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

Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

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 (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1TD9WRP

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 28 focal events and 10 molecular subtypes across 288 patients, 177 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_2p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_2q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
amp_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5q35.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2p12 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_3p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5p15.33 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_5q35.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_6q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q21.1 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q22.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q23.3 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q24.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q24.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_19q13.42 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_22q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 28 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 177 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 7p11 2	175 (61%)	113	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.0113 (0.0229)	1e-05 (5.38e-05)	1e-05 (5.38e-05)	1e-05 (5.38e-05)	8e-05 (0.000329)	0.00041 (0.00145)	1e-05 (5.38e-05)	3e-05 (0.000135)
amp 7q31 2	177 (61%)	111	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.0203 (0.0368)	3e-05 (0.000135)	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.00068 (0.00227)	0.00059 (0.00201)	1e-05 (5.38e-05)	3e-05 (0.000135)
amp 17q23 2	199 (69%)	89	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.00346 (0.00838)	9e-05 (0.00036)	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.00882 (0.0182)	0.00773 (0.0162)	0.0002 (0.000757)	0.00036 (0.00129)
del 5q35 2	11 (4%)	277	0.0403 (0.066)	1e-05 (5.38e-05)	0.0336 (0.0564)	0.00021 (0.000784)	0.00027 (0.000995)	1e-05 (5.38e-05)	0.0797 (0.119)	0.00077 (0.00254)	0.0032 (0.008)	0.0183 (0.0335)
del 9p21 3	40 (14%)	248	0.00269 (0.00703)	1e-05 (5.38e-05)	0.368 (0.444)	0.00112 (0.00348)	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.0125 (0.0246)	0.0124 (0.0246)	0.00111 (0.00348)	6e-05 (0.000255)
del 14q24 2	50 (17%)	238	2e-05 (9.82e-05)	4e-05 (0.000178)	0.0237 (0.0423)	0.00271 (0.00703)	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.0243 (0.0431)	1 (1.00)	0.0153 (0.0285)	0.00357 (0.00854)
amp 3q26 31	101 (35%)	187	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.238 (0.303)	0.00151 (0.00448)	1e-05 (5.38e-05)	0.0121 (0.0242)	0.00255 (0.00693)	0.00344 (0.00838)	0.557 (0.621)	0.00484 (0.0111)
del 3p22 1	25 (9%)	263	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.385 (0.46)	0.0296 (0.0508)	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.0143 (0.0277)	0.0455 (0.0724)	0.0503 (0.0791)	0.00266 (0.00703)
del 4q34 3	32 (11%)	256	0.00116 (0.00357)	1e-05 (5.38e-05)	0.275 (0.345)	0.0128 (0.0251)	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.0552 (0.0857)	0.468 (0.533)	0.0269 (0.0467)	0.00347 (0.00838)
del 10q21 1	19 (7%)	269	0.12 (0.166)	0.00016 (0.000614)	0.762 (0.805)	0.0422 (0.0679)	1e-05 (5.38e-05)	0.0009 (0.0029)	0.0231 (0.0414)	0.794 (0.833)	0.0446 (0.0714)	0.00733 (0.0154)
del 11q23 3	29 (10%)	259	0.211 (0.274)	0.00047 (0.00164)	0.338 (0.417)	0.041 (0.0666)	0.0001 (0.000394)	0.00159 (0.00459)	0.0319 (0.0538)	0.371 (0.446)	0.0148 (0.028)	0.00573 (0.0128)
del 22q12 2	63 (22%)	225	0.00231 (0.00647)	1e-05 (5.38e-05)	0.441 (0.51)	0.00637 (0.014)	1e-05 (5.38e-05)	1e-05 (5.38e-05)	5e-05 (0.000215)	0.749 (0.798)	0.0956 (0.139)	0.00646 (0.0141)
del 1p36 31	54 (19%)	234	2e-05 (9.82e-05)	1e-05 (5.38e-05)	0.416 (0.49)	0.0894 (0.133)	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.00489 (0.0111)	0.874 (0.907)	0.0531 (0.083)	0.0027 (0.00703)
del 2q22 1	10 (3%)	278	0.0359 (0.0594)	0.00152 (0.00448)	0.00622 (0.0138)	0.717 (0.766)	3e-05 (0.000135)	0.00729 (0.0154)	0.0135 (0.0262)	1 (1.00)	0.368 (0.444)	0.411 (0.488)
del 2q37 3	12 (4%)	276	0.00816 (0.0169)	0.00156 (0.00455)	0.00055 (0.0019)	0.214 (0.277)	0.0246 (0.0433)	0.00241 (0.00667)	0.0174 (0.0321)	0.291 (0.363)	0.0576 (0.0881)	0.444 (0.512)
del 6q25 3	32 (11%)	256	0.0119 (0.0239)	1e-05 (5.38e-05)	0.697 (0.748)	0.0188 (0.0342)	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.0278 (0.0481)	1 (1.00)	0.0696 (0.105)	0.0554 (0.0857)
del 14q11 2	51 (18%)	237	0.00016 (0.000614)	0.00119 (0.00362)	0.0635 (0.0967)	0.00447 (0.0104)	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.118 (0.166)	0.959 (0.981)	0.0557 (0.0857)	0.0148 (0.028)
del 15q13 3	35 (12%)	253	0.00282 (0.00724)	3e-05 (0.000135)	0.12 (0.166)	0.0312 (0.0533)	1e-05 (5.38e-05)	1e-05 (5.38e-05)	0.103 (0.148)	0.108 (0.155)	0.0926 (0.136)	0.0174 (0.0321)
amp 5q35 3	37 (13%)	251	9e-05 (0.00036)	0.00028 (0.00102)	0.535 (0.602)	0.618 (0.681)	0.00142 (0.00428)	1e-05 (5.38e-05)	0.436 (0.507)	0.0412 (0.0666)	0.422 (0.495)	0.126 (0.173)
del 11q22 3	31 (11%)	257	0.185 (0.246)	0.00472 (0.0109)	0.639 (0.702)	0.102 (0.148)	5e-05 (0.000215)	0.00243 (0.00667)	0.112 (0.158)	0.429 (0.501)	0.00672 (0.0144)	0.00271 (0.00703)
del 19q13 42	19 (7%)	269	1e-05 (5.38e-05)	0.00068 (0.00227)	0.792 (0.833)	0.415 (0.49)	8e-05 (0.000329)	0.00344 (0.00838)	0.00658 (0.0143)	0.472 (0.536)	0.664 (0.723)	0.21 (0.274)
amp 2p23 2	45 (16%)	243	1e-05 (5.38e-05)	2e-05 (9.82e-05)	0.762 (0.805)	0.0487 (0.077)	0.459 (0.527)	0.952 (0.977)	0.0317 (0.0538)	0.179 (0.239)	0.654 (0.715)	0.541 (0.606)
del 6p12 3	26 (9%)	262	0.0147 (0.028)	1e-05 (5.38e-05)	1 (1.00)	0.237 (0.303)	2e-05 (9.82e-05)	0.001 (0.00318)	0.461 (0.527)	0.594 (0.657)	0.393 (0.468)	0.189 (0.249)
del 16q24 2	12 (4%)	276	0.171 (0.23)	0.00306 (0.00772)	0.224 (0.289)	0.0953 (0.139)	0.00573 (0.0128)	0.0021 (0.00594)	0.513 (0.579)	0.313 (0.388)	0.0259 (0.0454)	0.172 (0.23)
del 19p13 3	23 (8%)	265	1e-05 (5.38e-05)	0.003 (0.00764)	0.891 (0.921)	0.81 (0.846)	0.00396 (0.0094)	0.00442 (0.0104)	0.123 (0.17)	0.195 (0.257)	0.156 (0.212)	0.106 (0.153)
amp 2q32 1	53 (18%)	235	1e-05 (5.38e-05)	2e-05 (9.82e-05)	0.837 (0.871)	0.116 (0.163)	0.143 (0.196)	0.937 (0.965)	0.0342 (0.0569)	0.351 (0.43)	1 (1.00)	0.307 (0.382)
del 2p12	8 (3%)	280	0.265 (0.336)	0.00188 (0.00537)	0.17 (0.23)	0.671 (0.728)	0.0374 (0.0615)	0.11 (0.157)	0.00944 (0.0193)	0.27 (0.34)	0.697 (0.748)	1 (1.00)
del 5p15 33	13 (5%)	275	0.0925 (0.136)	0.00667 (0.0144)	0.68 (0.735)	0.0783 (0.118)	0.0152 (0.0285)	0.00089 (0.0029)	0.367 (0.444)	0.227 (0.292)	0.34 (0.418)	0.577 (0.641)

