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

Kidney Renal Papillary Cell Carcinoma (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/C18G8JM3

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 31 focal events and 10 molecular subtypes across 288 patients, 100 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_2p23.2 cnv correlated to 'CN_CNMF'.
amp_2q32.1 cnv correlated to 'CN_CNMF'.
amp_3q27.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_5q35.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p36.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'MRNASEQ_CNMF'.
del_3p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q35.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p12.3 cnv correlated to 'CN_CNMF'.
del_6q22.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_6q25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_11q22.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_11q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_14q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_14q24.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_16q24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF'.
del_19q13.42 cnv correlated to 'CN_CNMF'.
del_22q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_xp11.4 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq28 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 31 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, 100 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 7q31 2	177 (61%)	111	1e-05 (0.0031)	1e-05 (0.0031)	0.0134 (1.00)	5e-05 (0.0121)	1e-05 (0.0031)	1e-05 (0.0031)	0.0508 (1.00)	1e-05 (0.0031)	3e-05 (0.00756)	1e-05 (0.0031)
del 9p21 3	40 (14%)	248	1e-05 (0.0031)	1e-05 (0.0031)	0.37 (1.00)	0.00073 (0.159)	1e-05 (0.0031)	1e-05 (0.0031)	0.00038 (0.0844)	0.0302 (1.00)	0.0001 (0.0233)	3e-05 (0.00756)
amp 17q25 2	201 (70%)	87	1e-05 (0.0031)	3e-05 (0.00756)	0.0804 (1.00)	0.00011 (0.0255)	1e-05 (0.0031)	1e-05 (0.0031)	0.0702 (1.00)	0.00103 (0.218)	0.00161 (0.328)	0.00105 (0.222)
del 4q34 3	32 (11%)	256	1e-05 (0.0031)	1e-05 (0.0031)	0.572 (1.00)	0.00593 (1.00)	1e-05 (0.0031)	5e-05 (0.0121)	0.423 (1.00)	0.367 (1.00)	0.00893 (1.00)	3e-05 (0.00756)
del xp11 4	34 (12%)	254	1e-05 (0.0031)	1e-05 (0.0031)	0.373 (1.00)	0.00274 (0.535)	1e-05 (0.0031)	2e-05 (0.00508)	0.704 (1.00)	0.264 (1.00)	0.00138 (0.286)	0.0004 (0.0884)
amp 3q27 1	100 (35%)	188	1e-05 (0.0031)	0.0576 (1.00)	0.256 (1.00)	0.0117 (1.00)	1e-05 (0.0031)	0.00085 (0.184)	0.0336 (1.00)	0.00019 (0.0431)	0.761 (1.00)	0.0174 (1.00)
amp 5q35 2	37 (13%)	251	1e-05 (0.0031)	0.00016 (0.0365)	0.256 (1.00)	0.321 (1.00)	0.00065 (0.142)	8e-05 (0.0188)	0.051 (1.00)	0.00537 (0.967)	0.41 (1.00)	0.0548 (1.00)
del 1p36 31	55 (19%)	233	1e-05 (0.0031)	6e-05 (0.0144)	0.662 (1.00)	0.0521 (1.00)	1e-05 (0.0031)	1e-05 (0.0031)	0.771 (1.00)	0.855 (1.00)	0.0244 (1.00)	0.00554 (0.988)
del 3p22 1	25 (9%)	263	1e-05 (0.0031)	1e-05 (0.0031)	0.472 (1.00)	0.00168 (0.339)	1e-05 (0.0031)	1e-05 (0.0031)	0.202 (1.00)	0.00572 (1.00)	0.0256 (1.00)	0.00446 (0.834)
del 5q35 2	11 (4%)	277	0.028 (1.00)	4e-05 (0.00984)	0.414 (1.00)	0.00632 (1.00)	6e-05 (0.0144)	6e-05 (0.0144)	0.00712 (1.00)	0.00301 (0.581)	0.00166 (0.337)	1e-05 (0.0031)
del 6q25 3	32 (11%)	256	1e-05 (0.0031)	0.00044 (0.0968)	0.857 (1.00)	0.104 (1.00)	1e-05 (0.0031)	6e-05 (0.0144)	0.342 (1.00)	0.743 (1.00)	0.0414 (1.00)	0.0653 (1.00)
