Correlation between copy number variation genes (focal events) and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1ZW1JKB
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/C1ZW1JKB
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 28 focal events and 8 molecular subtypes across 197 patients, 61 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_2p23.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_2q32.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_3q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_7q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_17q25.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_19p13.2 cnv correlated to 'CN_CNMF'.

  • del_1p36.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_3p22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q34.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_5p14.2 cnv correlated to 'METHLYATION_CNMF'.

  • del_5q15 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_5q35.2 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_10p11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_11q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_11q24.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_14q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_14q32.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_15q15.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_16q24.1 cnv correlated to 'METHLYATION_CNMF'.

  • del_21q22.3 cnv correlated to 'CN_CNMF'.

  • del_xp11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_xq28 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 28 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, 61 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 Chi-square test Chi-square 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
del 3p22 1 15 (8%) 182 1.54e-05
(0.00289) 		1.44e-07
(2.96e-05) 		1.73e-05
(0.00324) 		0.000192
(0.0341) 		0.186
(1.00) 		0.00139
(0.23) 		0.0193
(1.00) 		7.47e-07
(0.000151)
amp 3q22 3 68 (35%) 129 2.54e-15
(5.61e-13) 		1.05e-05
(0.002) 		5.27e-07
(0.000107) 		0.000303
(0.0531) 		0.0532
(1.00) 		0.153
(1.00) 		0.163
(1.00) 		0.002
(0.324)
amp 7q22 1 119 (60%) 78 1.51e-15
(3.34e-13) 		5.14e-06
(0.001) 		5.55e-13
(1.2e-10) 		1.18e-12
(2.54e-10) 		0.161
(1.00) 		0.534
(1.00) 		0.0975
(1.00) 		0.00352
(0.553)
del 9p21 3 27 (14%) 170 3.56e-06
(0.000701) 		5.89e-11
(1.27e-08) 		4e-08
(8.37e-06) 		0.000148
(0.0266) 		0.039
(1.00) 		0.0218
(1.00) 		0.0923
(1.00) 		0.0037
(0.573)
amp 17q25 2 143 (73%) 54 1.02e-09
(2.17e-07) 		0.00381
(0.587) 		3.42e-06
(0.000678) 		1.25e-07
(2.59e-05) 		0.504
(1.00) 		1
(1.00) 		0.605
(1.00) 		0.617
(1.00)
del 1p36 31 37 (19%) 160 3.85e-13
(8.4e-11) 		8.32e-07
(0.000167) 		4.03e-07
(8.23e-05) 		0.053
(1.00) 		1
(1.00) 		0.945
(1.00) 		0.918
(1.00) 		0.1
(1.00)
del 4q34 3 21 (11%) 176 1.2e-07
(2.49e-05) 		5.95e-10
(1.27e-07) 		3.79e-08
(7.96e-06) 		0.00241
(0.386) 		0.625
(1.00) 		0.411
(1.00) 		0.734
(1.00) 		0.0763
(1.00)
del 5q35 2 11 (6%) 186 0.0862
(1.00) 		2.03e-08
(4.3e-06) 		0.000682
(0.115) 		0.00116
(0.193) 		0.337
(1.00) 		0.0731