'amp_2p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S1. Gene #1: 'amp_2p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
AMP PEAK 1(2P23.2) MUTATED	5	3	28	9
AMP PEAK 1(2P23.2) WILD-TYPE	101	70	21	51

Figure S1. Get High-res Image Gene #1: 'amp_2p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p23.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S2. Gene #1: 'amp_2p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
AMP PEAK 1(2P23.2) MUTATED	5	2	2	19	5	9
AMP PEAK 1(2P23.2) WILD-TYPE	51	40	57	38	24	20

Figure S2. Get High-res Image Gene #1: 'amp_2p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0487 (Fisher's exact test), Q value = 0.077

Table S3. Gene #1: 'amp_2p23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
AMP PEAK 1(2P23.2) MUTATED	7	8	15	2
AMP PEAK 1(2P23.2) WILD-TYPE	32	58	50	41

Figure S3. Get High-res Image Gene #1: 'amp_2p23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_2p23.2' versus 'MIRSEQ_CNMF'

P value = 0.0317 (Fisher's exact test), Q value = 0.054

Table S4. Gene #1: 'amp_2p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
AMP PEAK 1(2P23.2) MUTATED	3	1	17	9	11	4
AMP PEAK 1(2P23.2) WILD-TYPE	26	36	49	34	69	29

Figure S4. Get High-res Image Gene #1: 'amp_2p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_2q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S5. Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
AMP PEAK 2(2Q32.1) MUTATED	9	4	30	10
AMP PEAK 2(2Q32.1) WILD-TYPE	97	69	19	50

Figure S5. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q32.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S6. Gene #2: 'amp_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
AMP PEAK 2(2Q32.1) MUTATED	6	5	2	22	7	8
AMP PEAK 2(2Q32.1) WILD-TYPE	50	37	57	35	22	21

Figure S6. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q32.1' versus 'MIRSEQ_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.057

Table S7. Gene #2: 'amp_2q32.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
AMP PEAK 2(2Q32.1) MUTATED	4	2	17	13	13	4
AMP PEAK 2(2Q32.1) WILD-TYPE	25	35	49	30	67	29

Figure S7. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S8. Gene #3: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
AMP PEAK 3(3Q26.31) MUTATED	25	27	37	12
AMP PEAK 3(3Q26.31) WILD-TYPE	81	46	12	48

Figure S8. Get High-res Image Gene #3: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S9. Gene #3: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
AMP PEAK 3(3Q26.31) MUTATED	20	9	15	38	7	6
AMP PEAK 3(3Q26.31) WILD-TYPE	36	33	44	19	22	23

Figure S9. Get High-res Image Gene #3: 'amp_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00151 (Fisher's exact test), Q value = 0.0045

Table S10. Gene #3: 'amp_3q26.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
AMP PEAK 3(3Q26.31) MUTATED	23	24	16	10
AMP PEAK 3(3Q26.31) WILD-TYPE	16	42	49	33

Figure S10. Get High-res Image Gene #3: 'amp_3q26.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3q26.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S11. Gene #3: 'amp_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
AMP PEAK 3(3Q26.31) MUTATED	22	36	28	7	8
AMP PEAK 3(3Q26.31) WILD-TYPE	10	54	42	25	56

Figure S11. Get High-res Image Gene #3: 'amp_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.024

Table S12. Gene #3: 'amp_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
AMP PEAK 3(3Q26.31) MUTATED	37	54	10
AMP PEAK 3(3Q26.31) WILD-TYPE	81	69	37

Figure S12. Get High-res Image Gene #3: 'amp_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.0069

Table S13. Gene #3: 'amp_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
AMP PEAK 3(3Q26.31) MUTATED	11	12	33	7	22	16
AMP PEAK 3(3Q26.31) WILD-TYPE	18	25	33	36	58	17

Figure S13. Get High-res Image Gene #3: 'amp_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00344 (Fisher's exact test), Q value = 0.0084

Table S14. Gene #3: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
AMP PEAK 3(3Q26.31) MUTATED	41	39	21
AMP PEAK 3(3Q26.31) WILD-TYPE	79	41	67

Figure S14. Get High-res Image Gene #3: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00484 (Fisher's exact test), Q value = 0.011

Table S15. Gene #3: 'amp_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
AMP PEAK 3(3Q26.31) MUTATED	41	25	6
AMP PEAK 3(3Q26.31) WILD-TYPE	51	74	25

Figure S15. Get High-res Image Gene #3: 'amp_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.3' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00036

Table S16. Gene #4: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
AMP PEAK 4(5Q35.3) MUTATED	16	1	4	16
AMP PEAK 4(5Q35.3) WILD-TYPE	90	72	45	44

Figure S16. Get High-res Image Gene #4: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.001

Table S17. Gene #4: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
AMP PEAK 4(5Q35.3) MUTATED	10	5	2	2	10	5
AMP PEAK 4(5Q35.3) WILD-TYPE	46	37	57	55	19	24

Figure S17. Get High-res Image Gene #4: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0043

Table S18. Gene #4: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
AMP PEAK 4(5Q35.3) MUTATED	5	4	12	1	15
AMP PEAK 4(5Q35.3) WILD-TYPE	27	86	58	31	49

