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

Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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/C1V40T21

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 8 molecular subtypes across 295 patients, 75 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q21.3 cnv correlated to 'CN_CNMF'.
amp_1q44 cnv correlated to 'CN_CNMF'.
amp_2p24.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
amp_2q33.1 cnv correlated to 'CN_CNMF'.
amp_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q28 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF'.
amp_6p21.33 cnv correlated to 'CN_CNMF'.
amp_7p11.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
amp_11q13.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
amp_11q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_19q13.13 cnv correlated to 'CN_CNMF'.
amp_20q11.21 cnv correlated to 'CN_CNMF'.
del_1p36.23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_2q37.1 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q21.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_4q35.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'CN_CNMF'.
del_5q35.2 cnv correlated to 'CN_CNMF'.
del_6q26 cnv correlated to 'CN_CNMF'.
del_8p23.3 cnv correlated to 'CN_CNMF'.
del_8p23.1 cnv correlated to 'CN_CNMF'.
del_11q23.3 cnv correlated to 'CN_CNMF'.
del_11q25 cnv correlated to 'CN_CNMF'.
del_13q12.11 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.
del_14q32.31 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_15q21.1 cnv correlated to 'CN_CNMF'.
del_17q25.3 cnv correlated to 'MRNASEQ_CNMF'.
del_18q21.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF'.
del_xp11.3 cnv correlated to 'MIRSEQ_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 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 75 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 3q26 31	227 (77%)	68	1e-05 (0.00504)	2e-05 (0.00958)	4e-05 (0.0186)	1e-05 (0.00504)	0.313 (1.00)	1e-05 (0.00504)	0.053 (1.00)	0.00021 (0.0932)
amp 3q28	224 (76%)	71	1e-05 (0.00504)	2e-05 (0.00958)	5e-05 (0.0231)	1e-05 (0.00504)	0.301 (1.00)	1e-05 (0.00504)	0.0346 (1.00)	0.00013 (0.0589)
amp 11q22 1	47 (16%)	248	0.00035 (0.153)	1e-05 (0.00504)	1e-05 (0.00504)	1e-05 (0.00504)	0.00054 (0.233)	1e-05 (0.00504)	0.0721 (1.00)	0.00331 (1.00)
del 3p14 2	134 (45%)	161	2e-05 (0.00958)	0.00016 (0.072)	0.00603 (1.00)	5e-05 (0.0231)	0.00857 (1.00)	0.00033 (0.145)	0.00226 (0.911)	0.00012 (0.0545)
del 19p13 3	105 (36%)	190	1e-05 (0.00504)	1e-05 (0.00504)	2e-05 (0.00958)	2e-05 (0.00958)	0.0139 (1.00)	5e-05 (0.0231)	0.0474 (1.00)	0.047 (1.00)
