00)	0.0142 (1.00)
amp 19p13 2	68 (40%)	101	2e-05 (0.00894)	0.0459 (1.00)	0.105 (1.00)	0.047 (1.00)	0.819 (1.00)	0.48 (1.00)	0.758 (1.00)	0.785 (1.00)
amp 19q12	61 (36%)	108	1e-05 (0.00488)	0.00083 (0.317)	0.0157 (1.00)	0.0142 (1.00)	0.588 (1.00)	0.00153 (0.56)	0.382 (1.00)	0.4 (1.00)
amp 20q13 33	68 (40%)	101	8e-05 (0.0341)	0.00337 (1.00)	0.00174 (0.632)	0.0108 (1.00)	0.0256 (1.00)	0.00286 (0.99)	0.0159 (1.00)	0.0314 (1.00)
amp 21q21 1	51 (30%)	118	0.0002 (0.0826)	0.00115 (0.429)	0.134 (1.00)	0.14 (1.00)	0.224 (1.00)	0.0109 (1.00)	0.104 (1.00)	0.177 (1.00)
amp xp21 2	60 (36%)	109	1e-05 (0.00488)	0.00066 (0.259)	0.0412 (1.00)	0.137 (1.00)	0.814 (1.00)	0.0246 (1.00)	0.501 (1.00)	0.774 (1.00)
del 2q37 3	68 (40%)	101	1e-05 (0.00488)	0.0217 (1.00)	0.107 (1.00)	0.0397 (1.00)	0.386 (1.00)	0.4 (1.00)	0.573 (1.00)	0.578 (1.00)
del 2q37 3	70 (41%)	99	1e-05 (0.00488)	0.00731 (1.00)	0.326 (1.00)	0.0131 (1.00)	0.805 (1.00)	0.417 (1.00)	0.956 (1.00)	0.841 (1.00)
del 3q29	39 (23%)	130	0.0442 (1.00)	0.00034 (0.137)	0.207 (1.00)	0.55 (1.00)	0.434 (1.00)	0.0542 (1.00)	0.241 (1.00)	0.0755 (1.00)
del 4q35 1	63 (37%)	106	2e-05 (0.00894)	0.0255 (1.00)	0.564 (1.00)	0.615 (1.00)	0.474 (1.00)	0.459 (1.00)	0.205 (1.00)	0.977 (1.00)
del 6q14 1	49 (29%)	120	0.00028 (0.114)	0.0112 (1.00)	0.308 (1.00)	0.452 (1.00)	0.946 (1.00)	0.705 (1.00)	0.848 (1.00)	0.123 (1.00)
del 7q36 3	44 (26%)	125	6e-05 (0.0259)	0.077 (1.00)	0.132 (1.00)	0.448 (1.00)	0.284 (1.00)	0.308 (1.00)	0.331 (1.00)	0.461 (1.00)
del 8p23 3	52 (31%)	117	0.0482 (1.00)	1e-05 (0.00488)	0.00723 (1.00)	0.00948 (1.00)	0.0007 (0.274)	0.0196 (1.00)	0.00432 (1.00)	0.0121 (1.00)
del 9q34 3	46 (27%)	123	0.00043 (0.172)	0.13 (1.00)	0.146 (1.00)	0.199 (1.00)	0.153 (1.00)	0.0515 (1.00)	0.0808 (1.00)	0.0351 (1.00)
del 10p15 3	88 (52%)	81	0.00311 (1.00)	0.00036 (0.145)	0.59 (1.00)	0.0284 (1.00)	0.792 (1.00)	0.644 (1.00)	0.818 (1.00)	0.74 (1.00)
del 11p15 5	73 (43%)	96	5e-05 (0.0217)	0.0008 (0.309)	0.927 (1.00)	0.496 (1.00)	0.522 (1.00)	0.925 (1.00)	0.553 (1.00)	0.879 (1.00)
del 12p13 1	57 (34%)	112	0.00131 (0.485)	0.00045 (0.18)	0.0203 (1.00)	0.178 (1.00)	0.0749 (1.00)	0.0821 (1.00)	0.14 (1.00)	0.108 (1.00)
del 14q24 1	56 (33%)	113	0.526 (1.00)	0.0275 (1.00)	0.75 (1.00)	0.00022 (0.0902)	0.165 (1.00)	0.0315 (1.00)	0.0501 (1.00)	0.0799 (1.00)
del 15q11 2	32 (19%)	137	0.19 (1.00)	0.0384 (1.00)	0.00022 (0.0902)	0.00517 (1.00)	0.0122 (1.00)	0.0272 (1.00)	0.0201 (1.00)	0.0415 (1.00)
del 16q12 1	95 (56%)	74	1e-05 (0.00488)	0.00076 (0.295)	0.0243 (1.00)	0.02 (1.00)	0.123 (1.00)	0.0692 (1.00)	0.0234 (1.00)	0.101 (1.00)
del 16q23 1	94 (56%)	75	4e-05 (0.0174)	0.00069 (0.27)	0.00834 (1.00)	0.00681 (1.00)	0.0222 (1.00)	0.0329 (1.00)	0.00304 (1.00)	0.0103 (1.00)
del 17q25 3	45 (27%)	124	0.00062 (0.245)	0.00325 (1.00)	0.0552 (1.00)	0.0627 (1.00)	0.514 (1.00)	0.166 (1.00)	0.473 (1.00)	0.385 (1.00)