Figure S18. Get High-res Image Gene #4: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S19. Gene #4: 'amp_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
AMP PEAK 4(5Q35.3) MUTATED	29	4	4
AMP PEAK 4(5Q35.3) WILD-TYPE	89	119	43

Figure S19. Get High-res Image Gene #4: 'amp_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.067

Table S20. Gene #4: 'amp_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
AMP PEAK 4(5Q35.3) MUTATED	22	5	10
AMP PEAK 4(5Q35.3) WILD-TYPE	98	75	78

Figure S20. Get High-res Image Gene #4: 'amp_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S21. Gene #5: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
AMP PEAK 5(7P11.2) MUTATED	30	71	38	36
AMP PEAK 5(7P11.2) WILD-TYPE	76	2	11	24

Figure S21. Get High-res Image Gene #5: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S22. Gene #5: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
AMP PEAK 5(7P11.2) MUTATED	28	21	47	50	7	11
AMP PEAK 5(7P11.2) WILD-TYPE	28	21	12	7	22	18

Figure S22. Get High-res Image Gene #5: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.023

Table S23. Gene #5: 'amp_7p11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
AMP PEAK 5(7P11.2) MUTATED	46	60	27
AMP PEAK 5(7P11.2) WILD-TYPE	29	22	29

Figure S23. Get High-res Image Gene #5: 'amp_7p11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S24. Gene #5: 'amp_7p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
AMP PEAK 5(7P11.2) MUTATED	31	53	29	20
AMP PEAK 5(7P11.2) WILD-TYPE	8	13	36	23

Figure S24. Get High-res Image Gene #5: 'amp_7p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S25. Gene #5: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
AMP PEAK 5(7P11.2) MUTATED	28	79	39	13	16
AMP PEAK 5(7P11.2) WILD-TYPE	4	11	31	19	48

Figure S25. Get High-res Image Gene #5: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S26. Gene #5: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
AMP PEAK 5(7P11.2) MUTATED	55	104	16
AMP PEAK 5(7P11.2) WILD-TYPE	63	19	31

Figure S26. Get High-res Image Gene #5: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00033

Table S27. Gene #5: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
AMP PEAK 5(7P11.2) MUTATED	18	20	52	14	47	24
AMP PEAK 5(7P11.2) WILD-TYPE	11	17	14	29	33	9

Figure S27. Get High-res Image Gene #5: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0015

Table S28. Gene #5: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
AMP PEAK 5(7P11.2) MUTATED	66	63	46
AMP PEAK 5(7P11.2) WILD-TYPE	54	17	42

Figure S28. Get High-res Image Gene #5: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S29. Gene #5: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
AMP PEAK 5(7P11.2) MUTATED	33	61	38
AMP PEAK 5(7P11.2) WILD-TYPE	38	14	38

Figure S29. Get High-res Image Gene #5: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S30. Gene #5: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
AMP PEAK 5(7P11.2) MUTATED	61	44	27
AMP PEAK 5(7P11.2) WILD-TYPE	31	55	4

Figure S30. Get High-res Image Gene #5: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S31. Gene #6: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
AMP PEAK 6(7Q31.2) MUTATED	31	73	38	35
AMP PEAK 6(7Q31.2) WILD-TYPE	75	0	11	25

Figure S31. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S32. Gene #6: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
AMP PEAK 6(7Q31.2) MUTATED	28	21	48	50	7	12
AMP PEAK 6(7Q31.2) WILD-TYPE	28	21	11	7	22	17

Figure S32. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.037

Table S33. Gene #6: 'amp_7q31.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
AMP PEAK 6(7Q31.2) MUTATED	46	60	28
AMP PEAK 6(7Q31.2) WILD-TYPE	29	22	28

Figure S33. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S34. Gene #6: 'amp_7q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
AMP PEAK 6(7Q31.2) MUTATED	31	53	30	20
AMP PEAK 6(7Q31.2) WILD-TYPE	8	13	35	23

Figure S34. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S35. Gene #6: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
AMP PEAK 6(7Q31.2) MUTATED	28	80	39	13	17
AMP PEAK 6(7Q31.2) WILD-TYPE	4	10	31	19	47

Figure S35. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S36. Gene #6: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
AMP PEAK 6(7Q31.2) MUTATED	54	105	18
AMP PEAK 6(7Q31.2) WILD-TYPE	64	18	29

Figure S36. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0023

Table S37. Gene #6: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
AMP PEAK 6(7Q31.2) MUTATED	18	20	52	16	48	23
AMP PEAK 6(7Q31.2) WILD-TYPE	11	17	14	27	32	10

Figure S37. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.002

Table S38. Gene #6: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
AMP PEAK 6(7Q31.2) MUTATED	67	63	47
AMP PEAK 6(7Q31.2) WILD-TYPE	53	17	41

Figure S38. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S39. Gene #6: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
AMP PEAK 6(7Q31.2) MUTATED	33	62	38
AMP PEAK 6(7Q31.2) WILD-TYPE	38	13	38

Figure S39. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S40. Gene #6: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
AMP PEAK 6(7Q31.2) MUTATED	62	44	27
AMP PEAK 6(7Q31.2) WILD-TYPE	30	55	4

Figure S40. Get High-res Image Gene #6: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S41. Gene #7: 'amp_17q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
AMP PEAK 7(17Q23.2) MUTATED	31	71	44	53
AMP PEAK 7(17Q23.2) WILD-TYPE	75	2	5	7

Figure S41. Get High-res Image Gene #7: 'amp_17q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S42. Gene #7: 'amp_17q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
AMP PEAK 7(17Q23.2) MUTATED	32	24	49	54	14	14
AMP PEAK 7(17Q23.2) WILD-TYPE	24	18	10	3	15	15

Figure S42. Get High-res Image Gene #7: 'amp_17q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q23.2' versus 'RPPA_CNMF'

P value = 0.00346 (Fisher's exact test), Q value = 0.0084

Table S43. Gene #7: 'amp_17q23.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
AMP PEAK 7(17Q23.2) MUTATED	55	64	29
AMP PEAK 7(17Q23.2) WILD-TYPE	20	18	27

Figure S43. Get High-res Image Gene #7: 'amp_17q23.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_17q23.2' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00036

Table S44. Gene #7: 'amp_17q23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
AMP PEAK 7(17Q23.2) MUTATED	35	53	36	24
AMP PEAK 7(17Q23.2) WILD-TYPE	4	13	29	19

Figure S44. Get High-res Image Gene #7: 'amp_17q23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S45. Gene #7: 'amp_17q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
AMP PEAK 7(17Q23.2) MUTATED	28	82	43	14	32
AMP PEAK 7(17Q23.2) WILD-TYPE	4	8	27	18	32

Figure S45. Get High-res Image Gene #7: 'amp_17q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S46. Gene #7: 'amp_17q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
AMP PEAK 7(17Q23.2) MUTATED	72	109	18
AMP PEAK 7(17Q23.2) WILD-TYPE	46	14	29