del 2q37 1	129 (44%)	166	0.00384 (1.00)	0.0002 (0.089)	1e-05 (0.00504)	3e-05 (0.0141)	0.0154 (1.00)	0.00128 (0.525)	0.0889 (1.00)	1e-05 (0.00504)
del 18q21 2	82 (28%)	213	0.137 (1.00)	3e-05 (0.0141)	1e-05 (0.00504)	5e-05 (0.0231)	0.016 (1.00)	2e-05 (0.00958)	0.0389 (1.00)	0.00259 (1.00)
del 1p36 23	40 (14%)	255	0.00058 (0.249)	0.0353 (1.00)	0.00323 (1.00)	5e-05 (0.0231)	0.173 (1.00)	0.00015 (0.0678)	0.128 (1.00)	0.0233 (1.00)
amp 2p24 3	79 (27%)	216	2e-05 (0.00958)	0.0859 (1.00)	0.0594 (1.00)	0.0462 (1.00)	0.0704 (1.00)	6e-05 (0.0275)	0.113 (1.00)	0.114 (1.00)
amp 7p11 2	52 (18%)	243	0.00017 (0.0763)	0.0188 (1.00)	0.00185 (0.753)	0.0644 (1.00)	0.0003 (0.132)	0.0886 (1.00)	0.028 (1.00)	0.0144 (1.00)
amp 11q13 3	41 (14%)	254	0.00037 (0.161)	0.0463 (1.00)	0.00137 (0.56)	0.00091 (0.378)	0.0164 (1.00)	2e-05 (0.00958)	0.371 (1.00)	0.321 (1.00)
del 4q21 3	103 (35%)	192	1e-05 (0.00504)	0.128 (1.00)	0.0354 (1.00)	0.00015 (0.0678)	0.487 (1.00)	0.235 (1.00)	0.563 (1.00)	0.329 (1.00)
del 4q22 1	100 (34%)	195	1e-05 (0.00504)	0.245 (1.00)	0.0526 (1.00)	0.00035 (0.153)	0.632 (1.00)	0.0446 (1.00)	0.229 (1.00)	0.414 (1.00)
del 4q35 2	114 (39%)	181	1e-05 (0.00504)	0.115 (1.00)	0.0151 (1.00)	3e-05 (0.0141)	0.381 (1.00)	0.124 (1.00)	0.414 (1.00)	0.0855 (1.00)
del 13q12 11	98 (33%)	197	0.00265 (1.00)	0.00771 (1.00)	0.00017 (0.0763)	0.00026 (0.115)	0.00211 (0.855)	0.00488 (1.00)	0.248 (1.00)	0.00247 (0.986)
del 13q14 2	118 (40%)	177	0.00382 (1.00)	0.00386 (1.00)	0.00111 (0.456)	0.0003 (0.132)	0.0146 (1.00)	0.00052 (0.225)	0.0797 (1.00)	0.00326 (1.00)
del 14q32 31	50 (17%)	245	0.00011 (0.05)	0.144 (1.00)	0.00054 (0.233)	0.00305 (1.00)	0.237 (1.00)	0.026 (1.00)	0.0899 (1.00)	0.13 (1.00)
amp 1q21 3	158 (54%)	137	1e-05 (0.00504)	0.277 (1.00)	0.053 (1.00)	0.23 (1.00)	0.989 (1.00)	0.00085 (0.354)	0.794 (1.00)	0.0547 (1.00)
amp 1q44	152 (52%)	143	1e-05 (0.00504)	0.108 (1.00)	0.0221 (1.00)	0.08 (1.00)	0.853 (1.00)	0.00146 (0.596)	0.434 (1.00)	0.0203 (1.00)
amp 2q33 1	41 (14%)	254	4e-05 (0.0186)	0.0529 (1.00)	0.00284 (1.00)	0.0939 (1.00)	0.304 (1.00)	0.0074 (1.00)	0.327 (1.00)	0.821 (1.00)
amp 5p15 33	138 (47%)	157	1e-05 (0.00504)	0.0151 (1.00)	0.00229 (0.921)	0.00064 (0.273)	0.00543 (1.00)	0.00082 (0.344)	0.192 (1.00)	0.0156 (1.00)
amp 6p21 33	82 (28%)	213	0.00026 (0.115)	0.0247 (1.00)	0.00352 (1.00)	0.0395 (1.00)	0.722 (1.00)	0.0155 (1.00)	0.413 (1.00)	0.688 (1.00)
amp 19q13 13	93 (32%)	202	1e-05 (0.00504)	0.188 (1.00)	0.562 (1.00)	0.46 (1.00)	0.656 (1.00)	0.271 (1.00)	0.88 (1.00)	0.848 (1.00)
amp 20q11 21	135 (46%)	160	0.00047 (0.204)	0.0828 (1.00)	0.245 (1.00)	0.0452 (1.00)	0.182 (1.00)	0.035 (1.00)	0.676 (1.00)	0.186 (1.00)