(1.00) 		0.217
(1.00) 		0.00466
(0.712)
del 10p11 21 12 (6%) 185 0.000379
(0.0651) 		7.12e-06
(0.00137) 		0.000342
(0.0594) 		0.0509
(1.00) 		0.566
(1.00) 		0.0171
(1.00) 		0.235
(1.00) 		0.00328
(0.518)
del 11q22 3 18 (9%) 179 0.000257
(0.0453) 		9.21e-05
(0.0167) 		0.00128
(0.213) 		0.053
(1.00) 		0.594
(1.00) 		0.0886
(1.00) 		0.137
(1.00) 		0.0712
(1.00)
del 14q32 2 39 (20%) 158 1.78e-14
(3.91e-12) 		0.000432
(0.0734) 		0.000256
(0.0453) 		0.00159
(0.26) 		0.665
(1.00) 		0.55
(1.00) 		0.572
(1.00) 		0.224
(1.00)
del 15q15 2 22 (11%) 175 5.4e-06
(0.00105) 		1.94e-05
(0.00361) 		0.00041
(0.07) 		0.0248
(1.00) 		0.0794
(1.00) 		0.158
(1.00) 		0.0562
(1.00) 		0.0479
(1.00)
del xp11 22 18 (9%) 179 2.42e-06
(0.000481) 		3.02e-08
(6.37e-06) 		6.48e-06
(0.00125) 		0.00997
(1.00) 		0.17
(1.00) 		0.0549
(1.00) 		0.203
(1.00) 		0.0117
(1.00)
amp 2p23 2 37 (19%) 160 1.12e-27
(2.51e-25) 		5.61e-05
(0.0103) 		0.0312
(1.00) 		0.104
(1.00) 		0.0519
(1.00) 		0.757
(1.00) 		0.00731
(1.00) 		0.68
(1.00)
amp 2q32 1 45 (23%) 152 4.21e-24
(9.39e-22) 		0.000342
(0.0594) 		0.0428
(1.00) 		0.0295
(1.00) 		0.138
(1.00) 		0.831
(1.00) 		0.0286
(1.00) 		0.418
(1.00)
del 5q15 11 (6%) 186 0.35
(1.00) 		3.35e-05
(0.00617) 		0.00493
(0.749) 		0.000185
(0.0331) 		0.287
(1.00) 		0.0731
(1.00) 		0.398
(1.00) 		0.0441
(1.00)
del 11q24 2 19 (10%) 178 0.000848
(0.143) 		1.1e-05
(0.0021) 		0.00239
(0.384) 		0.134
(1.00) 		0.823
(1.00) 		0.177
(1.00) 		0.255
(1.00) 		0.0527
(1.00)
del 14q11 2 39 (20%) 158 2.99e-14
(6.55e-12) 		0.00152
(0.249) 		0.00359
(0.56) 		0.00545
(0.823) 		0.665
(1.00) 		0.55
(1.00) 		0.572
(1.00) 		0.381
(1.00)
del xq28 17 (9%) 180 1.38e-05
(0.0026) 		1.54e-06
(0.000308) 		0.00266
(0.423) 		0.265
(1.00) 		0.217
(1.00) 		0.417
(1.00) 		0.335
(1.00) 		0.065
(1.00)
amp 19p13 2 21 (11%) 176 3.09e-07
(6.33e-05) 		0.185
(1.00) 		0.0358
(1.00) 		0.0688
(1.00) 		0.668
(1.00) 		0.798
(1.00) 		0.533
(1.00) 		0.834
(1.00)
del 5p14 2 10 (5%) 187 0.506
(1.00) 		3.64e-06
(0.000713) 		0.144
(1.00) 		0.0599
(1.00) 		0.108
(1.00) 		0.337
(1.00) 		0.173
(1.00) 		0.327
(1.00)
del 16q24 1 7 (4%) 190 0.0899
(1.00) 		8e-05
(0.0146) 		0.0309
(1.00) 		0.0778
(1.00) 		0.703
(1.00) 		0.589
(1.00) 		1
(1.00) 		0.0944
(1.00)
del 21q22 3 33 (17%) 164 3.02e-05
(0.00559) 		0.166
(1.00) 		0.676
(1.00) 		1
(1.00) 		0.514
(1.00) 		0.6
(1.00) 		0.22
(1.00) 		0.808
(1.00)
del 2q37 3 9 (5%) 188 0.1
(1.00) 		0.0283
(1.00) 		0.151
(1.00) 		0.0124
(1.00) 		0.25
(1.00) 		1
(1.00) 		0.0643
(1.00) 		0.496
(1.00)
del 6q21 17 (9%) 180 0.00736
(1.00) 		0.00699
(1.00) 		0.012
(1.00) 		0.265
(1.00) 		1
(1.00) 		0.422
(1.00) 		0.503
(1.00) 		0.0983
(1.00)
del 6q22 31 18 (9%) 179 0.0113
(1.00) 		0.0126
(1.00) 		0.00582
(0.872) 		0.183
(1.00) 		0.846
(1.00) 		0.321
(1.00) 		0.376
(1.00) 		0.0712
(1.00)
del 19p13 3 16 (8%) 181 0.0192
(1.00) 		0.0331
(1.00) 		0.0321
(1.00) 		0.0361
(1.00) 		0.385
(1.00) 		0.182
(1.00) 		0.114
(1.00) 		0.0547
(1.00)
del 19q13 42 15 (8%) 182 0.0394
(1.00) 		0.0767
(1.00) 		0.0108
(1.00) 		0.173
(1.00) 		0.5
(1.00) 		0.831
(1.00) 		0.0193
(1.00) 		0.914
(1.00)
'amp_2p23.2' versus 'CN_CNMF'

