Correlation between copy number variation genes (focal events) and molecular subtypes
Uveal Melanoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C190239W
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/C190239W
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 20 focal events and 8 molecular subtypes across 80 patients, 102 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_6p24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8q24.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p36.12 cnv correlated to 'CN_CNMF'.

  • del_1p12 cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • del_3p25.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p25.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p22.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p14.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3q24 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3q29 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q25.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q27 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11q24.3 cnv correlated to 'METHLYATION_CNMF'.

  • del_16q12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_16q23.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_16q24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17q12 cnv correlated to 'MIRSEQ_MATURE_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 20 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 102 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 6p24 3 45 (56%) 35 3e-05
(7.62e-05) 		4e-05
(1e-04) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		0.00043
(0.000997) 		1e-05
(2.67e-05)
amp 8q24 22 61 (76%) 19 0.00257
(0.00545) 		2e-05
(5.25e-05) 		0.0358
(0.0584) 		0.00085
(0.00192) 		0.00012
(0.000291) 		0.00071
(0.00162) 		0.0375
(0.0606) 		0.00089
(0.00198)
del 3p25 2 43 (54%) 37 1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05)
del 3p25 1 43 (54%) 37 1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05)
del 3p22 2 43 (54%) 37 1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05)
del 3p14 2 44 (55%) 36 1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05)
del 3q24 44 (55%) 36 1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05)
del 3q29 44 (55%) 36 1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05)
del 8p11 22 19 (24%) 61 1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		0.00025
(0.000597) 		1e-05
(2.67e-05) 		1e-05
(2.67e-05) 		3e-05
(7.62e-05) 		5e-05
(0.000123) 		1e-05
(2.67e-05)
del 6q27 24 (30%) 56 1e-05
(2.67e-05) 		0.00527
(0.0102) 		0.33
(0.362) 		0.00504
(0.00983) 		0.252
(0.286) 		0.75
(0.755) 		0.0413
(0.0648) 		0.0386
(0.0611)
del 16q24 3 17 (21%) 63 0.00659
(0.0124) 		0.00259
(0.00545) 		0.14
(0.181) 		0.00471
(0.00954) 		0.0584
(0.0889) 		0.0383
(0.0611) 		0.155
(0.193) 		0.0064
(0.0122)
amp 17q25 3 14 (18%) 66 0.00485
(0.00966) 		0.00231
(0.00499) 		0.412
(0.449) 		0.111
(0.151) 		0.0581
(0.0889) 		0.0003
(0.000706) 		0.227
(0.27) 		0.00446
(0.00927)
del 6q25 2 23 (29%) 57 1e-05
(2.67e-05) 		0.0109
(0.0193) 		0.421
(0.456) 		0.0104
(0.0187) 		0.482
(0.511) 		0.704
(0.718) 		0.129
(0.169) 		0.0131
(0.0229)
del 16q23 3 17 (21%) 63 0.00994
(0.0181) 		0.0143
(0.0246) 		0.139
(0.181) 		0.00463
(0.0095) 		0.11
(0.151) 		0.0979
(0.136) 		0.0338
(0.0558) 		0.0759
(0.11)
del 16q12 1 16 (20%) 64 0.022
(0.0371) 		0.0287
(0.0478) 		0.153
(0.193) 		0.0124
(0.0217) 		0.198
(0.236) 		0.125
(0.167) 		0.0688
(0.102) 		0.161
(0.2)
del 1p12 18 (22%) 62 0.128
(0.169) 		0.0771
(0.111) 		0.00933
(0.0172) 		0.171
(0.209) 		0.837
(0.837) 		0.0842
(0.118) 		0.00184
(0.00403) 		0.238
(0.276)
del 1p36 12 25 (31%) 55 0.00778
(0.0145) 		0.237
(0.276) 		0.0789
(0.113) 		0.102
(0.14) 		0.741
(0.751) 		0.32
(0.353) 		0.0582
(0.0889) 		0.0589
(0.0889)
del 11q24 3 7 (9%) 73 0.196
(0.236) 		0.00489
(0.00966) 		0.122
(0.164) 		0.0741
(0.109) 		0.176
(0.213) 		0.148
(0.188) 		0.0841
(0.118) 		0.145
(0.186)
del 17q12 3 (4%) 77 0.589
(0.614) 		0.0642
(0.096) 		0.245
(0.281) 		0.171
(0.209) 		0.262
(0.293) 		0.443
(0.472) 		0.0193
(0.0329) 		0.5
(0.526)
del 2q37 2 3 (4%) 77 0.591
(0.614) 		0.315
(0.349) 		0.681
(0.699) 		0.235
(0.276) 		0.652
(0.673) 		0.441
(0.472) 		0.248
(0.283) 		0.261
(0.293)
'amp_6p24.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S1.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
AMP PEAK 1(6P24.3) MUTATED 7 4 4 27 3 0
AMP PEAK 1(6P24.3) WILD-TYPE 15 3 6 4 3 4