del 5q12 1	76 (26%)	219	2e-05 (0.00958)	0.726 (1.00)	0.143 (1.00)	0.532 (1.00)	0.0204 (1.00)	0.344 (1.00)	0.816 (1.00)	0.0301 (1.00)
del 5q35 2	71 (24%)	224	0.00017 (0.0763)	0.993 (1.00)	0.3 (1.00)	0.782 (1.00)	0.0293 (1.00)	0.557 (1.00)	0.484 (1.00)	0.128 (1.00)
del 6q26	100 (34%)	195	1e-05 (0.00504)	0.0542 (1.00)	0.33 (1.00)	0.128 (1.00)	0.317 (1.00)	0.319 (1.00)	0.179 (1.00)	0.229 (1.00)
del 8p23 3	104 (35%)	191	2e-05 (0.00958)	0.0687 (1.00)	0.0006 (0.257)	0.106 (1.00)	0.072 (1.00)	0.0177 (1.00)	0.0329 (1.00)	0.193 (1.00)
del 8p23 1	97 (33%)	198	6e-05 (0.0275)	0.0678 (1.00)	0.00371 (1.00)	0.43 (1.00)	0.024 (1.00)	0.0225 (1.00)	0.0088 (1.00)	0.0817 (1.00)
del 11q23 3	162 (55%)	133	1e-05 (0.00504)	0.0473 (1.00)	0.135 (1.00)	0.0504 (1.00)	0.812 (1.00)	0.00242 (0.97)	0.113 (1.00)	0.00639 (1.00)
del 11q25	160 (54%)	135	1e-05 (0.00504)	0.0308 (1.00)	0.224 (1.00)	0.101 (1.00)	0.534 (1.00)	0.00608 (1.00)	0.0759 (1.00)	0.00853 (1.00)
del 15q21 1	70 (24%)	225	0.0001 (0.0456)	0.15 (1.00)	0.0462 (1.00)	0.0863 (1.00)	0.0105 (1.00)	0.0317 (1.00)	0.019 (1.00)	0.0502 (1.00)
del 17q25 3	51 (17%)	244	0.333 (1.00)	0.00363 (1.00)	4e-05 (0.0186)	0.00317 (1.00)	0.00333 (1.00)	0.00081 (0.341)	0.415 (1.00)	0.00519 (1.00)
del 21q11 2	58 (20%)	237	0.00019 (0.0847)	0.101 (1.00)	0.134 (1.00)	0.002 (0.812)	0.479 (1.00)	0.232 (1.00)	0.432 (1.00)	1 (1.00)
del xp11 3	72 (24%)	223	0.00071 (0.3)	0.00067 (0.285)	0.00383 (1.00)	0.115 (1.00)	0.00026 (0.115)	0.0306 (1.00)	0.00276 (1.00)	0.158 (1.00)
amp 1p31 3	96 (33%)	199	0.00082 (0.344)	0.467 (1.00)	0.0585 (1.00)	0.0219 (1.00)	0.341 (1.00)	0.0011 (0.453)	0.546 (1.00)	0.284 (1.00)
amp 4q12	21 (7%)	274	0.879 (1.00)	0.0626 (1.00)	0.709 (1.00)	0.589 (1.00)	1 (1.00)	0.37 (1.00)	0.4 (1.00)	0.112 (1.00)
amp 8q24 21	127 (43%)	168	0.252 (1.00)	0.313 (1.00)	0.547 (1.00)	0.193 (1.00)	0.0884 (1.00)	0.0985 (1.00)	0.02 (1.00)	0.00079 (0.333)
amp 9p24 1	63 (21%)	232	0.344 (1.00)	0.467 (1.00)	0.637 (1.00)	0.108 (1.00)	0.646 (1.00)	0.0684 (1.00)	0.119 (1.00)	0.178 (1.00)
amp 11p12	23 (8%)	272	0.528 (1.00)	0.22 (1.00)	0.16 (1.00)	0.387 (1.00)	0.454 (1.00)	0.0678 (1.00)	0.562 (1.00)	0.708 (1.00)
amp 13q22 1	65 (22%)	230	0.196 (1.00)	0.00855 (1.00)	0.981 (1.00)	0.925 (1.00)	0.759 (1.00)	0.428 (1.00)	0.355 (1.00)	0.641 (1.00)
amp 13q34	69 (23%)	226	0.0335 (1.00)	0.269 (1.00)	0.835 (1.00)	0.821 (1.00)	0.763 (1.00)	0.772 (1.00)	0.584 (1.00)	0.467 (1.00)
amp 15q26 1	76 (26%)	219	0.0884 (1.00)	0.589 (1.00)	0.64 (1.00)	0.219 (1.00)	0.55 (1.00)	0.606 (1.00)	0.472 (1.00)	0.385 (1.00)