del 19q13 43	73 (43%)	96	0.00042 (0.169)	0.0126 (1.00)	0.102 (1.00)	0.185 (1.00)	0.0714 (1.00)	0.0272 (1.00)	0.0669 (1.00)	0.161 (1.00)
del 22q13 31	54 (32%)	115	7e-05 (0.03)	0.027 (1.00)	0.891 (1.00)	0.111 (1.00)	0.441 (1.00)	0.428 (1.00)	0.675 (1.00)	0.206 (1.00)
del xq27 1	82 (49%)	87	3e-05 (0.0132)	0.00175 (0.633)	0.00072 (0.281)	0.00226 (0.798)	0.00262 (0.917)	0.00266 (0.926)	0.00212 (0.753)	0.0013 (0.482)
amp 3p11 2	40 (24%)	129	0.00967 (1.00)	0.0356 (1.00)	0.00642 (1.00)	0.00198 (0.709)	0.506 (1.00)	0.0437 (1.00)	0.274 (1.00)	0.285 (1.00)
amp 7q31 1	49 (29%)	120	0.00075 (0.292)	0.0153 (1.00)	0.0547 (1.00)	0.206 (1.00)	0.0384 (1.00)	0.00876 (1.00)	0.0196 (1.00)	0.00246 (0.866)
amp 8q21 12	61 (36%)	108	0.054 (1.00)	0.0364 (1.00)	0.236 (1.00)	0.609 (1.00)	1 (1.00)	0.0453 (1.00)	0.587 (1.00)	0.956 (1.00)
amp 11q22 2	26 (15%)	143	0.0549 (1.00)	0.0579 (1.00)	0.00579 (1.00)	0.14 (1.00)	0.136 (1.00)	0.0178 (1.00)	0.0857 (1.00)	0.115 (1.00)
amp 12p13 32	32 (19%)	137	0.0665 (1.00)	0.4 (1.00)	0.149 (1.00)	0.314 (1.00)	0.098 (1.00)	0.173 (1.00)	0.187 (1.00)	0.244 (1.00)
amp 12p12 1	42 (25%)	127	0.00137 (0.506)	0.0245 (1.00)	0.00947 (1.00)	0.0779 (1.00)	0.161 (1.00)	0.00727 (1.00)	0.144 (1.00)	0.0912 (1.00)
amp 13q34	31 (18%)	138	0.00149 (0.548)	0.00081 (0.312)	0.077 (1.00)	0.103 (1.00)	0.699 (1.00)	0.17 (1.00)	0.964 (1.00)	0.607 (1.00)
amp xq21 2	25 (15%)	144	0.00745 (1.00)	0.0796 (1.00)	0.6 (1.00)	0.237 (1.00)	0.425 (1.00)	0.255 (1.00)	0.559 (1.00)	0.508 (1.00)
del 1p32 3	26 (15%)	143	0.407 (1.00)	0.0959 (1.00)	0.989 (1.00)	0.118 (1.00)	0.617 (1.00)	0.286 (1.00)	0.555 (1.00)	0.62 (1.00)
del 6p25 1	61 (36%)	108	0.408 (1.00)	0.0422 (1.00)	0.0025 (0.877)	0.0128 (1.00)	0.0544 (1.00)	0.00297 (1.00)	0.0348 (1.00)	0.0202 (1.00)
del 6q16 1	48 (28%)	121	0.00442 (1.00)	0.211 (1.00)	0.241 (1.00)	0.792 (1.00)	0.865 (1.00)	0.524 (1.00)	0.476 (1.00)	0.0583 (1.00)
del 9p23	58 (34%)	111	0.00675 (1.00)	0.315 (1.00)	0.027 (1.00)	0.272 (1.00)	0.108 (1.00)	0.0297 (1.00)	0.0961 (1.00)	0.00583 (1.00)
del 9p21 3	72 (43%)	97	0.00129 (0.48)	0.0382 (1.00)	0.00151 (0.554)	0.0212 (1.00)	0.0293 (1.00)	0.00076 (0.295)	0.00206 (0.735)	0.00426 (1.00)
del 12q12	34 (20%)	135	0.0431 (1.00)	0.0327 (1.00)	0.83 (1.00)	0.202 (1.00)	0.171 (1.00)	0.664 (1.00)	0.597 (1.00)	0.506 (1.00)
del 18q23	57 (34%)	112	0.00952 (1.00)	0.0329 (1.00)	0.0178 (1.00)	0.0798 (1.00)	0.0352 (1.00)	0.0835 (1.00)	0.0291 (1.00)	0.269 (1.00)
del 21q11 2	31 (18%)	138	0.362 (1.00)	0.408 (1.00)	0.268 (1.00)	0.328 (1.00)	0.0151 (1.00)	0.327 (1.00)	0.102 (1.00)	0.139 (1.00)
del 21q22 3	44 (26%)	125	0.0698 (1.00)	0.0371 (1.00)	0.482 (1.00)	0.575 (1.00)	0.217 (1.00)	0.553 (1.00)	0.386 (1.00)	0.722 (1.00)
del xp22 33	54 (32%)	115	0.0181 (1.00)	0.00158 (0.577)	0.00971 (1.00)	0.185 (1.00)	0.119 (1.00)	0.148 (1.00)	0.175 (1.00)	0.138 (1.00)
del xq21 1	80 (47%)	89	0.035 (1.00)	0.00087 (0.331)	0.00391 (1.00)	0.00499 (1.00)	0.0137 (1.00)	0.00637 (1.00)	0.00452 (1.00)	0.0166 (1.00)