Figure S1.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p24.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 1e-04

Table S2.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
AMP PEAK 1(6P24.3) MUTATED 9 9 5 22
AMP PEAK 1(6P24.3) WILD-TYPE 19 5 9 2

Figure S2.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S3.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
AMP PEAK 1(6P24.3) MUTATED 4 6 29 6
AMP PEAK 1(6P24.3) WILD-TYPE 14 9 3 9

Figure S3.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S4.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
AMP PEAK 1(6P24.3) MUTATED 9 30 6
AMP PEAK 1(6P24.3) WILD-TYPE 20 3 12

Figure S4.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S5.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
AMP PEAK 1(6P24.3) MUTATED 1 4 8 24 7 1
AMP PEAK 1(6P24.3) WILD-TYPE 7 4 3 1 16 4

Figure S5.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_6p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S6.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
AMP PEAK 1(6P24.3) MUTATED 4 9 27 5
AMP PEAK 1(6P24.3) WILD-TYPE 13 4 1 17

Figure S6.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.001

Table S7.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
AMP PEAK 1(6P24.3) MUTATED 8 2 17 3 4 4 3
AMP PEAK 1(6P24.3) WILD-TYPE 12 5 0 6 4 3 3

Figure S7.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S8.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
AMP PEAK 1(6P24.3) MUTATED 7 25 1 8
AMP PEAK 1(6P24.3) WILD-TYPE 11 3 15 4

Figure S8.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.22' versus 'CN_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.0055

Table S9.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
AMP PEAK 2(8Q24.22) MUTATED 18 7 10 16 6 4
AMP PEAK 2(8Q24.22) WILD-TYPE 4 0 0 15 0 0

Figure S9.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.22' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.2e-05

Table S10.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
AMP PEAK 2(8Q24.22) MUTATED 28 5 11 17
AMP PEAK 2(8Q24.22) WILD-TYPE 0 9 3 7

Figure S10.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.058

Table S11.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
AMP PEAK 2(8Q24.22) MUTATED 16 12 19 14
AMP PEAK 2(8Q24.22) WILD-TYPE 2 3 13 1

Figure S11.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0019

Table S12.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
AMP PEAK 2(8Q24.22) MUTATED 28 19 14
AMP PEAK 2(8Q24.22) WILD-TYPE 1 14 4

Figure S12.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00029

Table S13.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
AMP PEAK 2(8Q24.22) MUTATED 7 8 5 16 23 2
AMP PEAK 2(8Q24.22) WILD-TYPE 1 0 6 9 0 3

Figure S13.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0016

Table S14.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
AMP PEAK 2(8Q24.22) MUTATED 16 6 18 21
AMP PEAK 2(8Q24.22) WILD-TYPE 1 7 10 1