amp 16p13 13	65 (22%)	230	0.242 (1.00)	0.268 (1.00)	0.393 (1.00)	0.0857 (1.00)	0.299 (1.00)	0.224 (1.00)	0.613 (1.00)	0.457 (1.00)
amp 17q12	55 (19%)	240	0.00493 (1.00)	0.0251 (1.00)	0.0187 (1.00)	0.00876 (1.00)	0.0287 (1.00)	0.0325 (1.00)	0.0188 (1.00)	0.0438 (1.00)
amp 17q25 1	74 (25%)	221	0.00104 (0.43)	0.233 (1.00)	0.411 (1.00)	0.125 (1.00)	0.157 (1.00)	0.942 (1.00)	0.263 (1.00)	0.774 (1.00)
amp 19p13 3	39 (13%)	256	0.354 (1.00)	0.00245 (0.98)	0.437 (1.00)	0.00641 (1.00)	0.514 (1.00)	0.018 (1.00)	0.443 (1.00)	0.157 (1.00)
amp 19p13 2	43 (15%)	252	0.793 (1.00)	0.105 (1.00)	0.572 (1.00)	0.455 (1.00)	0.697 (1.00)	0.0962 (1.00)	0.929 (1.00)	0.278 (1.00)
amp 21q22 13	48 (16%)	247	0.223 (1.00)	0.979 (1.00)	0.54 (1.00)	0.843 (1.00)	0.884 (1.00)	0.834 (1.00)	0.802 (1.00)	0.465 (1.00)
amp xq28	75 (25%)	220	0.624 (1.00)	0.281 (1.00)	0.365 (1.00)	0.426 (1.00)	0.00099 (0.41)	0.167 (1.00)	0.0232 (1.00)	0.0716 (1.00)
del 1p13 2	34 (12%)	261	0.058 (1.00)	0.00961 (1.00)	0.00087 (0.362)	0.286 (1.00)	0.0115 (1.00)	0.177 (1.00)	0.634 (1.00)	0.0271 (1.00)
del 2q22 1	65 (22%)	230	0.584 (1.00)	0.858 (1.00)	0.231 (1.00)	0.0637 (1.00)	0.967 (1.00)	0.18 (1.00)	0.601 (1.00)	0.0756 (1.00)
del 6p24 2	46 (16%)	249	0.286 (1.00)	0.0611 (1.00)	0.0746 (1.00)	0.227 (1.00)	0.287 (1.00)	0.0256 (1.00)	0.172 (1.00)	0.0898 (1.00)
del 7q34	60 (20%)	235	0.00062 (0.265)	0.368 (1.00)	0.495 (1.00)	0.894 (1.00)	0.693 (1.00)	0.466 (1.00)	0.74 (1.00)	0.599 (1.00)
del 10q23 31	86 (29%)	209	0.00789 (1.00)	0.481 (1.00)	0.89 (1.00)	0.336 (1.00)	0.946 (1.00)	0.238 (1.00)	0.854 (1.00)	0.585 (1.00)
del 11p15 1	102 (35%)	193	0.00081 (0.341)	0.0544 (1.00)	0.161 (1.00)	0.0415 (1.00)	0.266 (1.00)	0.077 (1.00)	0.987 (1.00)	0.143 (1.00)
del 16q11 2	53 (18%)	242	0.203 (1.00)	0.00954 (1.00)	0.0265 (1.00)	0.0828 (1.00)	0.0113 (1.00)	0.011 (1.00)	0.198 (1.00)	0.0139 (1.00)
del 16q23 1	55 (19%)	240	0.0133 (1.00)	0.00212 (0.856)	0.00301 (1.00)	0.00663 (1.00)	0.0266 (1.00)	0.00069 (0.293)	0.0492 (1.00)	0.00333 (1.00)
del 17p12	109 (37%)	186	0.00059 (0.253)	0.547 (1.00)	0.266 (1.00)	0.109 (1.00)	0.195 (1.00)	0.202 (1.00)	0.625 (1.00)	0.773 (1.00)
del 19q13 33	38 (13%)	257	0.628 (1.00)	0.097 (1.00)	0.162 (1.00)	0.196 (1.00)	0.0951 (1.00)	0.167 (1.00)	0.073 (1.00)	0.158 (1.00)
del 20p12 1	36 (12%)	259	0.585 (1.00)	0.0315 (1.00)	0.0635 (1.00)	0.324 (1.00)	0.0774 (1.00)	0.143 (1.00)	0.0918 (1.00)	0.362 (1.00)
del 22q13 32	88 (30%)	207	0.00475 (1.00)	0.128 (1.00)	0.0589 (1.00)	0.0066 (1.00)	0.973 (1.00)	0.655 (1.00)	1 (1.00)	0.906 (1.00)
del xq21 33	60 (20%)	235	0.129 (1.00)	0.00607 (1.00)	0.252 (1.00)	0.0921 (1.00)	0.248 (1.00)	0.952 (1.00)	0.0867 (1.00)	0.704 (1.00)