'amp_1p32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
AMP PEAK 1(1P32.1) MUTATED	17	37	8
AMP PEAK 1(1P32.1) WILD-TYPE	29	29	49

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 = 1e-05 (Fisher's exact test), Q value = 0.0049

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	42	21	16	28	4
AMP PEAK 1(1P32.1) MUTATED	10	10	10	3	2	24	3
AMP PEAK 1(1P32.1) WILD-TYPE	20	18	32	18	14	4	1

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

'amp_1p32.1' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S3. Gene #1: 'amp_1p32.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	45	24	58
AMP PEAK 1(1P32.1) MUTATED	27	15	6	13
AMP PEAK 1(1P32.1) WILD-TYPE	12	30	18	45

Figure S3. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_1p32.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S4. Gene #1: 'amp_1p32.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	32	33	37	19
AMP PEAK 1(1P32.1) MUTATED	17	6	25	9	4
AMP PEAK 1(1P32.1) WILD-TYPE	28	26	8	28	15

Figure S4. Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1q24.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S5. Gene #2: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
AMP PEAK 2(1Q24.3) MUTATED	22	39	10
AMP PEAK 2(1Q24.3) WILD-TYPE	24	27	47

Figure S5. Get High-res Image Gene #2: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.2' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.038

Table S6. Gene #4: 'amp_5p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
AMP PEAK 4(5P15.2) MUTATED	18	41	14
AMP PEAK 4(5P15.2) WILD-TYPE	28	25	43

Figure S6. Get High-res Image Gene #4: 'amp_5p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.11

Table S7. Gene #4: 'amp_5p15.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	32	33	37	19
AMP PEAK 4(5P15.2) MUTATED	27	8	19	17	2
AMP PEAK 4(5P15.2) WILD-TYPE	18	24	14	20	17

Figure S7. Get High-res Image Gene #4: 'amp_5p15.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

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

Table S8. Gene #5: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
AMP PEAK 5(6P21.1) MUTATED	11	26	3
AMP PEAK 5(6P21.1) WILD-TYPE	35	40	54

Figure S8. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S9. 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	42	21	16	28	4
AMP PEAK 5(6P21.1) MUTATED	13	5	2	5	0	12	3
AMP PEAK 5(6P21.1) WILD-TYPE	17	23	40	16	16	16	1