Figure S14.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.061

Table S15.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
AMP PEAK 2(8Q24.22) MUTATED 20 6 11 6 5 5 5
AMP PEAK 2(8Q24.22) WILD-TYPE 0 1 6 3 3 2 1

Figure S15.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.002

Table S16.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
AMP PEAK 2(8Q24.22) MUTATED 18 16 15 9
AMP PEAK 2(8Q24.22) WILD-TYPE 0 12 1 3

Figure S16.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.00485 (Fisher's exact test), Q value = 0.0097

Table S17.  Gene #3: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
AMP PEAK 3(17Q25.3) MUTATED 1 0 6 7 0 0
AMP PEAK 3(17Q25.3) WILD-TYPE 21 7 4 24 6 4

Figure S17.  Get High-res Image Gene #3: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'METHLYATION_CNMF'

P value = 0.00231 (Fisher's exact test), Q value = 0.005

Table S18.  Gene #3: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
AMP PEAK 3(17Q25.3) MUTATED 2 0 2 10
AMP PEAK 3(17Q25.3) WILD-TYPE 26 14 12 14

Figure S18.  Get High-res Image Gene #3: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00071

Table S19.  Gene #3: 'amp_17q25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
AMP PEAK 3(17Q25.3) MUTATED 3 0 11 0
AMP PEAK 3(17Q25.3) WILD-TYPE 14 13 17 22

Figure S19.  Get High-res Image Gene #3: 'amp_17q25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00446 (Fisher's exact test), Q value = 0.0093

Table S20.  Gene #3: 'amp_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
AMP PEAK 3(17Q25.3) MUTATED 0 8 1 5
AMP PEAK 3(17Q25.3) WILD-TYPE 18 20 15 7

Figure S20.  Get High-res Image Gene #3: 'amp_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.12' versus 'CN_CNMF'

P value = 0.00778 (Fisher's exact test), Q value = 0.014

Table S21.  Gene #4: 'del_1p36.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
DEL PEAK 1(1P36.12) MUTATED 7 2 7 6 0 3
DEL PEAK 1(1P36.12) WILD-TYPE 15 5 3 25 6 1

Figure S21.  Get High-res Image Gene #4: 'del_1p36.12' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p12' versus 'MRNASEQ_CNMF'

P value = 0.00933 (Fisher's exact test), Q value = 0.017

Table S22.  Gene #5: 'del_1p12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
DEL PEAK 2(1P12) MUTATED 9 4 4 1
DEL PEAK 2(1P12) WILD-TYPE 9 11 28 14

Figure S22.  Get High-res Image Gene #5: 'del_1p12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.004

Table S23.  Gene #5: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
DEL PEAK 2(1P12) MUTATED 7 1 1 0 5 4 0
DEL PEAK 2(1P12) WILD-TYPE 13 6 16 9 3 3 6

Figure S23.  Get High-res Image Gene #5: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S24.  Gene #7: 'del_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
DEL PEAK 4(3P25.2) MUTATED 17 7 8 2 6 3
DEL PEAK 4(3P25.2) WILD-TYPE 5 0 2 29 0 1

Figure S24.  Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p25.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S25.  Gene #7: 'del_3p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
DEL PEAK 4(3P25.2) MUTATED 28 3 10 2
DEL PEAK 4(3P25.2) WILD-TYPE 0 11 4 22

Figure S25.  Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p25.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S26.  Gene #7: 'del_3p25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
DEL PEAK 4(3P25.2) MUTATED 18 10 2 13
DEL PEAK 4(3P25.2) WILD-TYPE 0 5 30 2

Figure S26.  Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S27.  Gene #7: 'del_3p25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 4(3P25.2) MUTATED 29 2 12
DEL PEAK 4(3P25.2) WILD-TYPE 0 31 6

Figure S27.  Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p25.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S28.  Gene #7: 'del_3p25.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
DEL PEAK 4(3P25.2) MUTATED 8 5 2 2 23 3
DEL PEAK 4(3P25.2) WILD-TYPE 0 3 9 23 0 2