del 10q21 1	19 (7%)	269	1e-05 (0.0031)	4e-05 (0.00984)	0.332 (1.00)	0.00408 (0.767)	8e-05 (0.0188)	0.00078 (0.169)	0.636 (1.00)	0.975 (1.00)	0.0374 (1.00)	0.00616 (1.00)
del 11q23 3	29 (10%)	259	1e-05 (0.0031)	0.00015 (0.0345)	0.418 (1.00)	0.192 (1.00)	6e-05 (0.0144)	0.00028 (0.0627)	0.323 (1.00)	0.333 (1.00)	0.00598 (1.00)	0.00513 (0.939)
del 15q13 3	35 (12%)	253	1e-05 (0.0031)	4e-05 (0.00984)	0.135 (1.00)	0.00947 (1.00)	1e-05 (0.0031)	1e-05 (0.0031)	0.0766 (1.00)	0.601 (1.00)	0.0409 (1.00)	0.0033 (0.634)
del 22q12 2	63 (22%)	225	1e-05 (0.0031)	1e-05 (0.0031)	0.742 (1.00)	0.00595 (1.00)	1e-05 (0.0031)	1e-05 (0.0031)	1 (1.00)	0.4 (1.00)	0.0379 (1.00)	0.00525 (0.95)
amp 19p13 2	31 (11%)	257	1e-05 (0.0031)	0.00816 (1.00)	0.00467 (0.864)	0.00448 (0.834)	0.0009 (0.193)	0.00096 (0.204)	0.122 (1.00)	0.564 (1.00)	0.0612 (1.00)	0.0078 (1.00)
del 6q22 31	29 (10%)	259	1e-05 (0.0031)	0.00755 (1.00)	0.96 (1.00)	0.0379 (1.00)	2e-05 (0.00508)	3e-05 (0.00756)	0.418 (1.00)	0.266 (1.00)	0.0138 (1.00)	0.0376 (1.00)
del 11q22 3	31 (11%)	257	1e-05 (0.0031)	0.00144 (0.297)	0.738 (1.00)	0.234 (1.00)	0.00015 (0.0345)	0.0002 (0.0452)	0.239 (1.00)	0.191 (1.00)	0.00281 (0.545)	0.0024 (0.475)
del 14q11 2	51 (18%)	237	1e-05 (0.0031)	0.0141 (1.00)	0.0777 (1.00)	0.00398 (0.752)	1e-05 (0.0031)	1e-05 (0.0031)	0.523 (1.00)	0.561 (1.00)	0.0238 (1.00)	0.0286 (1.00)
del 14q24 2	50 (17%)	238	1e-05 (0.0031)	0.00134 (0.279)	0.0384 (1.00)	0.00266 (0.524)	1e-05 (0.0031)	1e-05 (0.0031)	0.54 (1.00)	0.573 (1.00)	0.00657 (1.00)	0.0081 (1.00)
del 16q24 1	12 (4%)	276	0.00026 (0.0585)	4e-05 (0.00984)	0.307 (1.00)	0.548 (1.00)	0.00089 (0.191)	0.0183 (1.00)	1 (1.00)	0.054 (1.00)	0.0103 (1.00)	0.0499 (1.00)
del xq28	28 (10%)	260	1e-05 (0.0031)	0.00012 (0.0277)	0.903 (1.00)	0.078 (1.00)	1e-05 (0.0031)	0.0017 (0.342)	0.75 (1.00)	0.794 (1.00)	0.00725 (1.00)	0.00509 (0.937)
amp 2p23 2	45 (16%)	243	1e-05 (0.0031)	0.0109 (1.00)	0.804 (1.00)	0.051 (1.00)	0.66 (1.00)	0.0655 (1.00)	0.152 (1.00)	0.062 (1.00)	0.437 (1.00)	0.079 (1.00)
amp 2q32 1	53 (18%)	235	1e-05 (0.0031)	0.0645 (1.00)	0.811 (1.00)	0.0839 (1.00)	0.435 (1.00)	0.029 (1.00)	0.302 (1.00)	0.127 (1.00)	0.975 (1.00)	0.511 (1.00)
del 2q22 1	10 (3%)	278	0.0033 (0.634)	0.00552 (0.988)	0.541 (1.00)	0.313 (1.00)	0.00031 (0.0691)	0.0518 (1.00)	0.671 (1.00)	0.808 (1.00)	0.178 (1.00)	0.426 (1.00)
del 6p12 3	26 (9%)	262	1e-05 (0.0031)	0.00905 (1.00)	1 (1.00)	0.631 (1.00)	0.00133 (0.278)	0.00124 (0.26)	0.131 (1.00)	0.506 (1.00)	0.264 (1.00)	0.22 (1.00)
del 19p13 3	23 (8%)	265	1e-05 (0.0031)	0.0449 (1.00)	0.779 (1.00)	0.294 (1.00)	0.0376 (1.00)	0.00519 (0.945)	0.238 (1.00)	0.313 (1.00)	0.0873 (1.00)	0.0363 (1.00)
del 19q13 42	19 (7%)	269	3e-05 (0.00756)	0.0453 (1.00)	0.888 (1.00)	0.134 (1.00)	0.01 (1.00)	0.00273 (0.535)	0.398 (1.00)	0.304 (1.00)	0.229 (1.00)	0.346 (1.00)
del 2p12	8 (3%)	280	0.0844 (1.00)	0.122 (1.00)	0.129 (1.00)	0.103 (1.00)	0.25 (1.00)	0.238 (1.00)	0.176 (1.00)	0.283 (1.00)	0.694 (1.00)	1 (1.00)
del 2q37 3	12 (4%)	276	0.0947 (1.00)	0.00188 (0.376)	0.00727 (1.00)	0.0478 (1.00)	0.00706 (1.00)	0.0214 (1.00)	0.144 (1.00)	0.151 (1.00)	0.0455 (1.00)	0.235 (1.00)
del 5p15 33	13 (5%)	275	0.26 (1.00)	0.00233 (0.464)	0.854 (1.00)	0.0138 (1.00)	0.0198 (1.00)	0.00352 (0.669)	0.559 (1.00)	0.203 (1.00)	0.332 (1.00)	0.00159 (0.326)