Figure S9. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.24

Table S10. Gene #5: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	45	24	58
AMP PEAK 5(6P21.1) MUTATED	13	16	7	4
AMP PEAK 5(6P21.1) WILD-TYPE	26	29	17	54

Figure S10. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.055

Table S11. Gene #5: 'amp_6p21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	14	29	12	60
AMP PEAK 5(6P21.1) MUTATED	19	4	10	3	3
AMP PEAK 5(6P21.1) WILD-TYPE	33	10	19	9	57

Figure S11. Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_6q24.3' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.046

Table S12. Gene #6: 'amp_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
AMP PEAK 6(6Q24.3) MUTATED	21	26	6
AMP PEAK 6(6Q24.3) WILD-TYPE	25	40	51

Figure S12. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S13. 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	42	21	16	28	4
AMP PEAK 6(6Q24.3) MUTATED	21	12	3	3	1	12	1
AMP PEAK 6(6Q24.3) WILD-TYPE	9	16	39	18	15	16	3

Figure S13. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S14. Gene #6: 'amp_6q24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	45	24	58
AMP PEAK 6(6Q24.3) MUTATED	15	28	5	4
AMP PEAK 6(6Q24.3) WILD-TYPE	24	17	19	54

Figure S14. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S15. Gene #6: 'amp_6q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	32	33	37	19
AMP PEAK 6(6Q24.3) MUTATED	27	9	12	2	2
AMP PEAK 6(6Q24.3) WILD-TYPE	18	23	21	35	17

Figure S15. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6q24.3' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S16. Gene #6: 'amp_6q24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	71	23
AMP PEAK 6(6Q24.3) MUTATED	32	10	11
AMP PEAK 6(6Q24.3) WILD-TYPE	41	61	12

Figure S16. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_6q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S17. Gene #6: 'amp_6q24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	14	29	12	60
AMP PEAK 6(6Q24.3) MUTATED	27	7	12	3	4
AMP PEAK 6(6Q24.3) WILD-TYPE	25	7	17	9	56

Figure S17. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_6q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S18. Gene #6: 'amp_6q24.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	71	27
AMP PEAK 6(6Q24.3) MUTATED	31	8	14
AMP PEAK 6(6Q24.3) WILD-TYPE	38	63	13

Figure S18. 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 = 0.00021 (Fisher's exact test), Q value = 0.087

Table S19. Gene #6: 'amp_6q24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	72	33
AMP PEAK 6(6Q24.3) MUTATED	28	11	14
AMP PEAK 6(6Q24.3) WILD-TYPE	34	61	19

Figure S19. Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S20. Gene #12: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
AMP PEAK 12(12Q15) MUTATED	41	18	5
AMP PEAK 12(12Q15) WILD-TYPE	5	48	52

Figure S20. Get High-res Image Gene #12: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S21. Gene #12: '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	42	21	16	28	4
AMP PEAK 12(12Q15) MUTATED	22	17	1	9	2	11	2
AMP PEAK 12(12Q15) WILD-TYPE	8	11	41	12	14	17	2

Figure S21. Get High-res Image Gene #12: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S22. Gene #12: 'amp_12q15' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	45	24	58
AMP PEAK 12(12Q15) MUTATED	17	32	12	2
AMP PEAK 12(12Q15) WILD-TYPE	22	13	12	56

Figure S22. Get High-res Image Gene #12: 'amp_12q15' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S23. Gene #12: 'amp_12q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	32	33	37	19
AMP PEAK 12(12Q15) MUTATED	30	17	14	1	1
AMP PEAK 12(12Q15) WILD-TYPE	15	15	19	36	18

Figure S23. Get High-res Image Gene #12: 'amp_12q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S24. Gene #12: 'amp_12q15' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	71	23
AMP PEAK 12(12Q15) MUTATED	41	9	12
AMP PEAK 12(12Q15) WILD-TYPE	32	62	11

Figure S24. Get High-res Image Gene #12: 'amp_12q15' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S25. Gene #12: 'amp_12q15' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	14	29	12	60
AMP PEAK 12(12Q15) MUTATED	36	8	14	3	1
AMP PEAK 12(12Q15) WILD-TYPE	16	6	15	9	59

Figure S25. Get High-res Image Gene #12: 'amp_12q15' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S26. Gene #12: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	71	27
AMP PEAK 12(12Q15) MUTATED	43	7	12
AMP PEAK 12(12Q15) WILD-TYPE	26	64	15