P value = 1.12e-27 (Chi-square test), Q value = 2.5e-25

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
AMP PEAK 1(2P23.2) MUTATED 2 2 6 0 27
AMP PEAK 1(2P23.2) WILD-TYPE 69 38 31 21 1

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

'amp_2p23.2' versus 'METHLYATION_CNMF'

P value = 5.61e-05 (Chi-square test), Q value = 0.01

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
AMP PEAK 1(2P23.2) MUTATED 3 8 4 18 1
AMP PEAK 1(2P23.2) WILD-TYPE 35 16 29 30 37

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

'amp_2q32.1' versus 'CN_CNMF'

P value = 4.21e-24 (Chi-square test), Q value = 9.4e-22

Table S3.  Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
AMP PEAK 2(2Q32.1) MUTATED 5 2 9 1 28
AMP PEAK 2(2Q32.1) WILD-TYPE 66 38 28 20 0

Figure S3.  Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q32.1' versus 'METHLYATION_CNMF'

P value = 0.000342 (Chi-square test), Q value = 0.059

Table S4.  Gene #2: 'amp_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
AMP PEAK 2(2Q32.1) MUTATED 6 8 7 20 1
AMP PEAK 2(2Q32.1) WILD-TYPE 32 16 26 28 37

Figure S4.  Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q22.3' versus 'CN_CNMF'

P value = 2.54e-15 (Chi-square test), Q value = 5.6e-13

Table S5.  Gene #3: 'amp_3q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
AMP PEAK 3(3Q22.3) MUTATED 12 9 6 21 20
AMP PEAK 3(3Q22.3) WILD-TYPE 59 31 31 0 8

Figure S5.  Get High-res Image Gene #3: 'amp_3q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q22.3' versus 'METHLYATION_CNMF'

P value = 1.05e-05 (Chi-square test), Q value = 0.002

Table S6.  Gene #3: 'amp_3q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
AMP PEAK 3(3Q22.3) MUTATED 12 5 6 31 8
AMP PEAK 3(3Q22.3) WILD-TYPE 26 19 27 17 30

Figure S6.  Get High-res Image Gene #3: 'amp_3q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q22.3' versus 'MRNASEQ_CNMF'

P value = 5.27e-07 (Fisher's exact test), Q value = 0.00011

Table S7.  Gene #3: 'amp_3q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
AMP PEAK 3(3Q22.3) MUTATED 22 7 23 16
AMP PEAK 3(3Q22.3) WILD-TYPE 17 60 36 16

Figure S7.  Get High-res Image Gene #3: 'amp_3q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000303 (Fisher's exact test), Q value = 0.053