Figure S46. Get High-res Image Gene #7: 'amp_17q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q23.2' versus 'MIRSEQ_CNMF'

P value = 0.00882 (Fisher's exact test), Q value = 0.018

Table S47. Gene #7: 'amp_17q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
AMP PEAK 7(17Q23.2) MUTATED	21	23	56	23	56	20
AMP PEAK 7(17Q23.2) WILD-TYPE	8	14	10	20	24	13

Figure S47. Get High-res Image Gene #7: 'amp_17q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00773 (Fisher's exact test), Q value = 0.016

Table S48. Gene #7: 'amp_17q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
AMP PEAK 7(17Q23.2) MUTATED	76	66	57
AMP PEAK 7(17Q23.2) WILD-TYPE	44	14	31

Figure S48. Get High-res Image Gene #7: 'amp_17q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00076

Table S49. Gene #7: 'amp_17q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
AMP PEAK 7(17Q23.2) MUTATED	44	64	43
AMP PEAK 7(17Q23.2) WILD-TYPE	27	11	33

Figure S49. Get High-res Image Gene #7: 'amp_17q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0013

Table S50. Gene #7: 'amp_17q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
AMP PEAK 7(17Q23.2) MUTATED	68	55	28
AMP PEAK 7(17Q23.2) WILD-TYPE	24	44	3

Figure S50. Get High-res Image Gene #7: 'amp_17q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S51. Gene #8: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 1(1P36.31) MUTATED	24	1	10	19
DEL PEAK 1(1P36.31) WILD-TYPE	82	72	39	41

Figure S51. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S52. Gene #8: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 1(1P36.31) MUTATED	12	2	1	5	19	12
DEL PEAK 1(1P36.31) WILD-TYPE	44	40	58	52	10	17

Figure S52. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S53. Gene #8: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 1(1P36.31) MUTATED	1	4	9	5	35
DEL PEAK 1(1P36.31) WILD-TYPE	31	86	61	27	29

Figure S53. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S54. Gene #8: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 1(1P36.31) MUTATED	28	7	19
DEL PEAK 1(1P36.31) WILD-TYPE	90	116	28

Figure S54. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CNMF'

P value = 0.00489 (Fisher's exact test), Q value = 0.011

Table S55. Gene #8: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
DEL PEAK 1(1P36.31) MUTATED	5	10	6	16	14	3
DEL PEAK 1(1P36.31) WILD-TYPE	24	27	60	27	66	30

Figure S55. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0027 (Fisher's exact test), Q value = 0.007

Table S56. Gene #8: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
DEL PEAK 1(1P36.31) MUTATED	15	24	0
DEL PEAK 1(1P36.31) WILD-TYPE	77	75	31

Figure S56. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2p12' versus 'METHLYATION_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.0054

Table S57. Gene #9: 'del_2p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 2(2P12) MUTATED	1	1	1	0	5	0
DEL PEAK 2(2P12) WILD-TYPE	55	41	58	57	24	29

Figure S57. Get High-res Image Gene #9: 'del_2p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p12' versus 'MRNASEQ_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.062

Table S58. Gene #9: 'del_2p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 2(2P12) MUTATED	0	0	2	1	5
DEL PEAK 2(2P12) WILD-TYPE	32	90	68	31	59

Figure S58. Get High-res Image Gene #9: 'del_2p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2p12' versus 'MIRSEQ_CNMF'

P value = 0.00944 (Fisher's exact test), Q value = 0.019

Table S59. Gene #9: 'del_2p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
DEL PEAK 2(2P12) MUTATED	1	2	0	4	0	1
DEL PEAK 2(2P12) WILD-TYPE	28	35	66	39	80	32

Figure S59. Get High-res Image Gene #9: 'del_2p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.059

Table S60. Gene #10: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 3(2Q22.1) MUTATED	6	0	0	4
DEL PEAK 3(2Q22.1) WILD-TYPE	100	73	49	56

Figure S60. Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.0045

Table S61. Gene #10: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 3(2Q22.1) MUTATED	4	0	0	0	4	1
DEL PEAK 3(2Q22.1) WILD-TYPE	52	42	59	57	25	28

Figure S61. Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CNMF'

P value = 0.00622 (Fisher's exact test), Q value = 0.014

Table S62. Gene #10: 'del_2q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
DEL PEAK 3(2Q22.1) MUTATED	2	0	5
DEL PEAK 3(2Q22.1) WILD-TYPE	73	82	51

Figure S62. Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S63. Gene #10: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 3(2Q22.1) MUTATED	0	0	1	0	9
DEL PEAK 3(2Q22.1) WILD-TYPE	32	90	69	32	55

Figure S63. Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00729 (Fisher's exact test), Q value = 0.015

Table S64. Gene #10: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 3(2Q22.1) MUTATED	7	0	3
DEL PEAK 3(2Q22.1) WILD-TYPE	111	123	44

Figure S64. Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.026

Table S65. Gene #10: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
DEL PEAK 3(2Q22.1) MUTATED	4	2	0	2	1	1
DEL PEAK 3(2Q22.1) WILD-TYPE	25	35	66	41	79	32

Figure S65. Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 0.00816 (Fisher's exact test), Q value = 0.017

Table S66. Gene #11: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 4(2Q37.3) MUTATED	10	0	1	1
DEL PEAK 4(2Q37.3) WILD-TYPE	96	73	48	59

Figure S66. Get High-res Image Gene #11: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.0045

Table S67. Gene #11: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 4(2Q37.3) MUTATED	2	2	0	0	5	1
DEL PEAK 4(2Q37.3) WILD-TYPE	54	40	59	57	24	28

Figure S67. Get High-res Image Gene #11: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0019

Table S68. Gene #11: 'del_2q37.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
DEL PEAK 4(2Q37.3) MUTATED	0	1	7
DEL PEAK 4(2Q37.3) WILD-TYPE	75	81	49

Figure S68. Get High-res Image Gene #11: 'del_2q37.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.043

Table S69. Gene #11: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 4(2Q37.3) MUTATED	1	0	4	1	6
DEL PEAK 4(2Q37.3) WILD-TYPE	31	90	66	31	58

Figure S69. Get High-res Image Gene #11: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00241 (Fisher's exact test), Q value = 0.0067

Table S70. Gene #11: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 4(2Q37.3) MUTATED	9	0	3
DEL PEAK 4(2Q37.3) WILD-TYPE	109	123	44

Figure S70. Get High-res Image Gene #11: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.032

Table S71. Gene #11: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
DEL PEAK 4(2Q37.3) MUTATED	4	3	0	2	3	0
DEL PEAK 4(2Q37.3) WILD-TYPE	25	34	66	41	77	33

Figure S71. Get High-res Image Gene #11: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S72. Gene #12: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 5(3P22.1) MUTATED	9	0	1	15
DEL PEAK 5(3P22.1) WILD-TYPE	97	73	48	45