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S1. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 2(1Q21.3) MUTATED	49	42	67
AMP PEAK 2(1Q21.3) WILD-TYPE	80	31	26

Figure S1. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S2. Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 3(1Q44) MUTATED	46	41	65
AMP PEAK 3(1Q44) WILD-TYPE	83	32	28

Figure S2. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p24.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S3. Gene #4: 'amp_2p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 4(2P24.3) MUTATED	21	35	23
AMP PEAK 4(2P24.3) WILD-TYPE	108	38	70

Figure S3. Get High-res Image Gene #4: 'amp_2p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.027

Table S4. Gene #4: 'amp_2p24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 4(2P24.3) MUTATED	21	26	6	13	13
AMP PEAK 4(2P24.3) WILD-TYPE	39	69	66	12	30

Figure S4. Get High-res Image Gene #4: 'amp_2p24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_2q33.1' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

Table S5. Gene #5: 'amp_2q33.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 5(2Q33.1) MUTATED	7	21	13
AMP PEAK 5(2Q33.1) WILD-TYPE	122	52	80

Figure S5. Get High-res Image Gene #5: 'amp_2q33.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S6. Gene #6: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 6(3Q26.31) MUTATED	77	57	93
AMP PEAK 6(3Q26.31) WILD-TYPE	52	16	0

Figure S6. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.31' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S7. Gene #6: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	57	41	45	52	36	13
AMP PEAK 6(3Q26.31) MUTATED	34	34	40	34	34	13
AMP PEAK 6(3Q26.31) WILD-TYPE	23	7	5	18	2	0

Figure S7. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.31' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

Table S8. Gene #6: 'amp_3q26.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	101	65
AMP PEAK 6(3Q26.31) MUTATED	51	92	45
AMP PEAK 6(3Q26.31) WILD-TYPE	26	9	20

Figure S8. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S9. Gene #6: 'amp_3q26.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	154	33
AMP PEAK 6(3Q26.31) MUTATED	34	135	19
AMP PEAK 6(3Q26.31) WILD-TYPE	22	19	14

Figure S9. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S10. Gene #6: 'amp_3q26.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 6(3Q26.31) MUTATED	34	81	65	20	27
AMP PEAK 6(3Q26.31) WILD-TYPE	26	14	7	5	16

Figure S10. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.093

Table S11. Gene #6: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
AMP PEAK 6(3Q26.31) MUTATED	38	45	24	109
AMP PEAK 6(3Q26.31) WILD-TYPE	26	5	2	33

Figure S11. Get High-res Image Gene #6: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S12. Gene #7: 'amp_3q28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 7(3Q28) MUTATED	77	54	93
AMP PEAK 7(3Q28) WILD-TYPE	52	19	0

Figure S12. Get High-res Image Gene #7: 'amp_3q28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q28' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S13. Gene #7: 'amp_3q28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	57	41	45	52	36	13
AMP PEAK 7(3Q28) MUTATED	32	33	39	35	35	13
AMP PEAK 7(3Q28) WILD-TYPE	25	8	6	17	1	0

Figure S13. Get High-res Image Gene #7: 'amp_3q28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q28' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S14. Gene #7: 'amp_3q28' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	101	65
AMP PEAK 7(3Q28) MUTATED	49	91	46
AMP PEAK 7(3Q28) WILD-TYPE	28	10	19

Figure S14. Get High-res Image Gene #7: 'amp_3q28' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3q28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S15. Gene #7: 'amp_3q28' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	154	33
AMP PEAK 7(3Q28) MUTATED	32	134	20
AMP PEAK 7(3Q28) WILD-TYPE	24	20	13

Figure S15. Get High-res Image Gene #7: 'amp_3q28' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3q28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S16. Gene #7: 'amp_3q28' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 7(3Q28) MUTATED	33	80	65	19	27
AMP PEAK 7(3Q28) WILD-TYPE	27	15	7	6	16

Figure S16. Get High-res Image Gene #7: 'amp_3q28' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_3q28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.059

Table S17. Gene #7: 'amp_3q28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
AMP PEAK 7(3Q28) MUTATED	36	44	24	109
AMP PEAK 7(3Q28) WILD-TYPE	28	6	2	33

Figure S17. Get High-res Image Gene #7: 'amp_3q28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S18. Gene #9: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 9(5P15.33) MUTATED	34	60	44
AMP PEAK 9(5P15.33) WILD-TYPE	95	13	49

Figure S18. Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.33' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.12

Table S19. Gene #10: 'amp_6p21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 10(6P21.33) MUTATED	26	34	22
AMP PEAK 10(6P21.33) WILD-TYPE	103	39	71

Figure S19. Get High-res Image Gene #10: 'amp_6p21.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.076

Table S20. Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 11(7P11.2) MUTATED	13	25	14
AMP PEAK 11(7P11.2) WILD-TYPE	116	48	79

Figure S20. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.13

Table S21. Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
AMP PEAK 11(7P11.2) MUTATED	12	6	34
AMP PEAK 11(7P11.2) WILD-TYPE	87	71	85

Figure S21. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.16

Table S22. Gene #15: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 15(11Q13.3) MUTATED	11	21	9
AMP PEAK 15(11Q13.3) WILD-TYPE	118	52	84