Table S8.  Gene #3: 'amp_3q22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
AMP PEAK 3(3Q22.3) MUTATED 37 19 12
AMP PEAK 3(3Q22.3) WILD-TYPE 33 52 44

Figure S8.  Get High-res Image Gene #3: 'amp_3q22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'CN_CNMF'

P value = 1.51e-15 (Chi-square test), Q value = 3.3e-13

Table S9.  Gene #4: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
AMP PEAK 4(7Q22.1) MUTATED 23 40 13 20 23
AMP PEAK 4(7Q22.1) WILD-TYPE 48 0 24 1 5

Figure S9.  Get High-res Image Gene #4: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q22.1' versus 'METHLYATION_CNMF'

P value = 5.14e-06 (Chi-square test), Q value = 0.001

Table S10.  Gene #4: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
AMP PEAK 4(7Q22.1) MUTATED 18 9 12 39 30
AMP PEAK 4(7Q22.1) WILD-TYPE 20 15 21 9 8

Figure S10.  Get High-res Image Gene #4: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CNMF'

P value = 5.55e-13 (Fisher's exact test), Q value = 1.2e-10

Table S11.  Gene #4: 'amp_7q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
AMP PEAK 4(7Q22.1) MUTATED 21 19 53 26
AMP PEAK 4(7Q22.1) WILD-TYPE 18 48 6 6

Figure S11.  Get High-res Image Gene #4: 'amp_7q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-12 (Fisher's exact test), Q value = 2.5e-10

Table S12.  Gene #4: 'amp_7q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
AMP PEAK 4(7Q22.1) MUTATED 65 28 26
AMP PEAK 4(7Q22.1) WILD-TYPE 5 43 30

Figure S12.  Get High-res Image Gene #4: 'amp_7q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'CN_CNMF'

P value = 1.02e-09 (Chi-square test), Q value = 2.2e-07

Table S13.  Gene #5: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
AMP PEAK 5(17Q25.2) MUTATED 38 40 19 19 27
AMP PEAK 5(17Q25.2) WILD-TYPE 33 0 18 2 1

Figure S13.  Get High-res Image Gene #5: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.2' versus 'MRNASEQ_CNMF'

P value = 3.42e-06 (Fisher's exact test), Q value = 0.00068

Table S14.  Gene #5: 'amp_17q25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
AMP PEAK 5(17Q25.2) MUTATED 31 34 54 24
AMP PEAK 5(17Q25.2) WILD-TYPE 8 33 5 8

Figure S14.  Get High-res Image Gene #5: 'amp_17q25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_17q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.25e-07 (Fisher's exact test), Q value = 2.6e-05

Table S15.  Gene #5: 'amp_17q25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
AMP PEAK 5(17Q25.2) MUTATED 66 47 30
AMP PEAK 5(17Q25.2) WILD-TYPE 4 24 26

Figure S15.  Get High-res Image Gene #5: 'amp_17q25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 3.09e-07 (Chi-square test), Q value = 6.3e-05

Table S16.  Gene #6: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
AMP PEAK 6(19P13.2) MUTATED 0 14 4 0 3
AMP PEAK 6(19P13.2) WILD-TYPE 71 26 33 21 25

Figure S16.  Get High-res Image Gene #6: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'CN_CNMF'

P value = 3.85e-13 (Chi-square test), Q value = 8.4e-11

Table S17.  Gene #7: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
DEL PEAK 1(1P36.31) MUTATED 7 0 23 0 7
DEL PEAK 1(1P36.31) WILD-TYPE 64 40 14 21 21

Figure S17.  Get High-res Image Gene #7: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 8.32e-07 (Chi-square test), Q value = 0.00017

Table S18.  Gene #7: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 1(1P36.31) MUTATED 6 14 6 8 0
DEL PEAK 1(1P36.31) WILD-TYPE 32 10 27 40 38

Figure S18.  Get High-res Image Gene #7: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 4.03e-07 (Fisher's exact test), Q value = 8.2e-05