'amp_2p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 1(2P23.2) MUTATED	2	3	14	26
AMP PEAK 1(2P23.2) WILD-TYPE	112	73	32	26

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

'amp_2q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S2. Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 2(2Q32.1) MUTATED	4	4	15	30
AMP PEAK 2(2Q32.1) WILD-TYPE	110	72	31	22

Figure S2. Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q27.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S3. Gene #3: 'amp_3q27.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 3(3Q27.1) MUTATED	20	17	45	18
AMP PEAK 3(3Q27.1) WILD-TYPE	94	59	1	34

Figure S3. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q27.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S4. Gene #3: 'amp_3q27.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
AMP PEAK 3(3Q27.1) MUTATED	39	48	13
AMP PEAK 3(3Q27.1) WILD-TYPE	39	66	82

Figure S4. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q27.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.18

Table S5. Gene #3: 'amp_3q27.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
AMP PEAK 3(3Q27.1) MUTATED	39	39	12	10
AMP PEAK 3(3Q27.1) WILD-TYPE	86	33	32	36

Figure S5. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q27.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.043

Table S6. Gene #3: 'amp_3q27.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	66	81	86
AMP PEAK 3(3Q27.1) MUTATED	20	18	43	19
AMP PEAK 3(3Q27.1) WILD-TYPE	35	48	38	67

Figure S6. Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S7. Gene #4: 'amp_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 4(5Q35.2) MUTATED	19	2	0	16
AMP PEAK 4(5Q35.2) WILD-TYPE	95	74	46	36

Figure S7. Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.2' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.036