Figure S72. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S73. Gene #12: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 5(3P22.1) MUTATED	5	4	0	0	11	4
DEL PEAK 5(3P22.1) WILD-TYPE	51	38	59	57	18	25

Figure S73. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.051

Table S74. Gene #12: 'del_3p22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 5(3P22.1) MUTATED	3	4	12	1
DEL PEAK 5(3P22.1) WILD-TYPE	36	62	53	42

Figure S74. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3p22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S75. Gene #12: 'del_3p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 5(3P22.1) MUTATED	0	0	6	1	18
DEL PEAK 5(3P22.1) WILD-TYPE	32	90	64	31	46

Figure S75. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S76. Gene #12: 'del_3p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 5(3P22.1) MUTATED	21	0	4
DEL PEAK 5(3P22.1) WILD-TYPE	97	123	43

Figure S76. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.1' versus 'MIRSEQ_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.028

Table S77. Gene #12: 'del_3p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
DEL PEAK 5(3P22.1) MUTATED	1	4	1	9	8	2
DEL PEAK 5(3P22.1) WILD-TYPE	28	33	65	34	72	31

Figure S77. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.072

Table S78. Gene #12: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
DEL PEAK 5(3P22.1) MUTATED	13	2	10
DEL PEAK 5(3P22.1) WILD-TYPE	107	78	78

Figure S78. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00266 (Fisher's exact test), Q value = 0.007

Table S79. Gene #12: 'del_3p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
DEL PEAK 5(3P22.1) MUTATED	6	18	0
DEL PEAK 5(3P22.1) WILD-TYPE	86	81	31

Figure S79. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0036

Table S80. Gene #13: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 6(4Q34.3) MUTATED	11	1	7	13
DEL PEAK 6(4Q34.3) WILD-TYPE	95	72	42	47

Figure S80. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S81. Gene #13: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 6(4Q34.3) MUTATED	4	5	0	2	8	11
DEL PEAK 6(4Q34.3) WILD-TYPE	52	37	59	55	21	18

Figure S81. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.025

Table S82. Gene #13: 'del_4q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 6(4Q34.3) MUTATED	2	4	15	4
DEL PEAK 6(4Q34.3) WILD-TYPE	37	62	50	39

Figure S82. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S83. Gene #13: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 6(4Q34.3) MUTATED	0	1	7	4	20
DEL PEAK 6(4Q34.3) WILD-TYPE	32	89	63	28	44

Figure S83. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S84. Gene #13: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 6(4Q34.3) MUTATED	18	2	12
DEL PEAK 6(4Q34.3) WILD-TYPE	100	121	35

Figure S84. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.047

Table S85. Gene #13: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
DEL PEAK 6(4Q34.3) MUTATED	11	3	12
DEL PEAK 6(4Q34.3) WILD-TYPE	60	72	64

Figure S85. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00347 (Fisher's exact test), Q value = 0.0084

Table S86. Gene #13: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
DEL PEAK 6(4Q34.3) MUTATED	7	19	0
DEL PEAK 6(4Q34.3) WILD-TYPE	85	80	31

Figure S86. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.00667 (Fisher's exact test), Q value = 0.014

Table S87. Gene #14: 'del_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 7(5P15.33) MUTATED	1	1	1	2	2	6
DEL PEAK 7(5P15.33) WILD-TYPE	55	41	58	55	27	23

Figure S87. Get High-res Image Gene #14: 'del_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.029

Table S88. Gene #14: 'del_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 7(5P15.33) MUTATED	0	1	4	5	3
DEL PEAK 7(5P15.33) WILD-TYPE	32	89	66	27	61

Figure S88. Get High-res Image Gene #14: 'del_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0029

Table S89. Gene #14: 'del_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 7(5P15.33) MUTATED	5	1	7
DEL PEAK 7(5P15.33) WILD-TYPE	113	122	40

Figure S89. Get High-res Image Gene #14: 'del_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q35.2' versus 'CN_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.066

Table S90. Gene #15: 'del_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 8(5Q35.2) MUTATED	6	0	4	1
DEL PEAK 8(5Q35.2) WILD-TYPE	100	73	45	59

Figure S90. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S91. Gene #15: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 8(5Q35.2) MUTATED	1	1	0	0	0	8
DEL PEAK 8(5Q35.2) WILD-TYPE	55	41	59	57	29	21

Figure S91. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q35.2' versus 'RPPA_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.056

Table S92. Gene #15: 'del_5q35.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
DEL PEAK 8(5Q35.2) MUTATED	5	0	3
DEL PEAK 8(5Q35.2) WILD-TYPE	70	82	53

Figure S92. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q35.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00078

Table S93. Gene #15: 'del_5q35.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 8(5Q35.2) MUTATED	0	0	8	0
DEL PEAK 8(5Q35.2) WILD-TYPE	39	66	57	43

Figure S93. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_5q35.2' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00099

Table S94. Gene #15: 'del_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 8(5Q35.2) MUTATED	0	0	1	5	5
DEL PEAK 8(5Q35.2) WILD-TYPE	32	90	69	27	59

Figure S94. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S95. Gene #15: 'del_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 8(5Q35.2) MUTATED	3	0	8
DEL PEAK 8(5Q35.2) WILD-TYPE	115	123	39

Figure S95. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0025

Table S96. Gene #15: 'del_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
DEL PEAK 8(5Q35.2) MUTATED	2	0	9
DEL PEAK 8(5Q35.2) WILD-TYPE	118	80	79

Figure S96. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q35.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.008

Table S97. Gene #15: 'del_5q35.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
DEL PEAK 8(5Q35.2) MUTATED	2	0	8
DEL PEAK 8(5Q35.2) WILD-TYPE	69	75	68

Figure S97. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.033

Table S98. Gene #15: 'del_5q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
DEL PEAK 8(5Q35.2) MUTATED	1	9	0
DEL PEAK 8(5Q35.2) WILD-TYPE	91	90	31

Figure S98. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p12.3' versus 'CN_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.028

Table S99. Gene #16: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 9(6P12.3) MUTATED	7	2	8	9
DEL PEAK 9(6P12.3) WILD-TYPE	99	71	41	51

Figure S99. Get High-res Image Gene #16: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p12.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S100. Gene #16: 'del_6p12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 9(6P12.3) MUTATED	4	2	0	2	8	9
DEL PEAK 9(6P12.3) WILD-TYPE	52	40	59	55	21	20

Figure S100. Get High-res Image Gene #16: 'del_6p12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p12.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S101. Gene #16: 'del_6p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 9(6P12.3) MUTATED	0	3	5	1	17
DEL PEAK 9(6P12.3) WILD-TYPE	32	87	65	31	47

Figure S101. Get High-res Image Gene #16: 'del_6p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.0032

Table S102. Gene #16: 'del_6p12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 9(6P12.3) MUTATED	12	4	10
DEL PEAK 9(6P12.3) WILD-TYPE	106	119	37

Figure S102. Get High-res Image Gene #16: 'del_6p12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q25.3' versus 'CN_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.024