Table S19.  Gene #7: 'del_1p36.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
DEL PEAK 1(1P36.31) MUTATED 5 27 5 0
DEL PEAK 1(1P36.31) WILD-TYPE 34 40 54 32

Figure S19.  Get High-res Image Gene #7: 'del_1p36.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p22.1' versus 'CN_CNMF'

P value = 1.54e-05 (Chi-square test), Q value = 0.0029

Table S20.  Gene #9: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
DEL PEAK 3(3P22.1) MUTATED 2 0 10 0 3
DEL PEAK 3(3P22.1) WILD-TYPE 69 40 27 21 25

Figure S20.  Get High-res Image Gene #9: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p22.1' versus 'METHLYATION_CNMF'

P value = 1.44e-07 (Chi-square test), Q value = 3e-05

Table S21.  Gene #9: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 3(3P22.1) MUTATED 0 8 6 0 0
DEL PEAK 3(3P22.1) WILD-TYPE 38 16 27 48 38

Figure S21.  Get High-res Image Gene #9: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p22.1' versus 'MRNASEQ_CNMF'

P value = 1.73e-05 (Fisher's exact test), Q value = 0.0032

Table S22.  Gene #9: 'del_3p22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
DEL PEAK 3(3P22.1) MUTATED 1 14 0 0
DEL PEAK 3(3P22.1) WILD-TYPE 38 53 59 32

Figure S22.  Get High-res Image Gene #9: 'del_3p22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000192 (Fisher's exact test), Q value = 0.034

Table S23.  Gene #9: 'del_3p22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
DEL PEAK 3(3P22.1) MUTATED 0 12 3
DEL PEAK 3(3P22.1) WILD-TYPE 70 59 53

Figure S23.  Get High-res Image Gene #9: 'del_3p22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.23

Table S24.  Gene #9: 'del_3p22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 78 90
DEL PEAK 3(3P22.1) MUTATED 7 6 2
DEL PEAK 3(3P22.1) WILD-TYPE 22 72 88

Figure S24.  Get High-res Image Gene #9: 'del_3p22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.47e-07 (Fisher's exact test), Q value = 0.00015

Table S25.  Gene #9: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 99 23
DEL PEAK 3(3P22.1) MUTATED 5 1 9
DEL PEAK 3(3P22.1) WILD-TYPE 70 98 14

Figure S25.  Get High-res Image Gene #9: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1.2e-07 (Chi-square test), Q value = 2.5e-05

Table S26.  Gene #10: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
DEL PEAK 4(4Q34.3) MUTATED 4 0 14 0 3
DEL PEAK 4(4Q34.3) WILD-TYPE 67 40 23 21 25

Figure S26.  Get High-res Image Gene #10: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 5.95e-10 (Chi-square test), Q value = 1.3e-07

Table S27.  Gene #10: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 4(4Q34.3) MUTATED 1 12 4 2 0
DEL PEAK 4(4Q34.3) WILD-TYPE 37 12 29 46 38

Figure S27.  Get High-res Image Gene #10: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 3.79e-08 (Fisher's exact test), Q value = 8e-06

Table S28.  Gene #10: 'del_4q34.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
DEL PEAK 4(4Q34.3) MUTATED 1 20 0 0
DEL PEAK 4(4Q34.3) WILD-TYPE 38 47 59 32

Figure S28.  Get High-res Image Gene #10: 'del_4q34.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_5p14.2' versus 'METHLYATION_CNMF'

P value = 3.64e-06 (Chi-square test), Q value = 0.00071

Table S29.  Gene #11: 'del_5p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 5(5P14.2) MUTATED 1 7 0 2 0
DEL PEAK 5(5P14.2) WILD-TYPE 37 17 33 46 38

Figure S29.  Get High-res Image Gene #11: 'del_5p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q15' versus 'METHLYATION_CNMF'