Table S8. Gene #4: 'amp_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
AMP PEAK 4(5Q35.2) MUTATED	11	15	4
AMP PEAK 4(5Q35.2) WILD-TYPE	52	43	99

Figure S8. Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.2' versus 'MRNASEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.14

Table S9. Gene #4: 'amp_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
AMP PEAK 4(5Q35.2) MUTATED	12	5	20
AMP PEAK 4(5Q35.2) WILD-TYPE	66	109	75

Figure S9. Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S10. Gene #4: 'amp_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
AMP PEAK 4(5Q35.2) MUTATED	29	3	1	4
AMP PEAK 4(5Q35.2) WILD-TYPE	96	69	43	42

Figure S10. Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S11. Gene #5: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 5(7Q31.2) MUTATED	32	75	43	27
AMP PEAK 5(7Q31.2) WILD-TYPE	82	1	3	25

Figure S11. Get High-res Image Gene #5: '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 = 0.0031

Table S12. Gene #5: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
AMP PEAK 5(7Q31.2) MUTATED	34	19	85
AMP PEAK 5(7Q31.2) WILD-TYPE	29	39	18

Figure S12. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.012

Table S13. Gene #5: 'amp_7q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	17	22	29	22	27	39	25	25
AMP PEAK 5(7Q31.2) MUTATED	14	17	27	9	12	18	18	14
AMP PEAK 5(7Q31.2) WILD-TYPE	3	5	2	13	15	21	7	11

Figure S13. Get High-res Image Gene #5: '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 = 0.0031

Table S14. Gene #5: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
AMP PEAK 5(7Q31.2) MUTATED	50	97	29
AMP PEAK 5(7Q31.2) WILD-TYPE	28	17	66

Figure S14. Get High-res Image Gene #5: '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 = 0.0031

Table S15. Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
AMP PEAK 5(7Q31.2) MUTATED	59	68	32	17
AMP PEAK 5(7Q31.2) WILD-TYPE	66	4	12	29

Figure S15. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S16. Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	66	81	86
AMP PEAK 5(7Q31.2) MUTATED	23	41	67	46
AMP PEAK 5(7Q31.2) WILD-TYPE	32	25	14	40

Figure S16. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S17. Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	81	71
AMP PEAK 5(7Q31.2) MUTATED	33	64	35
AMP PEAK 5(7Q31.2) WILD-TYPE	36	17	36

Figure S17. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S18. Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
AMP PEAK 5(7Q31.2) MUTATED	67	35	4	26
AMP PEAK 5(7Q31.2) WILD-TYPE	31	42	12	4

Figure S18. Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S19. Gene #6: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 6(17Q25.2) MUTATED	43	76	45	37
AMP PEAK 6(17Q25.2) WILD-TYPE	71	0	1	15

Figure S19. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S20. Gene #6: 'amp_17q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
AMP PEAK 6(17Q25.2) MUTATED	38	34	89
AMP PEAK 6(17Q25.2) WILD-TYPE	25	24	14

Figure S20. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.026

Table S21. Gene #6: 'amp_17q25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	17	22	29	22	27	39	25	25
AMP PEAK 6(17Q25.2) MUTATED	15	20	26	11	13	23	21	17
AMP PEAK 6(17Q25.2) WILD-TYPE	2	2	3	11	14	16	4	8

Figure S21. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q25.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S22. Gene #6: 'amp_17q25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
AMP PEAK 6(17Q25.2) MUTATED	54	101	45
AMP PEAK 6(17Q25.2) WILD-TYPE	24	13	50

Figure S22. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S23. Gene #6: 'amp_17q25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
AMP PEAK 6(17Q25.2) MUTATED	79	68	35	18
AMP PEAK 6(17Q25.2) WILD-TYPE	46	4	9	28

Figure S23. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.22

Table S24. Gene #6: 'amp_17q25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	66	81	86
AMP PEAK 6(17Q25.2) MUTATED	30	46	69	56
AMP PEAK 6(17Q25.2) WILD-TYPE	25	20	12	30

Figure S24. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00105 (Fisher's exact test), Q value = 0.22