Table S103. Gene #17: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 10(6Q25.3) MUTATED	11	2	8	11
DEL PEAK 10(6Q25.3) WILD-TYPE	95	71	41	49

Figure S103. Get High-res Image Gene #17: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q25.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S104. Gene #17: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 10(6Q25.3) MUTATED	6	2	0	2	11	10
DEL PEAK 10(6Q25.3) WILD-TYPE	50	40	59	55	18	19

Figure S104. Get High-res Image Gene #17: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.034

Table S105. Gene #17: 'del_6q25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 10(6Q25.3) MUTATED	4	5	15	2
DEL PEAK 10(6Q25.3) WILD-TYPE	35	61	50	41

Figure S105. Get High-res Image Gene #17: 'del_6q25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6q25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S106. Gene #17: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 10(6Q25.3) MUTATED	0	2	6	2	22
DEL PEAK 10(6Q25.3) WILD-TYPE	32	88	64	30	42

Figure S106. Get High-res Image Gene #17: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S107. Gene #17: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 10(6Q25.3) MUTATED	17	3	12
DEL PEAK 10(6Q25.3) WILD-TYPE	101	120	35

Figure S107. Get High-res Image Gene #17: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q25.3' versus 'MIRSEQ_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.048

Table S108. Gene #17: 'del_6q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
DEL PEAK 10(6Q25.3) MUTATED	4	5	5	10	8	0
DEL PEAK 10(6Q25.3) WILD-TYPE	25	32	61	33	72	33

Figure S108. Get High-res Image Gene #17: 'del_6q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.007

Table S109. Gene #18: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 11(9P21.3) MUTATED	19	3	4	14
DEL PEAK 11(9P21.3) WILD-TYPE	87	70	45	46

Figure S109. Get High-res Image Gene #18: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S110. Gene #18: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 11(9P21.3) MUTATED	8	3	1	1	9	15
DEL PEAK 11(9P21.3) WILD-TYPE	48	39	58	56	20	14

Figure S110. Get High-res Image Gene #18: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.0035

Table S111. Gene #18: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 11(9P21.3) MUTATED	3	5	19	3
DEL PEAK 11(9P21.3) WILD-TYPE	36	61	46	40

Figure S111. Get High-res Image Gene #18: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S112. Gene #18: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 11(9P21.3) MUTATED	1	1	5	5	28
DEL PEAK 11(9P21.3) WILD-TYPE	31	89	65	27	36

Figure S112. Get High-res Image Gene #18: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S113. Gene #18: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 11(9P21.3) MUTATED	20	0	20
DEL PEAK 11(9P21.3) WILD-TYPE	98	123	27

Figure S113. Get High-res Image Gene #18: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.025

Table S114. Gene #18: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
DEL PEAK 11(9P21.3) MUTATED	4	4	4	11	16	1
DEL PEAK 11(9P21.3) WILD-TYPE	25	33	62	32	64	32

Figure S114. Get High-res Image Gene #18: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.025

Table S115. Gene #18: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
DEL PEAK 11(9P21.3) MUTATED	10	10	20
DEL PEAK 11(9P21.3) WILD-TYPE	110	70	68

Figure S115. Get High-res Image Gene #18: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0035

Table S116. Gene #18: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
DEL PEAK 11(9P21.3) MUTATED	9	4	20
DEL PEAK 11(9P21.3) WILD-TYPE	62	71	56

Figure S116. Get High-res Image Gene #18: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00025

Table S117. Gene #18: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
DEL PEAK 11(9P21.3) MUTATED	7	26	0
DEL PEAK 11(9P21.3) WILD-TYPE	85	73	31

Figure S117. Get High-res Image Gene #18: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00061

Table S118. Gene #19: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 12(10Q21.1) MUTATED	2	3	0	2	7	5
DEL PEAK 12(10Q21.1) WILD-TYPE	54	39	59	55	22	24

Figure S118. Get High-res Image Gene #19: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.068

Table S119. Gene #19: 'del_10q21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 12(10Q21.1) MUTATED	1	4	10	1
DEL PEAK 12(10Q21.1) WILD-TYPE	38	62	55	42

Figure S119. Get High-res Image Gene #19: 'del_10q21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S120. Gene #19: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 12(10Q21.1) MUTATED	0	0	5	1	13
DEL PEAK 12(10Q21.1) WILD-TYPE	32	90	65	31	51

Figure S120. Get High-res Image Gene #19: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0029

Table S121. Gene #19: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 12(10Q21.1) MUTATED	13	1	5
DEL PEAK 12(10Q21.1) WILD-TYPE	105	122	42

Figure S121. Get High-res Image Gene #19: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q21.1' versus 'MIRSEQ_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.041

Table S122. Gene #19: 'del_10q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
DEL PEAK 12(10Q21.1) MUTATED	2	4	0	6	6	1
DEL PEAK 12(10Q21.1) WILD-TYPE	27	33	66	37	74	32

Figure S122. Get High-res Image Gene #19: 'del_10q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 0.071

Table S123. Gene #19: 'del_10q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
DEL PEAK 12(10Q21.1) MUTATED	5	1	8
DEL PEAK 12(10Q21.1) WILD-TYPE	66	74	68

Figure S123. Get High-res Image Gene #19: 'del_10q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00733 (Fisher's exact test), Q value = 0.015

Table S124. Gene #19: 'del_10q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
DEL PEAK 12(10Q21.1) MUTATED	2	12	0
DEL PEAK 12(10Q21.1) WILD-TYPE	90	87	31

Figure S124. Get High-res Image Gene #19: 'del_10q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q22.3' versus 'METHLYATION_CNMF'

P value = 0.00472 (Fisher's exact test), Q value = 0.011

Table S125. Gene #20: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 13(11Q22.3) MUTATED	7	3	2	4	9	5
DEL PEAK 13(11Q22.3) WILD-TYPE	49	39	57	53	20	24

Figure S125. Get High-res Image Gene #20: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q22.3' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S126. Gene #20: 'del_11q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 13(11Q22.3) MUTATED	1	3	6	3	18
DEL PEAK 13(11Q22.3) WILD-TYPE	31	87	64	29	46

Figure S126. Get High-res Image Gene #20: 'del_11q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.0067

Table S127. Gene #20: 'del_11q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 13(11Q22.3) MUTATED	17	5	9
DEL PEAK 13(11Q22.3) WILD-TYPE	101	118	38

Figure S127. Get High-res Image Gene #20: 'del_11q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00672 (Fisher's exact test), Q value = 0.014

Table S128. Gene #20: 'del_11q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
DEL PEAK 13(11Q22.3) MUTATED	6	3	15
DEL PEAK 13(11Q22.3) WILD-TYPE	65	72	61

Figure S128. Get High-res Image Gene #20: 'del_11q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00271 (Fisher's exact test), Q value = 0.007

Table S129. Gene #20: 'del_11q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
DEL PEAK 13(11Q22.3) MUTATED	6	18	0
DEL PEAK 13(11Q22.3) WILD-TYPE	86	81	31