P value = 3.35e-05 (Chi-square test), Q value = 0.0062

Table S30.  Gene #12: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 6(5Q15) MUTATED 1 7 1 1 1
DEL PEAK 6(5Q15) WILD-TYPE 37 17 32 47 37

Figure S30.  Get High-res Image Gene #12: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000185 (Fisher's exact test), Q value = 0.033

Table S31.  Gene #12: 'del_5q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
DEL PEAK 6(5Q15) MUTATED 0 2 9
DEL PEAK 6(5Q15) WILD-TYPE 70 69 47

Figure S31.  Get High-res Image Gene #12: 'del_5q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q35.2' versus 'METHLYATION_CNMF'

P value = 2.03e-08 (Chi-square test), Q value = 4.3e-06

Table S32.  Gene #13: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 7(5Q35.2) MUTATED 1 8 1 0 0
DEL PEAK 7(5Q35.2) WILD-TYPE 37 16 32 48 38

Figure S32.  Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q35.2' versus 'MRNASEQ_CNMF'

P value = 0.000682 (Fisher's exact test), Q value = 0.12

Table S33.  Gene #13: 'del_5q35.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
DEL PEAK 7(5Q35.2) MUTATED 1 10 0 0
DEL PEAK 7(5Q35.2) WILD-TYPE 38 57 59 32

Figure S33.  Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_5q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.19

Table S34.  Gene #13: 'del_5q35.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
DEL PEAK 7(5Q35.2) MUTATED 0 3 8
DEL PEAK 7(5Q35.2) WILD-TYPE 70 68 48

Figure S34.  Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 3.56e-06 (Chi-square test), Q value = 7e-04

Table S35.  Gene #16: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
DEL PEAK 10(9P21.3) MUTATED 8 1 15 0 3
DEL PEAK 10(9P21.3) WILD-TYPE 63 39 22 21 25

Figure S35.  Get High-res Image Gene #16: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 5.89e-11 (Chi-square test), Q value = 1.3e-08

Table S36.  Gene #16: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 10(9P21.3) MUTATED 4 14 5 1 0
DEL PEAK 10(9P21.3) WILD-TYPE 34 10 28 47 38

Figure S36.  Get High-res Image Gene #16: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 4e-08 (Fisher's exact test), Q value = 8.4e-06

Table S37.  Gene #16: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
DEL PEAK 10(9P21.3) MUTATED 3 23 0 1
DEL PEAK 10(9P21.3) WILD-TYPE 36 44 59 31

Figure S37.  Get High-res Image Gene #16: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000148 (Fisher's exact test), Q value = 0.027

Table S38.  Gene #16: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 71 56
DEL PEAK 10(9P21.3) MUTATED 1 13 13
DEL PEAK 10(9P21.3) WILD-TYPE 69 58 43

Figure S38.  Get High-res Image Gene #16: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.21' versus 'CN_CNMF'

P value = 0.000379 (Chi-square test), Q value = 0.065

Table S39.  Gene #17: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
DEL PEAK 11(10P11.21) MUTATED 1 0 7 0 4
DEL PEAK 11(10P11.21) WILD-TYPE 70 40 30 21 24

Figure S39.  Get High-res Image Gene #17: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'METHLYATION_CNMF'

P value = 7.12e-06 (Chi-square test), Q value = 0.0014

Table S40.  Gene #17: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 11(10P11.21) MUTATED 0 7 3 1 0
DEL PEAK 11(10P11.21) WILD-TYPE 38 17 30 47 38

Figure S40.  Get High-res Image Gene #17: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'MRNASEQ_CNMF'

P value = 0.000342 (Fisher's exact test), Q value = 0.059

Table S41.  Gene #17: 'del_10p11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
DEL PEAK 11(10P11.21) MUTATED 0 11 1 0
DEL PEAK 11(10P11.21) WILD-TYPE 39 56 58 32