Table S25. Gene #6: 'amp_17q25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
AMP PEAK 6(17Q25.2) MUTATED	72	45	7	27
AMP PEAK 6(17Q25.2) WILD-TYPE	26	32	9	3

Figure S25. Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S26. Gene #7: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
AMP PEAK 7(19P13.2) MUTATED	1	22	0	8
AMP PEAK 7(19P13.2) WILD-TYPE	113	54	46	44

Figure S26. Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.19

Table S27. Gene #7: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
AMP PEAK 7(19P13.2) MUTATED	3	22	6
AMP PEAK 7(19P13.2) WILD-TYPE	75	92	89

Figure S27. Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.2

Table S28. Gene #7: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
AMP PEAK 7(19P13.2) MUTATED	4	11	9	7
AMP PEAK 7(19P13.2) WILD-TYPE	121	61	35	39

Figure S28. Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S29. Gene #8: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 1(1P36.31) MUTATED	21	0	2	32
DEL PEAK 1(1P36.31) WILD-TYPE	93	76	44	20

Figure S29. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S30. Gene #8: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
DEL PEAK 1(1P36.31) MUTATED	11	22	9
DEL PEAK 1(1P36.31) WILD-TYPE	52	36	94

Figure S30. 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 = 0.0031

Table S31. Gene #8: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 1(1P36.31) MUTATED	11	6	38
DEL PEAK 1(1P36.31) WILD-TYPE	67	108	57

Figure S31. 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 = 0.0031

Table S32. Gene #8: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 1(1P36.31) MUTATED	29	6	1	19
DEL PEAK 1(1P36.31) WILD-TYPE	96	66	43	27

Figure S32. Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.069

Table S33. Gene #10: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 3(2Q22.1) MUTATED	1	0	9
DEL PEAK 3(2Q22.1) WILD-TYPE	77	114	86

Figure S33. Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S34. Gene #12: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 5(3P22.1) MUTATED	6	0	0	19
DEL PEAK 5(3P22.1) WILD-TYPE	108	76	46	33

Figure S34. 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 = 0.0031

Table S35. Gene #12: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
DEL PEAK 5(3P22.1) MUTATED	3	14	1
DEL PEAK 5(3P22.1) WILD-TYPE	60	44	102

Figure S35. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S36. Gene #12: 'del_3p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 5(3P22.1) MUTATED	5	0	20
DEL PEAK 5(3P22.1) WILD-TYPE	73	114	75

Figure S36. 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 = 0.0031

Table S37. Gene #12: 'del_3p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 5(3P22.1) MUTATED	21	0	0	4
DEL PEAK 5(3P22.1) WILD-TYPE	104	72	44	42

Figure S37. Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S38. Gene #13: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 6(4Q34.3) MUTATED	8	1	1	22
DEL PEAK 6(4Q34.3) WILD-TYPE	106	75	45	30

Figure S38. 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 = 0.0031

Table S39. Gene #13: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
DEL PEAK 6(4Q34.3) MUTATED	4	20	2
DEL PEAK 6(4Q34.3) WILD-TYPE	59	38	101

Figure S39. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S40. Gene #13: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 6(4Q34.3) MUTATED	4	2	26
DEL PEAK 6(4Q34.3) WILD-TYPE	74	112	69

Figure S40. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.012

Table S41. Gene #13: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 6(4Q34.3) MUTATED	18	1	1	12
DEL PEAK 6(4Q34.3) WILD-TYPE	107	71	43	34

Figure S41. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S42. Gene #13: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
DEL PEAK 6(4Q34.3) MUTATED	7	11	8	0
DEL PEAK 6(4Q34.3) WILD-TYPE	91	66	8	30

Figure S42. Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q35.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0098

Table S43. Gene #15: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
DEL PEAK 8(5Q35.2) MUTATED	1	9	0
DEL PEAK 8(5Q35.2) WILD-TYPE	62	49	103

Figure S43. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q35.2' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S44. Gene #15: 'del_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 8(5Q35.2) MUTATED	1	0	10
DEL PEAK 8(5Q35.2) WILD-TYPE	77	114	85