Figure S26. Get High-res Image Gene #12: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S27. Gene #12: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	72	33
AMP PEAK 12(12Q15) MUTATED	37	9	16
AMP PEAK 12(12Q15) WILD-TYPE	25	63	17

Figure S27. Get High-res Image Gene #12: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S28. Gene #14: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
AMP PEAK 14(17P11.2) MUTATED	9	46	14
AMP PEAK 14(17P11.2) WILD-TYPE	37	20	43

Figure S28. Get High-res Image Gene #14: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p11.2' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.03

Table S29. Gene #14: 'amp_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	30	28	42	21	16	28	4
AMP PEAK 14(17P11.2) MUTATED	14	6	21	6	1	20	1
AMP PEAK 14(17P11.2) WILD-TYPE	16	22	21	15	15	8	3

Figure S29. Get High-res Image Gene #14: 'amp_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q24.3' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.058

Table S30. Gene #15: '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	42	21	16	28	4
AMP PEAK 15(17Q24.3) MUTATED	11	6	4	8	2	13	4
AMP PEAK 15(17Q24.3) WILD-TYPE	19	22	38	13	14	15	0

Figure S30. Get High-res Image Gene #15: 'amp_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S31. Gene #16: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
AMP PEAK 16(19P13.2) MUTATED	17	40	11
AMP PEAK 16(19P13.2) WILD-TYPE	29	26	46

Figure S31. Get High-res Image Gene #16: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S32. Gene #17: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
AMP PEAK 17(19Q12) MUTATED	14	39	8
AMP PEAK 17(19Q12) WILD-TYPE	32	27	49

Figure S32. Get High-res Image Gene #17: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.034

Table S33. Gene #18: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
AMP PEAK 18(20Q13.33) MUTATED	19	38	11
AMP PEAK 18(20Q13.33) WILD-TYPE	27	28	46

Figure S33. Get High-res Image Gene #18: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_21q21.1' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.083

Table S34. Gene #19: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
AMP PEAK 19(21Q21.1) MUTATED	9	32	10
AMP PEAK 19(21Q21.1) WILD-TYPE	37	34	47

Figure S34. Get High-res Image Gene #19: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S35. Gene #20: 'amp_xp21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
AMP PEAK 20(XP21.2) MUTATED	11	39	10
AMP PEAK 20(XP21.2) WILD-TYPE	35	27	47

Figure S35. Get High-res Image Gene #20: 'amp_xp21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S36. Gene #22: '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	42	21	16	28	4
DEL PEAK 1(1P36.32) MUTATED	7	1	27	5	6	3	2
DEL PEAK 1(1P36.32) WILD-TYPE	23	27	15	16	10	25	2

Figure S36. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S37. Gene #22: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	45	24	58
DEL PEAK 1(1P36.32) MUTATED	5	7	4	34
DEL PEAK 1(1P36.32) WILD-TYPE	34	38	20	24

Figure S37. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S38. Gene #22: 'del_1p36.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	32	33	37	19
DEL PEAK 1(1P36.32) MUTATED	7	5	3	23	12
DEL PEAK 1(1P36.32) WILD-TYPE	38	27	30	14	7

Figure S38. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S39. Gene #22: 'del_1p36.32' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	71	23
DEL PEAK 1(1P36.32) MUTATED	10	37	4
DEL PEAK 1(1P36.32) WILD-TYPE	63	34	19

Figure S39. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S40. Gene #22: 'del_1p36.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	14	29	12	60
DEL PEAK 1(1P36.32) MUTATED	7	3	4	1	36
DEL PEAK 1(1P36.32) WILD-TYPE	45	11	25	11	24

Figure S40. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S41. Gene #22: 'del_1p36.32' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	71	27
DEL PEAK 1(1P36.32) MUTATED	9	38	4
DEL PEAK 1(1P36.32) WILD-TYPE	60	33	23

Figure S41. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S42. Gene #22: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	72	33
DEL PEAK 1(1P36.32) MUTATED	9	38	4
DEL PEAK 1(1P36.32) WILD-TYPE	53	34	29

Figure S42. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S43. Gene #24: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 3(1Q44) MUTATED	16	33	4
DEL PEAK 3(1Q44) WILD-TYPE	30	33	53

Figure S43. Get High-res Image Gene #24: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.03

Table S44. Gene #24: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	30	28	42	21	16	28	4
DEL PEAK 3(1Q44) MUTATED	18	5	8	3	2	15	2
DEL PEAK 3(1Q44) WILD-TYPE	12	23	34	18	14	13	2