Figure S28.  Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S29.  Gene #7: 'del_3p25.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 4(3P25.2) MUTATED 17 1 3 22
DEL PEAK 4(3P25.2) WILD-TYPE 0 12 25 0

Figure S29.  Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S30.  Gene #7: 'del_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
DEL PEAK 4(3P25.2) MUTATED 20 6 2 4 5 2 3
DEL PEAK 4(3P25.2) WILD-TYPE 0 1 15 5 3 5 3

Figure S30.  Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S31.  Gene #7: 'del_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
DEL PEAK 4(3P25.2) MUTATED 17 3 16 6
DEL PEAK 4(3P25.2) WILD-TYPE 1 25 0 6

Figure S31.  Get High-res Image Gene #7: 'del_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S32.  Gene #8: 'del_3p25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
DEL PEAK 5(3P25.1) MUTATED 17 7 8 2 6 3
DEL PEAK 5(3P25.1) WILD-TYPE 5 0 2 29 0 1

Figure S32.  Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S33.  Gene #8: 'del_3p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
DEL PEAK 5(3P25.1) MUTATED 28 3 10 2
DEL PEAK 5(3P25.1) WILD-TYPE 0 11 4 22

Figure S33.  Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S34.  Gene #8: 'del_3p25.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
DEL PEAK 5(3P25.1) MUTATED 18 10 2 13
DEL PEAK 5(3P25.1) WILD-TYPE 0 5 30 2

Figure S34.  Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S35.  Gene #8: 'del_3p25.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 5(3P25.1) MUTATED 29 2 12
DEL PEAK 5(3P25.1) WILD-TYPE 0 31 6

Figure S35.  Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p25.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S36.  Gene #8: 'del_3p25.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
DEL PEAK 5(3P25.1) MUTATED 8 5 2 2 23 3
DEL PEAK 5(3P25.1) WILD-TYPE 0 3 9 23 0 2

Figure S36.  Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S37.  Gene #8: 'del_3p25.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 5(3P25.1) MUTATED 17 1 3 22
DEL PEAK 5(3P25.1) WILD-TYPE 0 12 25 0

Figure S37.  Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S38.  Gene #8: 'del_3p25.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
DEL PEAK 5(3P25.1) MUTATED 20 6 2 4 5 2 3
DEL PEAK 5(3P25.1) WILD-TYPE 0 1 15 5 3 5 3

Figure S38.  Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S39.  Gene #8: 'del_3p25.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
DEL PEAK 5(3P25.1) MUTATED 17 3 16 6
DEL PEAK 5(3P25.1) WILD-TYPE 1 25 0 6

Figure S39.  Get High-res Image Gene #8: 'del_3p25.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S40.  Gene #9: 'del_3p22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
DEL PEAK 6(3P22.2) MUTATED 17 7 8 2 6 3
DEL PEAK 6(3P22.2) WILD-TYPE 5 0 2 29 0 1

Figure S40.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S41.  Gene #9: 'del_3p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
DEL PEAK 6(3P22.2) MUTATED 28 3 10 2
DEL PEAK 6(3P22.2) WILD-TYPE 0 11 4 22

Figure S41.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S42.  Gene #9: 'del_3p22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
DEL PEAK 6(3P22.2) MUTATED 18 10 2 13
DEL PEAK 6(3P22.2) WILD-TYPE 0 5 30 2

Figure S42.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S43.  Gene #9: 'del_3p22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 6(3P22.2) MUTATED 29 2 12
DEL PEAK 6(3P22.2) WILD-TYPE 0 31 6

Figure S43.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S44.  Gene #9: 'del_3p22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
DEL PEAK 6(3P22.2) MUTATED 8 5 2 2 23 3
DEL PEAK 6(3P22.2) WILD-TYPE 0 3 9 23 0 2