Figure S44. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S45. Gene #15: 'del_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 8(5Q35.2) MUTATED	3	0	0	8
DEL PEAK 8(5Q35.2) WILD-TYPE	122	72	44	38

Figure S45. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S46. Gene #15: 'del_5q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
DEL PEAK 8(5Q35.2) MUTATED	1	1	8	0
DEL PEAK 8(5Q35.2) WILD-TYPE	97	76	8	30

Figure S46. Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S47. Gene #16: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 9(6P12.3) MUTATED	8	0	1	17
DEL PEAK 9(6P12.3) WILD-TYPE	106	76	45	35

Figure S47. Get High-res Image Gene #16: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S48. Gene #17: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 10(6Q22.31) MUTATED	8	0	1	20
DEL PEAK 10(6Q22.31) WILD-TYPE	106	76	45	32

Figure S48. Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0051

Table S49. Gene #17: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 10(6Q22.31) MUTATED	5	3	21
DEL PEAK 10(6Q22.31) WILD-TYPE	73	111	74

Figure S49. Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S50. Gene #17: 'del_6q22.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 10(6Q22.31) MUTATED	14	2	0	13
DEL PEAK 10(6Q22.31) WILD-TYPE	111	70	44	33

Figure S50. Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S51. Gene #18: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 11(6Q25.3) MUTATED	7	0	1	24
DEL PEAK 11(6Q25.3) WILD-TYPE	107	76	45	28

Figure S51. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q25.3' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.097

Table S52. Gene #18: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
DEL PEAK 11(6Q25.3) MUTATED	5	14	4
DEL PEAK 11(6Q25.3) WILD-TYPE	58	44	99

Figure S52. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S53. Gene #18: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 11(6Q25.3) MUTATED	6	3	23
DEL PEAK 11(6Q25.3) WILD-TYPE	72	111	72

Figure S53. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S54. Gene #18: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 11(6Q25.3) MUTATED	18	2	0	12
DEL PEAK 11(6Q25.3) WILD-TYPE	107	70	44	34

Figure S54. Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S55. Gene #19: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 12(9P21.3) MUTATED	11	2	1	26
DEL PEAK 12(9P21.3) WILD-TYPE	103	74	45	26

Figure S55. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S56. Gene #19: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
DEL PEAK 12(9P21.3) MUTATED	9	20	2
DEL PEAK 12(9P21.3) WILD-TYPE	54	38	101

Figure S56. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.16

Table S57. Gene #19: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	17	22	29	22	27	39	25	25
DEL PEAK 12(9P21.3) MUTATED	0	3	0	5	9	3	2	7
DEL PEAK 12(9P21.3) WILD-TYPE	17	19	29	17	18	36	23	18

Figure S57. Get High-res Image Gene #19: '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 = 0.0031

Table S58. Gene #19: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 12(9P21.3) MUTATED	6	2	32
DEL PEAK 12(9P21.3) WILD-TYPE	72	112	63

Figure S58. Get High-res Image Gene #19: '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 = 0.0031

Table S59. Gene #19: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 12(9P21.3) MUTATED	20	0	0	20
DEL PEAK 12(9P21.3) WILD-TYPE	105	72	44	26

Figure S59. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.084

Table S60. Gene #19: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	103	96
DEL PEAK 12(9P21.3) MUTATED	3	16	21
DEL PEAK 12(9P21.3) WILD-TYPE	86	87	75

Figure S60. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.023

Table S61. Gene #19: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	81	71
DEL PEAK 12(9P21.3) MUTATED	8	4	21
DEL PEAK 12(9P21.3) WILD-TYPE	61	77	50

Figure S61. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S62. Gene #19: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
DEL PEAK 12(9P21.3) MUTATED	7	19	7	0
DEL PEAK 12(9P21.3) WILD-TYPE	91	58	9	30

Figure S62. Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S63. Gene #20: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 13(10Q21.1) MUTATED	5	0	0	14
DEL PEAK 13(10Q21.1) WILD-TYPE	109	76	46	38