Figure S44. Get High-res Image Gene #24: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p25.3' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.071

Table S45. Gene #25: 'del_2p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 4(2P25.3) MUTATED	8	34	14
DEL PEAK 4(2P25.3) WILD-TYPE	38	32	43

Figure S45. Get High-res Image Gene #25: 'del_2p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p25.3' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.075

Table S46. Gene #25: '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	42	21	16	28	4
DEL PEAK 4(2P25.3) MUTATED	12	3	23	2	5	8	3
DEL PEAK 4(2P25.3) WILD-TYPE	18	25	19	19	11	20	1

Figure S46. Get High-res Image Gene #25: 'del_2p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p25.3' versus 'MRNASEQ_CNMF'

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

Table S47. Gene #25: 'del_2p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	45	24	58
DEL PEAK 4(2P25.3) MUTATED	10	12	1	31
DEL PEAK 4(2P25.3) WILD-TYPE	29	33	23	27

Figure S47. Get High-res Image Gene #25: 'del_2p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.12

Table S48. Gene #25: 'del_2p25.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	32	33	37	19
DEL PEAK 4(2P25.3) MUTATED	13	3	8	20	10
DEL PEAK 4(2P25.3) WILD-TYPE	32	29	25	17	9

Figure S48. Get High-res Image Gene #25: 'del_2p25.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S49. Gene #26: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 5(2Q37.3) MUTATED	13	46	9
DEL PEAK 5(2Q37.3) WILD-TYPE	33	20	48

Figure S49. Get High-res Image Gene #26: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S50. Gene #27: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 6(2Q37.3) MUTATED	14	47	9
DEL PEAK 6(2Q37.3) WILD-TYPE	32	19	48

Figure S50. Get High-res Image Gene #27: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S51. Gene #28: '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	42	21	16	28	4
DEL PEAK 7(3P21.31) MUTATED	16	3	1	7	2	8	0
DEL PEAK 7(3P21.31) WILD-TYPE	14	25	41	14	14	20	4

Figure S51. Get High-res Image Gene #28: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.055

Table S52. Gene #28: 'del_3p21.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	45	24	58
DEL PEAK 7(3P21.31) MUTATED	9	16	9	3
DEL PEAK 7(3P21.31) WILD-TYPE	30	29	15	55

Figure S52. Get High-res Image Gene #28: 'del_3p21.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.071

Table S53. Gene #28: 'del_3p21.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	14	29	12	60
DEL PEAK 7(3P21.31) MUTATED	19	6	4	4	4
DEL PEAK 7(3P21.31) WILD-TYPE	33	8	25	8	56

Figure S53. Get High-res Image Gene #28: 'del_3p21.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.14

Table S54. Gene #29: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	30	28	42	21	16	28	4
DEL PEAK 8(3Q29) MUTATED	13	2	7	5	0	9	3
DEL PEAK 8(3Q29) WILD-TYPE	17	26	35	16	16	19	1

Figure S54. Get High-res Image Gene #29: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S55. Gene #30: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 9(4Q35.1) MUTATED	15	39	9
DEL PEAK 9(4Q35.1) WILD-TYPE	31	27	48

Figure S55. Get High-res Image Gene #30: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.1' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.11

Table S56. Gene #32: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 11(6Q14.1) MUTATED	8	31	10
DEL PEAK 11(6Q14.1) WILD-TYPE	38	35	47

Figure S56. Get High-res Image Gene #32: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S57. Gene #34: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 13(7Q36.3) MUTATED	14	26	4
DEL PEAK 13(7Q36.3) WILD-TYPE	32	40	53

Figure S57. Get High-res Image Gene #34: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S58. Gene #35: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	30	28	42	21	16	28	4
DEL PEAK 14(8P23.3) MUTATED	14	5	4	9	2	15	3
DEL PEAK 14(8P23.3) WILD-TYPE	16	23	38	12	14	13	1

Figure S58. Get High-res Image Gene #35: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q34.3' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.17

Table S59. Gene #38: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 17(9Q34.3) MUTATED	7	29	10
DEL PEAK 17(9Q34.3) WILD-TYPE	39	37	47

Figure S59. Get High-res Image Gene #38: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.15

Table S60. Gene #39: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	30	28	42	21	16	28	4
DEL PEAK 18(10P15.3) MUTATED	20	6	28	10	4	18	2
DEL PEAK 18(10P15.3) WILD-TYPE	10	22	14	11	12	10	2