Figure S44.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S45.  Gene #9: 'del_3p22.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 6(3P22.2) MUTATED 17 1 3 22
DEL PEAK 6(3P22.2) WILD-TYPE 0 12 25 0

Figure S45.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S46.  Gene #9: 'del_3p22.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
DEL PEAK 6(3P22.2) MUTATED 20 6 2 4 5 2 3
DEL PEAK 6(3P22.2) WILD-TYPE 0 1 15 5 3 5 3

Figure S46.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S47.  Gene #9: 'del_3p22.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
DEL PEAK 6(3P22.2) MUTATED 17 3 16 6
DEL PEAK 6(3P22.2) WILD-TYPE 1 25 0 6

Figure S47.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S48.  Gene #10: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
DEL PEAK 7(3P14.2) MUTATED 17 7 8 2 6 4
DEL PEAK 7(3P14.2) WILD-TYPE 5 0 2 29 0 0

Figure S48.  Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S49.  Gene #10: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
DEL PEAK 7(3P14.2) MUTATED 28 4 10 2
DEL PEAK 7(3P14.2) WILD-TYPE 0 10 4 22

Figure S49.  Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S50.  Gene #10: 'del_3p14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
DEL PEAK 7(3P14.2) MUTATED 18 10 3 13
DEL PEAK 7(3P14.2) WILD-TYPE 0 5 29 2

Figure S50.  Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S51.  Gene #10: 'del_3p14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 7(3P14.2) MUTATED 29 2 13
DEL PEAK 7(3P14.2) WILD-TYPE 0 31 5

Figure S51.  Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S52.  Gene #10: 'del_3p14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
DEL PEAK 7(3P14.2) MUTATED 8 6 2 2 23 3
DEL PEAK 7(3P14.2) WILD-TYPE 0 2 9 23 0 2

Figure S52.  Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S53.  Gene #10: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 7(3P14.2) MUTATED 17 2 3 22
DEL PEAK 7(3P14.2) WILD-TYPE 0 11 25 0

Figure S53.  Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S54.  Gene #10: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
DEL PEAK 7(3P14.2) MUTATED 20 6 2 5 5 2 3
DEL PEAK 7(3P14.2) WILD-TYPE 0 1 15 4 3 5 3

Figure S54.  Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S55.  Gene #10: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
DEL PEAK 7(3P14.2) MUTATED 18 3 16 6
DEL PEAK 7(3P14.2) WILD-TYPE 0 25 0 6

Figure S55.  Get High-res Image Gene #10: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q24' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S56.  Gene #11: 'del_3q24' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
DEL PEAK 8(3Q24) MUTATED 17 7 8 2 6 4
DEL PEAK 8(3Q24) WILD-TYPE 5 0 2 29 0 0

Figure S56.  Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q24' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S57.  Gene #11: 'del_3q24' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
DEL PEAK 8(3Q24) MUTATED 28 4 10 2
DEL PEAK 8(3Q24) WILD-TYPE 0 10 4 22

Figure S57.  Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q24' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S58.  Gene #11: 'del_3q24' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
DEL PEAK 8(3Q24) MUTATED 18 10 3 13
DEL PEAK 8(3Q24) WILD-TYPE 0 5 29 2

Figure S58.  Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3q24' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S59.  Gene #11: 'del_3q24' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 8(3Q24) MUTATED 29 2 13
DEL PEAK 8(3Q24) WILD-TYPE 0 31 5

Figure S59.  Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3q24' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S60.  Gene #11: 'del_3q24' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
DEL PEAK 8(3Q24) MUTATED 8 6 2 2 23 3
DEL PEAK 8(3Q24) WILD-TYPE 0 2 9 23 0 2

Figure S60.  Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3q24' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S61.  Gene #11: 'del_3q24' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 8(3Q24) MUTATED 17 2 3 22
DEL PEAK 8(3Q24) WILD-TYPE 0 11 25 0