Figure S22. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S23. Gene #15: 'amp_11q13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 15(11Q13.3) MUTATED	3	10	5	6	17
AMP PEAK 15(11Q13.3) WILD-TYPE	57	85	67	19	26

Figure S23. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_11q22.1' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.15

Table S24. Gene #16: 'amp_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 16(11Q22.1) MUTATED	15	23	9
AMP PEAK 16(11Q22.1) WILD-TYPE	114	50	84

Figure S24. Get High-res Image Gene #16: 'amp_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S25. Gene #16: 'amp_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	57	41	45	52	36	13
AMP PEAK 16(11Q22.1) MUTATED	3	3	9	22	3	2
AMP PEAK 16(11Q22.1) WILD-TYPE	54	38	36	30	33	11

Figure S25. Get High-res Image Gene #16: 'amp_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S26. Gene #16: 'amp_11q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	101	65
AMP PEAK 16(11Q22.1) MUTATED	6	12	24
AMP PEAK 16(11Q22.1) WILD-TYPE	71	89	41

Figure S26. Get High-res Image Gene #16: 'amp_11q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_11q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S27. Gene #16: 'amp_11q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	154	33
AMP PEAK 16(11Q22.1) MUTATED	3	21	18
AMP PEAK 16(11Q22.1) WILD-TYPE	53	133	15

Figure S27. Get High-res Image Gene #16: 'amp_11q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_11q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.23

Table S28. Gene #16: 'amp_11q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
AMP PEAK 16(11Q22.1) MUTATED	8	8	31
AMP PEAK 16(11Q22.1) WILD-TYPE	91	69	88

Figure S28. Get High-res Image Gene #16: 'amp_11q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_11q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S29. Gene #16: 'amp_11q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
AMP PEAK 16(11Q22.1) MUTATED	2	8	11	3	23
AMP PEAK 16(11Q22.1) WILD-TYPE	58	87	61	22	20

Figure S29. Get High-res Image Gene #16: 'amp_11q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S30. Gene #25: 'amp_19q13.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 25(19Q13.13) MUTATED	21	46	26
AMP PEAK 25(19Q13.13) WILD-TYPE	108	27	67

Figure S30. Get High-res Image Gene #25: 'amp_19q13.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.2

Table S31. Gene #26: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
AMP PEAK 26(20Q11.21) MUTATED	43	44	48
AMP PEAK 26(20Q11.21) WILD-TYPE	86	29	45

Figure S31. Get High-res Image Gene #26: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.23' versus 'CN_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.25

Table S32. Gene #29: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 1(1P36.23) MUTATED	10	20	10
DEL PEAK 1(1P36.23) WILD-TYPE	119	53	83

Figure S32. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S33. Gene #29: 'del_1p36.23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	154	33
DEL PEAK 1(1P36.23) MUTATED	15	9	8
DEL PEAK 1(1P36.23) WILD-TYPE	41	145	25

Figure S33. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.068

Table S34. Gene #29: 'del_1p36.23' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 1(1P36.23) MUTATED	16	11	1	5	7
DEL PEAK 1(1P36.23) WILD-TYPE	44	84	71	20	36

Figure S34. Get High-res Image Gene #29: 'del_1p36.23' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.089

Table S35. Gene #32: 'del_2q37.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	57	41	45	52	36	13
DEL PEAK 4(2Q37.1) MUTATED	11	17	22	33	15	7
DEL PEAK 4(2Q37.1) WILD-TYPE	46	24	23	19	21	6

Figure S35. Get High-res Image Gene #32: 'del_2q37.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S36. Gene #32: 'del_2q37.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	101	65
DEL PEAK 4(2Q37.1) MUTATED	16	47	41
DEL PEAK 4(2Q37.1) WILD-TYPE	61	54	24

Figure S36. Get High-res Image Gene #32: 'del_2q37.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q37.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S37. Gene #32: 'del_2q37.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	154	33
DEL PEAK 4(2Q37.1) MUTATED	10	73	21
DEL PEAK 4(2Q37.1) WILD-TYPE	46	81	12

Figure S37. Get High-res Image Gene #32: 'del_2q37.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S38. Gene #32: 'del_2q37.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 4(2Q37.1) MUTATED	13	20	9	81
DEL PEAK 4(2Q37.1) WILD-TYPE	51	30	17	61

Figure S38. Get High-res Image Gene #32: 'del_2q37.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S39. Gene #33: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 5(3P14.2) MUTATED	40	47	47
DEL PEAK 5(3P14.2) WILD-TYPE	89	26	46