Figure S41.  Get High-res Image Gene #17: 'del_10p11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11q22.3' versus 'CN_CNMF'

P value = 0.000257 (Chi-square test), Q value = 0.045

Table S42.  Gene #18: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
DEL PEAK 12(11Q22.3) MUTATED 3 1 10 0 4
DEL PEAK 12(11Q22.3) WILD-TYPE 68 39 27 21 24

Figure S42.  Get High-res Image Gene #18: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.3' versus 'METHLYATION_CNMF'

P value = 9.21e-05 (Chi-square test), Q value = 0.017

Table S43.  Gene #18: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 12(11Q22.3) MUTATED 2 8 5 2 0
DEL PEAK 12(11Q22.3) WILD-TYPE 36 16 28 46 38

Figure S43.  Get High-res Image Gene #18: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q22.3' versus 'MRNASEQ_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.21

Table S44.  Gene #18: 'del_11q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
DEL PEAK 12(11Q22.3) MUTATED 2 14 1 1
DEL PEAK 12(11Q22.3) WILD-TYPE 37 53 58 31

Figure S44.  Get High-res Image Gene #18: 'del_11q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11q24.2' versus 'CN_CNMF'

P value = 0.000848 (Chi-square test), Q value = 0.14

Table S45.  Gene #19: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
DEL PEAK 13(11Q24.2) MUTATED 3 1 10 1 4
DEL PEAK 13(11Q24.2) WILD-TYPE 68 39 27 20 24

Figure S45.  Get High-res Image Gene #19: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.2' versus 'METHLYATION_CNMF'

P value = 1.1e-05 (Chi-square test), Q value = 0.0021

Table S46.  Gene #19: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 13(11Q24.2) MUTATED 2 9 5 2 0
DEL PEAK 13(11Q24.2) WILD-TYPE 36 15 28 46 38

Figure S46.  Get High-res Image Gene #19: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q11.2' versus 'CN_CNMF'

P value = 2.99e-14 (Chi-square test), Q value = 6.5e-12

Table S47.  Gene #20: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
DEL PEAK 14(14Q11.2) MUTATED 5 1 25 2 6
DEL PEAK 14(14Q11.2) WILD-TYPE 66 39 12 19 22

Figure S47.  Get High-res Image Gene #20: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 0.00152 (Chi-square test), Q value = 0.25

Table S48.  Gene #20: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 14(14Q11.2) MUTATED 11 10 3 8 2
DEL PEAK 14(14Q11.2) WILD-TYPE 27 14 30 40 36

Figure S48.  Get High-res Image Gene #20: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.2' versus 'CN_CNMF'

P value = 1.78e-14 (Chi-square test), Q value = 3.9e-12

Table S49.  Gene #21: 'del_14q32.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
DEL PEAK 15(14Q32.2) MUTATED 7 0 25 1 6
DEL PEAK 15(14Q32.2) WILD-TYPE 64 40 12 20 22

Figure S49.  Get High-res Image Gene #21: 'del_14q32.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.2' versus 'METHLYATION_CNMF'

P value = 0.000432 (Chi-square test), Q value = 0.073

Table S50.  Gene #21: 'del_14q32.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 15(14Q32.2) MUTATED 11 11 3 8 2
DEL PEAK 15(14Q32.2) WILD-TYPE 27 13 30 40 36

Figure S50.  Get High-res Image Gene #21: 'del_14q32.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.2' versus 'MRNASEQ_CNMF'

P value = 0.000256 (Fisher's exact test), Q value = 0.045

Table S51.  Gene #21: 'del_14q32.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
DEL PEAK 15(14Q32.2) MUTATED 8 24 4 3
DEL PEAK 15(14Q32.2) WILD-TYPE 31 43 55 29

Figure S51.  Get High-res Image Gene #21: 'del_14q32.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_15q15.2' versus 'CN_CNMF'