Figure S61.  Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3q24' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S62.  Gene #11: 'del_3q24' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
DEL PEAK 8(3Q24) MUTATED 20 6 2 5 5 2 3
DEL PEAK 8(3Q24) WILD-TYPE 0 1 15 4 3 5 3

Figure S62.  Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3q24' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S63.  Gene #11: 'del_3q24' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
DEL PEAK 8(3Q24) MUTATED 18 3 16 6
DEL PEAK 8(3Q24) WILD-TYPE 0 25 0 6

Figure S63.  Get High-res Image Gene #11: 'del_3q24' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S64.  Gene #12: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
DEL PEAK 9(3Q29) MUTATED 17 7 8 2 6 4
DEL PEAK 9(3Q29) WILD-TYPE 5 0 2 29 0 0

Figure S64.  Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S65.  Gene #12: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
DEL PEAK 9(3Q29) MUTATED 28 4 10 2
DEL PEAK 9(3Q29) WILD-TYPE 0 10 4 22

Figure S65.  Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S66.  Gene #12: 'del_3q29' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
DEL PEAK 9(3Q29) MUTATED 18 10 3 13
DEL PEAK 9(3Q29) WILD-TYPE 0 5 29 2

Figure S66.  Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S67.  Gene #12: 'del_3q29' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 9(3Q29) MUTATED 29 2 13
DEL PEAK 9(3Q29) WILD-TYPE 0 31 5

Figure S67.  Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S68.  Gene #12: 'del_3q29' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
DEL PEAK 9(3Q29) MUTATED 8 6 2 2 23 3
DEL PEAK 9(3Q29) WILD-TYPE 0 2 9 23 0 2

Figure S68.  Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3q29' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S69.  Gene #12: 'del_3q29' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 9(3Q29) MUTATED 17 2 3 22
DEL PEAK 9(3Q29) WILD-TYPE 0 11 25 0

Figure S69.  Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S70.  Gene #12: 'del_3q29' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
DEL PEAK 9(3Q29) MUTATED 20 6 2 5 5 2 3
DEL PEAK 9(3Q29) WILD-TYPE 0 1 15 4 3 5 3

Figure S70.  Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3q29' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S71.  Gene #12: 'del_3q29' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
DEL PEAK 9(3Q29) MUTATED 18 3 16 6
DEL PEAK 9(3Q29) WILD-TYPE 0 25 0 6

Figure S71.  Get High-res Image Gene #12: 'del_3q29' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S72.  Gene #13: 'del_6q25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
DEL PEAK 10(6Q25.2) MUTATED 0 7 2 9 5 0
DEL PEAK 10(6Q25.2) WILD-TYPE 22 0 8 22 1 4

Figure S72.  Get High-res Image Gene #13: 'del_6q25.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q25.2' versus 'METHLYATION_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.019

Table S73.  Gene #13: 'del_6q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
DEL PEAK 10(6Q25.2) MUTATED 13 1 1 8
DEL PEAK 10(6Q25.2) WILD-TYPE 15 13 13 16

Figure S73.  Get High-res Image Gene #13: 'del_6q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.019

Table S74.  Gene #13: 'del_6q25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 10(6Q25.2) MUTATED 13 9 1
DEL PEAK 10(6Q25.2) WILD-TYPE 16 24 17

Figure S74.  Get High-res Image Gene #13: 'del_6q25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_6q25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.023

Table S75.  Gene #13: 'del_6q25.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
DEL PEAK 10(6Q25.2) MUTATED 11 8 2 2
DEL PEAK 10(6Q25.2) WILD-TYPE 7 20 14 10

Figure S75.  Get High-res Image Gene #13: 'del_6q25.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S76.  Gene #14: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
DEL PEAK 11(6Q27) MUTATED 0 7 3 9 5 0
DEL PEAK 11(6Q27) WILD-TYPE 22 0 7 22 1 4