Figure S39. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.072

Table S40. Gene #33: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	57	41	45	52	36	13
DEL PEAK 5(3P14.2) MUTATED	13	24	15	31	21	5
DEL PEAK 5(3P14.2) WILD-TYPE	44	17	30	21	15	8

Figure S40. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S41. Gene #33: 'del_3p14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	154	33
DEL PEAK 5(3P14.2) MUTATED	13	85	11
DEL PEAK 5(3P14.2) WILD-TYPE	43	69	22

Figure S41. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.14

Table S42. Gene #33: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 5(3P14.2) MUTATED	13	54	34	13	20
DEL PEAK 5(3P14.2) WILD-TYPE	47	41	38	12	23

Figure S42. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.054

Table S43. Gene #33: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	50	26	142
DEL PEAK 5(3P14.2) MUTATED	14	30	14	69
DEL PEAK 5(3P14.2) WILD-TYPE	50	20	12	73

Figure S43. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S44. Gene #34: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 6(4Q21.3) MUTATED	21	48	34
DEL PEAK 6(4Q21.3) WILD-TYPE	108	25	59

Figure S44. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.068

Table S45. Gene #34: 'del_4q21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	154	33
DEL PEAK 6(4Q21.3) MUTATED	13	47	22
DEL PEAK 6(4Q21.3) WILD-TYPE	43	107	11

Figure S45. Get High-res Image Gene #34: 'del_4q21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S46. Gene #35: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 7(4Q22.1) MUTATED	17	51	32
DEL PEAK 7(4Q22.1) WILD-TYPE	112	22	61

Figure S46. Get High-res Image Gene #35: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.15

Table S47. Gene #35: 'del_4q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	154	33
DEL PEAK 7(4Q22.1) MUTATED	13	46	21
DEL PEAK 7(4Q22.1) WILD-TYPE	43	108	12

Figure S47. Get High-res Image Gene #35: 'del_4q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S48. Gene #36: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 8(4Q35.2) MUTATED	25	52	37
DEL PEAK 8(4Q35.2) WILD-TYPE	104	21	56

Figure S48. Get High-res Image Gene #36: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S49. Gene #36: 'del_4q35.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	154	33
DEL PEAK 8(4Q35.2) MUTATED	16	53	25
DEL PEAK 8(4Q35.2) WILD-TYPE	40	101	8

Figure S49. Get High-res Image Gene #36: 'del_4q35.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S50. Gene #37: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 9(5Q12.1) MUTATED	19	33	24
DEL PEAK 9(5Q12.1) WILD-TYPE	110	40	69

Figure S50. Get High-res Image Gene #37: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.2' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.076

Table S51. Gene #38: 'del_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 10(5Q35.2) MUTATED	19	30	22
DEL PEAK 10(5Q35.2) WILD-TYPE	110	43	71

Figure S51. Get High-res Image Gene #38: 'del_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S52. Gene #40: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 12(6Q26) MUTATED	39	43	18
DEL PEAK 12(6Q26) WILD-TYPE	90	30	75

Figure S52. Get High-res Image Gene #40: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S53. Gene #42: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 14(8P23.3) MUTATED	28	42	34
DEL PEAK 14(8P23.3) WILD-TYPE	101	31	59

Figure S53. Get High-res Image Gene #42: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.1' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.027

Table S54. Gene #43: 'del_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 15(8P23.1) MUTATED	28	39	30
DEL PEAK 15(8P23.1) WILD-TYPE	101	34	63

Figure S54. Get High-res Image Gene #43: 'del_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S55. Gene #46: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 18(11Q23.3) MUTATED	49	42	71
DEL PEAK 18(11Q23.3) WILD-TYPE	80	31	22

Figure S55. Get High-res Image Gene #46: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S56. Gene #47: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 19(11Q25) MUTATED	45	45	70
DEL PEAK 19(11Q25) WILD-TYPE	84	28	23

Figure S56. Get High-res Image Gene #47: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.076

Table S57. Gene #48: 'del_13q12.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	101	65
DEL PEAK 20(13Q12.11) MUTATED	14	36	34
DEL PEAK 20(13Q12.11) WILD-TYPE	63	65	31

Figure S57. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.12

Table S58. Gene #48: 'del_13q12.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	154	33
DEL PEAK 20(13Q12.11) MUTATED	8	59	17
DEL PEAK 20(13Q12.11) WILD-TYPE	48	95	16