Figure S129. Get High-res Image Gene #20: 'del_11q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.3' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0016

Table S130. Gene #21: 'del_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 14(11Q23.3) MUTATED	6	3	1	3	9	6
DEL PEAK 14(11Q23.3) WILD-TYPE	50	39	58	54	20	23

Figure S130. Get High-res Image Gene #21: 'del_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.067

Table S131. Gene #21: 'del_11q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 14(11Q23.3) MUTATED	3	3	13	4
DEL PEAK 14(11Q23.3) WILD-TYPE	36	63	52	39

Figure S131. Get High-res Image Gene #21: 'del_11q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q23.3' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00039

Table S132. Gene #21: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 14(11Q23.3) MUTATED	1	2	6	3	17
DEL PEAK 14(11Q23.3) WILD-TYPE	31	88	64	29	47

Figure S132. Get High-res Image Gene #21: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0046

Table S133. Gene #21: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 14(11Q23.3) MUTATED	17	4	8
DEL PEAK 14(11Q23.3) WILD-TYPE	101	119	39

Figure S133. Get High-res Image Gene #21: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.054

Table S134. Gene #21: 'del_11q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
DEL PEAK 14(11Q23.3) MUTATED	2	2	3	9	12	1
DEL PEAK 14(11Q23.3) WILD-TYPE	27	35	63	34	68	32

Figure S134. Get High-res Image Gene #21: 'del_11q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.028

Table S135. Gene #21: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
DEL PEAK 14(11Q23.3) MUTATED	6	3	14
DEL PEAK 14(11Q23.3) WILD-TYPE	65	72	62

Figure S135. Get High-res Image Gene #21: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00573 (Fisher's exact test), Q value = 0.013

Table S136. Gene #21: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
DEL PEAK 14(11Q23.3) MUTATED	6	17	0
DEL PEAK 14(11Q23.3) WILD-TYPE	86	82	31

Figure S136. Get High-res Image Gene #21: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00061

Table S137. Gene #22: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 15(14Q11.2) MUTATED	23	2	10	16
DEL PEAK 15(14Q11.2) WILD-TYPE	83	71	39	44

Figure S137. Get High-res Image Gene #22: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.0036

Table S138. Gene #22: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 15(14Q11.2) MUTATED	13	5	4	5	8	11
DEL PEAK 15(14Q11.2) WILD-TYPE	43	37	55	52	21	18

Figure S138. Get High-res Image Gene #22: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00447 (Fisher's exact test), Q value = 0.01

Table S139. Gene #22: 'del_14q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 15(14Q11.2) MUTATED	6	7	20	3
DEL PEAK 15(14Q11.2) WILD-TYPE	33	59	45	40

Figure S139. Get High-res Image Gene #22: 'del_14q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S140. Gene #22: 'del_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 15(14Q11.2) MUTATED	4	4	11	6	26
DEL PEAK 15(14Q11.2) WILD-TYPE	28	86	59	26	38

Figure S140. Get High-res Image Gene #22: 'del_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S141. Gene #22: 'del_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 15(14Q11.2) MUTATED	24	8	19
DEL PEAK 15(14Q11.2) WILD-TYPE	94	115	28

Figure S141. Get High-res Image Gene #22: 'del_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.028

Table S142. Gene #22: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
DEL PEAK 15(14Q11.2) MUTATED	11	25	2
DEL PEAK 15(14Q11.2) WILD-TYPE	81	74	29

Figure S142. Get High-res Image Gene #22: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S143. Gene #23: 'del_14q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 16(14Q24.2) MUTATED	23	1	8	18
DEL PEAK 16(14Q24.2) WILD-TYPE	83	72	41	42

Figure S143. Get High-res Image Gene #23: 'del_14q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00018

Table S144. Gene #23: 'del_14q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 16(14Q24.2) MUTATED	15	4	3	4	9	11
DEL PEAK 16(14Q24.2) WILD-TYPE	41	38	56	53	20	18

Figure S144. Get High-res Image Gene #23: 'del_14q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q24.2' versus 'RPPA_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.042

Table S145. Gene #23: 'del_14q24.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
DEL PEAK 16(14Q24.2) MUTATED	20	9	7
DEL PEAK 16(14Q24.2) WILD-TYPE	55	73	49

Figure S145. Get High-res Image Gene #23: 'del_14q24.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_14q24.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00271 (Fisher's exact test), Q value = 0.007

Table S146. Gene #23: 'del_14q24.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 16(14Q24.2) MUTATED	7	6	20	3
DEL PEAK 16(14Q24.2) WILD-TYPE	32	60	45	40

Figure S146. Get High-res Image Gene #23: 'del_14q24.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_14q24.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S147. Gene #23: 'del_14q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 16(14Q24.2) MUTATED	4	3	9	7	27
DEL PEAK 16(14Q24.2) WILD-TYPE	28	87	61	25	37

Figure S147. Get High-res Image Gene #23: 'del_14q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S148. Gene #23: 'del_14q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 16(14Q24.2) MUTATED	24	7	19
DEL PEAK 16(14Q24.2) WILD-TYPE	94	116	28

Figure S148. Get High-res Image Gene #23: 'del_14q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.2' versus 'MIRSEQ_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.043

Table S149. Gene #23: 'del_14q24.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
DEL PEAK 16(14Q24.2) MUTATED	2	5	7	14	18	4
DEL PEAK 16(14Q24.2) WILD-TYPE	27	32	59	29	62	29

Figure S149. Get High-res Image Gene #23: 'del_14q24.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.029

Table S150. Gene #23: 'del_14q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
DEL PEAK 16(14Q24.2) MUTATED	14	6	19
DEL PEAK 16(14Q24.2) WILD-TYPE	57	69	57

Figure S150. Get High-res Image Gene #23: 'del_14q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00357 (Fisher's exact test), Q value = 0.0085

Table S151. Gene #23: 'del_14q24.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
DEL PEAK 16(14Q24.2) MUTATED	12	26	1
DEL PEAK 16(14Q24.2) WILD-TYPE	80	73	30

Figure S151. Get High-res Image Gene #23: 'del_14q24.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q13.3' versus 'CN_CNMF'

P value = 0.00282 (Fisher's exact test), Q value = 0.0072

Table S152. Gene #24: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 17(15Q13.3) MUTATED	14	2	5	14
DEL PEAK 17(15Q13.3) WILD-TYPE	92	71	44	46

Figure S152. Get High-res Image Gene #24: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q13.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S153. Gene #24: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 17(15Q13.3) MUTATED	10	3	1	3	5	11
DEL PEAK 17(15Q13.3) WILD-TYPE	46	39	58	54	24	18

Figure S153. Get High-res Image Gene #24: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.053

Table S154. Gene #24: 'del_15q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 17(15Q13.3) MUTATED	4	5	16	4
DEL PEAK 17(15Q13.3) WILD-TYPE	35	61	49	39