Figure S76.  Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'METHLYATION_CNMF'

P value = 0.00527 (Fisher's exact test), Q value = 0.01

Table S77.  Gene #14: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
DEL PEAK 11(6Q27) MUTATED 14 1 1 8
DEL PEAK 11(6Q27) WILD-TYPE 14 13 13 16

Figure S77.  Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q27' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00504 (Fisher's exact test), Q value = 0.0098

Table S78.  Gene #14: 'del_6q27' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 11(6Q27) MUTATED 14 9 1
DEL PEAK 11(6Q27) WILD-TYPE 15 24 17

Figure S78.  Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_6q27' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.065

Table S79.  Gene #14: 'del_6q27' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
DEL PEAK 11(6Q27) MUTATED 12 2 3 3 0 2 2
DEL PEAK 11(6Q27) WILD-TYPE 8 5 14 6 8 5 4

Figure S79.  Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_6q27' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.061

Table S80.  Gene #14: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
DEL PEAK 11(6Q27) MUTATED 11 7 3 3
DEL PEAK 11(6Q27) WILD-TYPE 7 21 13 9

Figure S80.  Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S81.  Gene #15: 'del_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
DEL PEAK 12(8P11.22) MUTATED 6 7 0 1 4 1
DEL PEAK 12(8P11.22) WILD-TYPE 16 0 10 30 2 3

Figure S81.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S82.  Gene #15: 'del_8p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
DEL PEAK 12(8P11.22) MUTATED 16 1 1 1
DEL PEAK 12(8P11.22) WILD-TYPE 12 13 13 23

Figure S82.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p11.22' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 6e-04

Table S83.  Gene #15: 'del_8p11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
DEL PEAK 12(8P11.22) MUTATED 8 3 1 7
DEL PEAK 12(8P11.22) WILD-TYPE 10 12 31 8

Figure S83.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_8p11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S84.  Gene #15: 'del_8p11.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 12(8P11.22) MUTATED 16 1 2
DEL PEAK 12(8P11.22) WILD-TYPE 13 32 16

Figure S84.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_8p11.22' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S85.  Gene #15: 'del_8p11.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
DEL PEAK 12(8P11.22) MUTATED 1 5 0 0 12 1
DEL PEAK 12(8P11.22) WILD-TYPE 7 3 11 25 11 4

Figure S85.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_8p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S86.  Gene #15: 'del_8p11.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 12(8P11.22) MUTATED 7 1 0 11
DEL PEAK 12(8P11.22) WILD-TYPE 10 12 28 11

Figure S86.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_8p11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S87.  Gene #15: 'del_8p11.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
DEL PEAK 12(8P11.22) MUTATED 12 4 0 1 0 0 2
DEL PEAK 12(8P11.22) WILD-TYPE 8 3 17 8 8 7 4

Figure S87.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_8p11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.7e-05

Table S88.  Gene #15: 'del_8p11.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
DEL PEAK 12(8P11.22) MUTATED 11 0 7 1
DEL PEAK 12(8P11.22) WILD-TYPE 7 28 9 11

Figure S88.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q24.3' versus 'METHLYATION_CNMF'

P value = 0.00489 (Fisher's exact test), Q value = 0.0097

Table S89.  Gene #16: 'del_11q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
DEL PEAK 14(11Q24.3) MUTATED 0 0 1 6
DEL PEAK 14(11Q24.3) WILD-TYPE 28 14 13 18

Figure S89.  Get High-res Image Gene #16: 'del_11q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q12.1' versus 'CN_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.037

Table S90.  Gene #17: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
DEL PEAK 15(16Q12.1) MUTATED 4 5 1 4 2 0
DEL PEAK 15(16Q12.1) WILD-TYPE 18 2 9 27 4 4

Figure S90.  Get High-res Image Gene #17: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q12.1' versus 'METHLYATION_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 0.048