Figure S63. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0098

Table S64. Gene #20: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
DEL PEAK 13(10Q21.1) MUTATED	1	12	2
DEL PEAK 13(10Q21.1) WILD-TYPE	62	46	101

Figure S64. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S65. Gene #20: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 13(10Q21.1) MUTATED	3	1	15
DEL PEAK 13(10Q21.1) WILD-TYPE	75	113	80

Figure S65. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.17

Table S66. Gene #20: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 13(10Q21.1) MUTATED	14	0	0	5
DEL PEAK 13(10Q21.1) WILD-TYPE	111	72	44	41

Figure S66. Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S67. Gene #21: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 14(11Q22.3) MUTATED	8	4	1	18
DEL PEAK 14(11Q22.3) WILD-TYPE	106	72	45	34

Figure S67. Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.3' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.034

Table S68. Gene #21: 'del_11q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 14(11Q22.3) MUTATED	4	6	21
DEL PEAK 14(11Q22.3) WILD-TYPE	74	108	74

Figure S68. Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.045

Table S69. Gene #21: 'del_11q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 14(11Q22.3) MUTATED	18	0	4	9
DEL PEAK 14(11Q22.3) WILD-TYPE	107	72	40	37

Figure S69. Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S70. Gene #22: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 15(11Q23.3) MUTATED	6	4	0	19
DEL PEAK 15(11Q23.3) WILD-TYPE	108	72	46	33

Figure S70. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.034

Table S71. Gene #22: 'del_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
DEL PEAK 15(11Q23.3) MUTATED	6	14	3
DEL PEAK 15(11Q23.3) WILD-TYPE	57	44	100

Figure S71. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.3' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S72. Gene #22: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 15(11Q23.3) MUTATED	3	5	21
DEL PEAK 15(11Q23.3) WILD-TYPE	75	109	74

Figure S72. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.063

Table S73. Gene #22: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 15(11Q23.3) MUTATED	18	0	3	8
DEL PEAK 15(11Q23.3) WILD-TYPE	107	72	41	38

Figure S73. Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S74. Gene #23: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 16(14Q11.2) MUTATED	20	1	2	28
DEL PEAK 16(14Q11.2) WILD-TYPE	94	75	44	24

Figure S74. Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S75. Gene #23: 'del_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 16(14Q11.2) MUTATED	13	6	32
DEL PEAK 16(14Q11.2) WILD-TYPE	65	108	63

Figure S75. Get High-res Image Gene #23: '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 = 0.0031

Table S76. Gene #23: 'del_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 16(14Q11.2) MUTATED	26	2	4	19
DEL PEAK 16(14Q11.2) WILD-TYPE	99	70	40	27

Figure S76. Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S77. Gene #24: 'del_14q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 17(14Q24.2) MUTATED	21	0	1	28
DEL PEAK 17(14Q24.2) WILD-TYPE	93	76	45	24

Figure S77. Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S78. Gene #24: 'del_14q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 17(14Q24.2) MUTATED	11	5	34
DEL PEAK 17(14Q24.2) WILD-TYPE	67	109	61

Figure S78. Get High-res Image Gene #24: '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 = 0.0031

Table S79. Gene #24: 'del_14q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 17(14Q24.2) MUTATED	26	2	3	19
DEL PEAK 17(14Q24.2) WILD-TYPE	99	70	41	27

Figure S79. Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S80. Gene #25: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 18(15Q13.3) MUTATED	12	0	3	20
DEL PEAK 18(15Q13.3) WILD-TYPE	102	76	43	32

Figure S80. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q13.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0098

Table S81. Gene #25: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
DEL PEAK 18(15Q13.3) MUTATED	10	15	3
DEL PEAK 18(15Q13.3) WILD-TYPE	53	43	100

Figure S81. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S82. Gene #25: 'del_15q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 18(15Q13.3) MUTATED	7	3	25
DEL PEAK 18(15Q13.3) WILD-TYPE	71	111	70

Figure S82. Get High-res Image Gene #25: '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 = 0.0031