Figure S58. Get High-res Image Gene #48: 'del_13q12.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.13

Table S59. Gene #49: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	154	33
DEL PEAK 21(13Q14.2) MUTATED	10	72	16
DEL PEAK 21(13Q14.2) WILD-TYPE	46	82	17

Figure S59. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.23

Table S60. Gene #49: 'del_13q14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 21(13Q14.2) MUTATED	11	43	27	13	24
DEL PEAK 21(13Q14.2) WILD-TYPE	49	52	45	12	19

Figure S60. Get High-res Image Gene #49: 'del_13q14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.31' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.05

Table S61. Gene #50: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 22(14Q32.31) MUTATED	17	25	8
DEL PEAK 22(14Q32.31) WILD-TYPE	112	48	85

Figure S61. Get High-res Image Gene #50: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'MRNASEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.23

Table S62. Gene #50: 'del_14q32.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	101	65
DEL PEAK 22(14Q32.31) MUTATED	22	7	11
DEL PEAK 22(14Q32.31) WILD-TYPE	55	94	54

Figure S62. Get High-res Image Gene #50: 'del_14q32.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_15q21.1' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.046

Table S63. Gene #51: 'del_15q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 23(15Q21.1) MUTATED	20	31	19
DEL PEAK 23(15Q21.1) WILD-TYPE	109	42	74

Figure S63. Get High-res Image Gene #51: 'del_15q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q25.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

Table S64. Gene #55: 'del_17q25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	101	65
DEL PEAK 27(17Q25.3) MUTATED	3	18	20
DEL PEAK 27(17Q25.3) WILD-TYPE	74	83	45

Figure S64. Get High-res Image Gene #55: 'del_17q25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S65. Gene #56: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	57	41	45	52	36	13
DEL PEAK 28(18Q21.2) MUTATED	25	7	8	23	2	2
DEL PEAK 28(18Q21.2) WILD-TYPE	32	34	37	29	34	11

Figure S65. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S66. Gene #56: 'del_18q21.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	101	65
DEL PEAK 28(18Q21.2) MUTATED	29	8	30
DEL PEAK 28(18Q21.2) WILD-TYPE	48	93	35

Figure S66. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S67. Gene #56: 'del_18q21.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	154	33
DEL PEAK 28(18Q21.2) MUTATED	26	27	14
DEL PEAK 28(18Q21.2) WILD-TYPE	30	127	19

Figure S67. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S68. Gene #56: 'del_18q21.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 28(18Q21.2) MUTATED	29	18	11	4	20
DEL PEAK 28(18Q21.2) WILD-TYPE	31	77	61	21	23

Figure S68. Get High-res Image Gene #56: 'del_18q21.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S69. Gene #57: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 29(19P13.3) MUTATED	24	52	29
DEL PEAK 29(19P13.3) WILD-TYPE	105	21	64

Figure S69. Get High-res Image Gene #57: '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 = 0.005

Table S70. Gene #57: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	57	41	45	52	36	13
DEL PEAK 29(19P13.3) MUTATED	18	10	5	34	9	4
DEL PEAK 29(19P13.3) WILD-TYPE	39	31	40	18	27	9

Figure S70. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S71. Gene #57: 'del_19p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	101	65
DEL PEAK 29(19P13.3) MUTATED	26	19	35
DEL PEAK 29(19P13.3) WILD-TYPE	51	82	30

Figure S71. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S72. Gene #57: 'del_19p13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	154	33
DEL PEAK 29(19P13.3) MUTATED	16	40	24
DEL PEAK 29(19P13.3) WILD-TYPE	40	114	9

Figure S72. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S73. Gene #57: 'del_19p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	95	72	25	43
DEL PEAK 29(19P13.3) MUTATED	17	36	13	13	26
DEL PEAK 29(19P13.3) WILD-TYPE	43	59	59	12	17

Figure S73. Get High-res Image Gene #57: 'del_19p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.085

Table S74. Gene #60: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	73	93
DEL PEAK 32(21Q11.2) MUTATED	13	24	21
DEL PEAK 32(21Q11.2) WILD-TYPE	116	49	72

Figure S74. Get High-res Image Gene #60: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.3' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.12

Table S75. Gene #62: 'del_xp11.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	77	119
DEL PEAK 34(XP11.3) MUTATED	22	8	42
DEL PEAK 34(XP11.3) WILD-TYPE	77	69	77

Figure S75. Get High-res Image Gene #62: 'del_xp11.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = CESC-TP.transferedmergedcluster.txt
Number of patients = 295
Number of significantly focal cnvs = 63
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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