Figure S154. Get High-res Image Gene #24: 'del_15q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_15q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S155. Gene #24: 'del_15q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 17(15Q13.3) MUTATED	1	3	6	5	20
DEL PEAK 17(15Q13.3) WILD-TYPE	31	87	64	27	44

Figure S155. Get High-res Image Gene #24: 'del_15q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S156. Gene #24: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 17(15Q13.3) MUTATED	16	4	15
DEL PEAK 17(15Q13.3) WILD-TYPE	102	119	32

Figure S156. Get High-res Image Gene #24: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.032

Table S157. Gene #24: 'del_15q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
DEL PEAK 17(15Q13.3) MUTATED	11	18	0
DEL PEAK 17(15Q13.3) WILD-TYPE	81	81	31

Figure S157. Get High-res Image Gene #24: 'del_15q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.2' versus 'METHLYATION_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.0077

Table S158. Gene #25: 'del_16q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 18(16Q24.2) MUTATED	2	3	0	0	3	4
DEL PEAK 18(16Q24.2) WILD-TYPE	54	39	59	57	26	25

Figure S158. Get High-res Image Gene #25: 'del_16q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q24.2' versus 'MRNASEQ_CNMF'

P value = 0.00573 (Fisher's exact test), Q value = 0.013

Table S159. Gene #25: 'del_16q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 18(16Q24.2) MUTATED	0	0	4	1	7
DEL PEAK 18(16Q24.2) WILD-TYPE	32	90	66	31	57

Figure S159. Get High-res Image Gene #25: 'del_16q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0021 (Fisher's exact test), Q value = 0.0059

Table S160. Gene #25: 'del_16q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 18(16Q24.2) MUTATED	8	0	4
DEL PEAK 18(16Q24.2) WILD-TYPE	110	123	43

Figure S160. Get High-res Image Gene #25: 'del_16q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.045

Table S161. Gene #25: 'del_16q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
DEL PEAK 18(16Q24.2) MUTATED	6	0	5
DEL PEAK 18(16Q24.2) WILD-TYPE	65	75	71

Figure S161. Get High-res Image Gene #25: 'del_16q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S162. Gene #26: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 19(19P13.3) MUTATED	3	1	4	15
DEL PEAK 19(19P13.3) WILD-TYPE	103	72	45	45

Figure S162. Get High-res Image Gene #26: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.0076

Table S163. Gene #26: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 19(19P13.3) MUTATED	3	3	2	3	9	2
DEL PEAK 19(19P13.3) WILD-TYPE	53	39	57	54	20	27

Figure S163. Get High-res Image Gene #26: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00396 (Fisher's exact test), Q value = 0.0094

Table S164. Gene #26: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 19(19P13.3) MUTATED	0	2	9	2	10
DEL PEAK 19(19P13.3) WILD-TYPE	32	88	61	30	54

Figure S164. Get High-res Image Gene #26: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00442 (Fisher's exact test), Q value = 0.01

Table S165. Gene #26: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 19(19P13.3) MUTATED	17	4	2
DEL PEAK 19(19P13.3) WILD-TYPE	101	119	45

Figure S165. Get High-res Image Gene #26: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.42' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S166. Gene #27: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 20(19Q13.42) MUTATED	2	0	5	12
DEL PEAK 20(19Q13.42) WILD-TYPE	104	73	44	48

Figure S166. Get High-res Image Gene #27: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.42' versus 'METHLYATION_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0023

Table S167. Gene #27: 'del_19q13.42' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 20(19Q13.42) MUTATED	3	3	0	3	8	2
DEL PEAK 20(19Q13.42) WILD-TYPE	53	39	59	54	21	27

Figure S167. Get High-res Image Gene #27: 'del_19q13.42' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.42' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00033

Table S168. Gene #27: 'del_19q13.42' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 20(19Q13.42) MUTATED	0	0	5	2	12
DEL PEAK 20(19Q13.42) WILD-TYPE	32	90	65	30	52

Figure S168. Get High-res Image Gene #27: 'del_19q13.42' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00344 (Fisher's exact test), Q value = 0.0084

Table S169. Gene #27: 'del_19q13.42' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 20(19Q13.42) MUTATED	14	2	3
DEL PEAK 20(19Q13.42) WILD-TYPE	104	121	44

Figure S169. Get High-res Image Gene #27: 'del_19q13.42' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_CNMF'

P value = 0.00658 (Fisher's exact test), Q value = 0.014

Table S170. Gene #27: 'del_19q13.42' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
DEL PEAK 20(19Q13.42) MUTATED	0	6	1	5	7	0
DEL PEAK 20(19Q13.42) WILD-TYPE	29	31	65	38	73	33

Figure S170. Get High-res Image Gene #27: 'del_19q13.42' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q12.2' versus 'CN_CNMF'

P value = 0.00231 (Fisher's exact test), Q value = 0.0065

Table S171. Gene #28: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
DEL PEAK 21(22Q12.2) MUTATED	24	6	13	20
DEL PEAK 21(22Q12.2) WILD-TYPE	82	67	36	40

Figure S171. Get High-res Image Gene #28: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S172. Gene #28: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
DEL PEAK 21(22Q12.2) MUTATED	9	8	1	6	22	14
DEL PEAK 21(22Q12.2) WILD-TYPE	47	34	58	51	7	15

Figure S172. Get High-res Image Gene #28: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q12.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00637 (Fisher's exact test), Q value = 0.014

Table S173. Gene #28: 'del_22q12.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
DEL PEAK 21(22Q12.2) MUTATED	4	12	25	10
DEL PEAK 21(22Q12.2) WILD-TYPE	35	54	40	33

Figure S173. Get High-res Image Gene #28: 'del_22q12.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_22q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S174. Gene #28: 'del_22q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
DEL PEAK 21(22Q12.2) MUTATED	2	5	16	7	33
DEL PEAK 21(22Q12.2) WILD-TYPE	30	85	54	25	31

Figure S174. Get High-res Image Gene #28: 'del_22q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.4e-05

Table S175. Gene #28: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
DEL PEAK 21(22Q12.2) MUTATED	36	9	18
DEL PEAK 21(22Q12.2) WILD-TYPE	82	114	29

Figure S175. Get High-res Image Gene #28: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q12.2' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S176. Gene #28: 'del_22q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
DEL PEAK 21(22Q12.2) MUTATED	3	14	8	20	14	4
DEL PEAK 21(22Q12.2) WILD-TYPE	26	23	58	23	66	29

Figure S176. Get High-res Image Gene #28: 'del_22q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00646 (Fisher's exact test), Q value = 0.014

Table S177. Gene #28: 'del_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
DEL PEAK 21(22Q12.2) MUTATED	21	28	1
DEL PEAK 21(22Q12.2) WILD-TYPE	71	71	30

Figure S177. Get High-res Image Gene #28: 'del_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/22533930/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/22542911/KIRP-TP.transferedmergedcluster.txt
Number of patients = 288
Number of significantly focal cnvs = 28
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

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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