Table S83. Gene #25: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 18(15Q13.3) MUTATED	17	2	1	15
DEL PEAK 18(15Q13.3) WILD-TYPE	108	70	43	31

Figure S83. Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.1' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.058

Table S84. Gene #26: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 19(16Q24.1) MUTATED	4	0	0	8
DEL PEAK 19(16Q24.1) WILD-TYPE	110	76	46	44

Figure S84. Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q24.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0098

Table S85. Gene #26: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
DEL PEAK 19(16Q24.1) MUTATED	1	9	0
DEL PEAK 19(16Q24.1) WILD-TYPE	62	49	103

Figure S85. Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q24.1' versus 'MRNASEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.19

Table S86. Gene #26: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 19(16Q24.1) MUTATED	3	0	9
DEL PEAK 19(16Q24.1) WILD-TYPE	75	114	86

Figure S86. Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S87. Gene #27: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 20(19P13.3) MUTATED	4	4	1	14
DEL PEAK 20(19P13.3) WILD-TYPE	110	72	45	38

Figure S87. Get High-res Image Gene #27: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.42' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S88. Gene #28: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 21(19Q13.42) MUTATED	2	3	2	12
DEL PEAK 21(19Q13.42) WILD-TYPE	112	73	44	40

Figure S88. Get High-res Image Gene #28: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S89. Gene #29: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 22(22Q12.2) MUTATED	23	6	2	32
DEL PEAK 22(22Q12.2) WILD-TYPE	91	70	44	20

Figure S89. Get High-res Image Gene #29: '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 = 0.0031

Table S90. Gene #29: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
DEL PEAK 22(22Q12.2) MUTATED	9	32	11
DEL PEAK 22(22Q12.2) WILD-TYPE	54	26	92

Figure S90. Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S91. Gene #29: 'del_22q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 22(22Q12.2) MUTATED	15	8	40
DEL PEAK 22(22Q12.2) WILD-TYPE	63	106	55

Figure S91. Get High-res Image Gene #29: '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 = 0.0031

Table S92. Gene #29: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 22(22Q12.2) MUTATED	37	6	2	18
DEL PEAK 22(22Q12.2) WILD-TYPE	88	66	42	28

Figure S92. Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.4' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S93. Gene #30: 'del_xp11.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 23(XP11.4) MUTATED	12	1	1	20
DEL PEAK 23(XP11.4) WILD-TYPE	102	75	45	32

Figure S93. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.4' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S94. Gene #30: 'del_xp11.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
DEL PEAK 23(XP11.4) MUTATED	4	18	2
DEL PEAK 23(XP11.4) WILD-TYPE	59	40	101

Figure S94. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp11.4' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S95. Gene #30: 'del_xp11.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 23(XP11.4) MUTATED	5	3	26
DEL PEAK 23(XP11.4) WILD-TYPE	73	111	69

Figure S95. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp11.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0051

Table S96. Gene #30: 'del_xp11.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
DEL PEAK 23(XP11.4) MUTATED	19	1	2	12
DEL PEAK 23(XP11.4) WILD-TYPE	106	71	42	34

Figure S96. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.4' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.088

Table S97. Gene #30: 'del_xp11.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
DEL PEAK 23(XP11.4) MUTATED	5	16	4	0
DEL PEAK 23(XP11.4) WILD-TYPE	93	61	12	30

Figure S97. Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S98. Gene #31: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
DEL PEAK 24(XQ28) MUTATED	10	0	1	17
DEL PEAK 24(XQ28) WILD-TYPE	104	76	45	35

Figure S98. Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq28' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.028

Table S99. Gene #31: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
DEL PEAK 24(XQ28) MUTATED	3	13	3
DEL PEAK 24(XQ28) WILD-TYPE	60	45	100

Figure S99. Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq28' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S100. Gene #31: 'del_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
DEL PEAK 24(XQ28) MUTATED	4	3	21
DEL PEAK 24(XQ28) WILD-TYPE	74	111	74

Figure S100. Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = KIRP-TP.transferedmergedcluster.txt
Number of patients = 288
Number of significantly focal cnvs = 31
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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