Figure S60. Get High-res Image Gene #39: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S61. Gene #40: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 19(10Q23.31) MUTATED	8	54	33
DEL PEAK 19(10Q23.31) WILD-TYPE	38	12	24

Figure S61. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S62. Gene #40: '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	42	21	16	28	4
DEL PEAK 19(10Q23.31) MUTATED	17	4	39	5	6	21	3
DEL PEAK 19(10Q23.31) WILD-TYPE	13	24	3	16	10	7	1

Figure S62. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S63. Gene #40: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	45	24	58
DEL PEAK 19(10Q23.31) MUTATED	24	15	6	48
DEL PEAK 19(10Q23.31) WILD-TYPE	15	30	18	10

Figure S63. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S64. Gene #40: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	32	33	37	19
DEL PEAK 19(10Q23.31) MUTATED	18	8	20	36	11
DEL PEAK 19(10Q23.31) WILD-TYPE	27	24	13	1	8

Figure S64. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.11

Table S65. Gene #40: 'del_10q23.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	71	23
DEL PEAK 19(10Q23.31) MUTATED	29	52	13
DEL PEAK 19(10Q23.31) WILD-TYPE	44	19	10

Figure S65. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.022

Table S66. Gene #40: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	14	29	12	60
DEL PEAK 19(10Q23.31) MUTATED	24	6	14	2	48
DEL PEAK 19(10Q23.31) WILD-TYPE	28	8	15	10	12

Figure S66. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S67. Gene #40: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	71	27
DEL PEAK 19(10Q23.31) MUTATED	26	54	14
DEL PEAK 19(10Q23.31) WILD-TYPE	43	17	13

Figure S67. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S68. Gene #40: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	72	33
DEL PEAK 19(10Q23.31) MUTATED	24	52	18
DEL PEAK 19(10Q23.31) WILD-TYPE	38	20	15

Figure S68. Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.022

Table S69. Gene #41: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 20(11P15.5) MUTATED	21	40	12
DEL PEAK 20(11P15.5) WILD-TYPE	25	26	45

Figure S69. Get High-res Image Gene #41: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S70. Gene #42: 'del_11q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 21(11Q24.3) MUTATED	27	41	7
DEL PEAK 21(11Q24.3) WILD-TYPE	19	25	50

Figure S70. Get High-res Image Gene #42: 'del_11q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S71. Gene #42: 'del_11q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	30	28	42	21	16	28	4
DEL PEAK 21(11Q24.3) MUTATED	24	9	13	8	2	17	2
DEL PEAK 21(11Q24.3) WILD-TYPE	6	19	29	13	14	11	2

Figure S71. Get High-res Image Gene #42: 'del_11q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.18

Table S72. Gene #43: '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	42	21	16	28	4
DEL PEAK 22(12P13.1) MUTATED	18	5	13	3	2	15	1
DEL PEAK 22(12P13.1) WILD-TYPE	12	23	29	18	14	13	3

Figure S72. Get High-res Image Gene #43: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S73. Gene #45: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 24(13Q14.2) MUTATED	23	63	35
DEL PEAK 24(13Q14.2) WILD-TYPE	23	3	22

Figure S73. Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S74. Gene #45: '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	42	21	16	28	4
DEL PEAK 24(13Q14.2) MUTATED	24	11	41	9	7	25	4
DEL PEAK 24(13Q14.2) WILD-TYPE	6	17	1	12	9	3	0

Figure S74. Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.042

Table S75. Gene #45: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	45	24	58
DEL PEAK 24(13Q14.2) MUTATED	31	24	12	51
DEL PEAK 24(13Q14.2) WILD-TYPE	8	21	12	7

Figure S75. Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S76. Gene #45: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	32	33	37	19
DEL PEAK 24(13Q14.2) MUTATED	27	13	26	36	16
DEL PEAK 24(13Q14.2) WILD-TYPE	18	19	7	1	3

Figure S76. Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.09

Table S77. Gene #46: 'del_14q24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	32	33	37	19
DEL PEAK 25(14Q24.1) MUTATED	17	7	9	8	15
DEL PEAK 25(14Q24.1) WILD-TYPE	28	25	24	29	4

Figure S77. Get High-res Image Gene #46: 'del_14q24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.09