Table S91.  Gene #17: 'del_16q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
DEL PEAK 15(16Q12.1) MUTATED 10 0 3 3
DEL PEAK 15(16Q12.1) WILD-TYPE 18 14 11 21

Figure S91.  Get High-res Image Gene #17: 'del_16q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.022

Table S92.  Gene #17: 'del_16q12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 15(16Q12.1) MUTATED 11 4 1
DEL PEAK 15(16Q12.1) WILD-TYPE 18 29 17

Figure S92.  Get High-res Image Gene #17: 'del_16q12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.3' versus 'CN_CNMF'

P value = 0.00994 (Fisher's exact test), Q value = 0.018

Table S93.  Gene #18: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
DEL PEAK 16(16Q23.3) MUTATED 4 5 1 4 3 0
DEL PEAK 16(16Q23.3) WILD-TYPE 18 2 9 27 3 4

Figure S93.  Get High-res Image Gene #18: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.3' versus 'METHLYATION_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.025

Table S94.  Gene #18: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
DEL PEAK 16(16Q23.3) MUTATED 11 0 3 3
DEL PEAK 16(16Q23.3) WILD-TYPE 17 14 11 21

Figure S94.  Get High-res Image Gene #18: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00463 (Fisher's exact test), Q value = 0.0095

Table S95.  Gene #18: 'del_16q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 16(16Q23.3) MUTATED 12 4 1
DEL PEAK 16(16Q23.3) WILD-TYPE 17 29 17

Figure S95.  Get High-res Image Gene #18: 'del_16q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.056

Table S96.  Gene #18: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
DEL PEAK 16(16Q23.3) MUTATED 9 3 2 0 1 2 0
DEL PEAK 16(16Q23.3) WILD-TYPE 11 4 15 9 7 5 6

Figure S96.  Get High-res Image Gene #18: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q24.3' versus 'CN_CNMF'

P value = 0.00659 (Fisher's exact test), Q value = 0.012

Table S97.  Gene #19: 'del_16q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
DEL PEAK 17(16Q24.3) MUTATED 4 5 2 3 3 0
DEL PEAK 17(16Q24.3) WILD-TYPE 18 2 8 28 3 4

Figure S97.  Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q24.3' versus 'METHLYATION_CNMF'

P value = 0.00259 (Fisher's exact test), Q value = 0.0055

Table S98.  Gene #19: 'del_16q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
DEL PEAK 17(16Q24.3) MUTATED 12 0 3 2
DEL PEAK 17(16Q24.3) WILD-TYPE 16 14 11 22

Figure S98.  Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00471 (Fisher's exact test), Q value = 0.0095

Table S99.  Gene #19: 'del_16q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 17(16Q24.3) MUTATED 12 4 1
DEL PEAK 17(16Q24.3) WILD-TYPE 17 29 17

Figure S99.  Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.061

Table S100.  Gene #19: 'del_16q24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 17(16Q24.3) MUTATED 6 0 4 7
DEL PEAK 17(16Q24.3) WILD-TYPE 11 13 24 15

Figure S100.  Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0064 (Fisher's exact test), Q value = 0.012

Table S101.  Gene #19: 'del_16q24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
DEL PEAK 17(16Q24.3) MUTATED 9 4 4 0
DEL PEAK 17(16Q24.3) WILD-TYPE 9 24 12 12

Figure S101.  Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.033

Table S102.  Gene #20: 'del_17q12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
DEL PEAK 18(17Q12) MUTATED 0 1 0 0 0 2 0
DEL PEAK 18(17Q12) WILD-TYPE 20 6 17 9 8 5 6

Figure S102.  Get High-res Image Gene #20: 'del_17q12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

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/UVM-TP/22534464/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/22542449/UVM-TP.transferedmergedcluster.txt

  • Number of patients = 80

  • Number of significantly focal cnvs = 20

  • Number of molecular subtypes = 8

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

Download Results

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

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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