P value = 5.4e-06 (Chi-square test), Q value = 0.001

Table S52.  Gene #22: 'del_15q15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
DEL PEAK 16(15Q15.2) MUTATED 4 0 13 1 4
DEL PEAK 16(15Q15.2) WILD-TYPE 67 40 24 20 24

Figure S52.  Get High-res Image Gene #22: 'del_15q15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.2' versus 'METHLYATION_CNMF'

P value = 1.94e-05 (Chi-square test), Q value = 0.0036

Table S53.  Gene #22: 'del_15q15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 16(15Q15.2) MUTATED 7 9 2 2 0
DEL PEAK 16(15Q15.2) WILD-TYPE 31 15 31 46 38

Figure S53.  Get High-res Image Gene #22: 'del_15q15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.2' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.07

Table S54.  Gene #22: 'del_15q15.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
DEL PEAK 16(15Q15.2) MUTATED 4 16 2 0
DEL PEAK 16(15Q15.2) WILD-TYPE 35 51 57 32

Figure S54.  Get High-res Image Gene #22: 'del_15q15.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q24.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Chi-square test), Q value = 0.015

Table S55.  Gene #23: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 17(16Q24.1) MUTATED 0 5 2 0 0
DEL PEAK 17(16Q24.1) WILD-TYPE 38 19 31 48 38

Figure S55.  Get High-res Image Gene #23: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'CN_CNMF'

P value = 3.02e-05 (Chi-square test), Q value = 0.0056

Table S56.  Gene #26: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
DEL PEAK 20(21Q22.3) MUTATED 5 4 9 2 13
DEL PEAK 20(21Q22.3) WILD-TYPE 66 36 28 19 15

Figure S56.  Get High-res Image Gene #26: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.22' versus 'CN_CNMF'

P value = 2.42e-06 (Chi-square test), Q value = 0.00048

Table S57.  Gene #27: 'del_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
DEL PEAK 21(XP11.22) MUTATED 4 0 12 0 2
DEL PEAK 21(XP11.22) WILD-TYPE 67 40 25 21 26

Figure S57.  Get High-res Image Gene #27: 'del_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.22' versus 'METHLYATION_CNMF'

P value = 3.02e-08 (Chi-square test), Q value = 6.4e-06

Table S58.  Gene #27: 'del_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 21(XP11.22) MUTATED 1 10 4 1 0
DEL PEAK 21(XP11.22) WILD-TYPE 37 14 29 47 38

Figure S58.  Get High-res Image Gene #27: 'del_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp11.22' versus 'MRNASEQ_CNMF'

P value = 6.48e-06 (Fisher's exact test), Q value = 0.0012

Table S59.  Gene #27: 'del_xp11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 67 59 32
DEL PEAK 21(XP11.22) MUTATED 2 16 0 0
DEL PEAK 21(XP11.22) WILD-TYPE 37 51 59 32

Figure S59.  Get High-res Image Gene #27: 'del_xp11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_xq28' versus 'CN_CNMF'

P value = 1.38e-05 (Chi-square test), Q value = 0.0026

Table S60.  Gene #28: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 40 37 21 28
DEL PEAK 22(XQ28) MUTATED 5 0 11 0 1
DEL PEAK 22(XQ28) WILD-TYPE 66 40 26 21 27

Figure S60.  Get High-res Image Gene #28: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq28' versus 'METHLYATION_CNMF'

P value = 1.54e-06 (Chi-square test), Q value = 0.00031

Table S61.  Gene #28: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 24 33 48 38
DEL PEAK 22(XQ28) MUTATED 1 9 2 3 0
DEL PEAK 22(XQ28) WILD-TYPE 37 15 31 45 38

Figure S61.  Get High-res Image Gene #28: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = KIRP-TP.transferedmergedcluster.txt

  • Number of patients = 197

  • Number of significantly focal cnvs = 28

  • Number of molecular subtypes = 8

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[3] 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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