Table S78. Gene #47: 'del_15q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	45	24	58
DEL PEAK 26(15Q11.2) MUTATED	17	6	3	5
DEL PEAK 26(15Q11.2) WILD-TYPE	22	39	21	53

Figure S78. Get High-res Image Gene #47: 'del_15q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S79. Gene #48: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 27(16Q12.1) MUTATED	13	52	30
DEL PEAK 27(16Q12.1) WILD-TYPE	33	14	27

Figure S79. Get High-res Image Gene #48: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

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

Table S80. Gene #49: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 28(16Q23.1) MUTATED	16	50	28
DEL PEAK 28(16Q23.1) WILD-TYPE	30	16	29

Figure S80. Get High-res Image Gene #49: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'CN_CNMF'

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

Table S81. Gene #50: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 29(17P13.1) MUTATED	9	41	32
DEL PEAK 29(17P13.1) WILD-TYPE	37	25	25

Figure S81. Get High-res Image Gene #50: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.042

Table S82. Gene #50: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	30	28	42	21	16	28	4
DEL PEAK 29(17P13.1) MUTATED	9	7	33	10	6	16	1
DEL PEAK 29(17P13.1) WILD-TYPE	21	21	9	11	10	12	3

Figure S82. Get High-res Image Gene #50: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.055

Table S83. Gene #50: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	45	24	58
DEL PEAK 29(17P13.1) MUTATED	21	11	9	39
DEL PEAK 29(17P13.1) WILD-TYPE	18	34	15	19

Figure S83. Get High-res Image Gene #50: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.23

Table S84. Gene #50: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	32	33	37	19
DEL PEAK 29(17P13.1) MUTATED	15	12	16	29	8
DEL PEAK 29(17P13.1) WILD-TYPE	30	20	17	8	11

Figure S84. Get High-res Image Gene #50: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.087

Table S85. Gene #50: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	72	33
DEL PEAK 29(17P13.1) MUTATED	17	43	20
DEL PEAK 29(17P13.1) WILD-TYPE	45	29	13

Figure S85. Get High-res Image Gene #50: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S86. Gene #51: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 30(17Q11.2) MUTATED	15	31	5
DEL PEAK 30(17Q11.2) WILD-TYPE	31	35	52

Figure S86. Get High-res Image Gene #51: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S87. Gene #51: '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	42	21	16	28	4
DEL PEAK 30(17Q11.2) MUTATED	17	4	6	8	0	15	1
DEL PEAK 30(17Q11.2) WILD-TYPE	13	24	36	13	16	13	3

Figure S87. Get High-res Image Gene #51: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.18

Table S88. Gene #51: 'del_17q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	71	27
DEL PEAK 30(17Q11.2) MUTATED	28	10	12
DEL PEAK 30(17Q11.2) WILD-TYPE	41	61	15

Figure S88. Get High-res Image Gene #51: 'del_17q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_17q25.3' versus 'CN_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.24

Table S89. Gene #52: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 31(17Q25.3) MUTATED	10	28	7
DEL PEAK 31(17Q25.3) WILD-TYPE	36	38	50

Figure S89. Get High-res Image Gene #52: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S90. Gene #54: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 33(19P13.3) MUTATED	6	32	12
DEL PEAK 33(19P13.3) WILD-TYPE	40	34	45

Figure S90. Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.051

Table S91. Gene #54: '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	42	21	16	28	4
DEL PEAK 33(19P13.3) MUTATED	5	1	17	5	5	14	3
DEL PEAK 33(19P13.3) WILD-TYPE	25	27	25	16	11	14	1

Figure S91. Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.43' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.17

Table S92. Gene #55: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 34(19Q13.43) MUTATED	11	40	22
DEL PEAK 34(19Q13.43) WILD-TYPE	35	26	35

Figure S92. Get High-res Image Gene #55: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.03

Table S93. Gene #58: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 37(22Q13.31) MUTATED	15	32	7
DEL PEAK 37(22Q13.31) WILD-TYPE	31	34	50

Figure S93. Get High-res Image Gene #58: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq27.1' versus 'CN_CNMF'

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

Table S94. Gene #61: 'del_xq27.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	66	57
DEL PEAK 40(XQ27.1) MUTATED	13	46	23
DEL PEAK 40(XQ27.1) WILD-TYPE	33	20	34

Figure S94. Get High-res Image Gene #61: 'del_xq27.1' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = SARC-TP.transferedmergedcluster.txt
Number of patients = 169
Number of significantly focal cnvs = 61
Number of molecular subtypes = 8
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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