Correlation between copy number variation genes (focal events) and molecular subtypes
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 6 molecular subtypes across 191 patients, 69 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_1q43 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_11q23.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_13q31.3 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_19p13.2 cnv correlated to 'CN_CNMF'.

  • amp_20q11.21 cnv correlated to 'CN_CNMF'.

  • amp_21q22.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_3p13 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_5q31.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_7p12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_7q34 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_7q34 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_12p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_12q21.33 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_16q23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • del_17p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_17q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_18p11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_20q13.13 cnv correlated to 'CN_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 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 69 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
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
del 5q31 2 18 (9%) 173 1e-05
(0.000109) 		1e-05
(0.000109) 		0.00535
(0.014) 		0.00083
(0.00383) 		0.00069
(0.00345) 		0.00119
(0.00468)
del 7p12 1 16 (8%) 175 0.00021
(0.00157) 		0.00037
(0.00234) 		0.00183
(0.00627) 		1e-05
(0.000109) 		0.00568
(0.0145) 		0.00684
(0.0161)
del 7q34 24 (13%) 167 1e-05
(0.000109) 		0.00011
(0.000943) 		0.023
(0.0468) 		1e-05
(0.000109) 		0.00087
(0.00386) 		0.00068
(0.00345)
del 7q34 24 (13%) 167 1e-05
(0.000109) 		0.00012
(0.00096) 		0.0217
(0.0457) 		1e-05
(0.000109) 		0.0009
(0.00386) 		0.00072
(0.00346)
amp 21q22 2 14 (7%) 177 1e-05
(0.000109) 		0.00054
(0.00309) 		0.00335
(0.00966) 		0.0365
(0.0682) 		0.00164
(0.00579) 		0.0667
(0.108)
del 17p13 2 15 (8%) 176 1e-05
(0.000109) 		0.00025
(0.00167) 		0.0111
(0.0242) 		0.00023
(0.00162) 		0.086
(0.131) 		0.0012
(0.00468)
amp 1p33 7 (4%) 184 0.00049
(0.00294) 		0.00246
(0.00757) 		0.125
(0.184) 		0.132
(0.19) 		0.00946
(0.0214) 		0.0475
(0.0838)
amp 1q43 7 (4%) 184 0.00338
(0.00966) 		0.00237
(0.00757) 		0.373
(0.444) 		0.036
(0.0682) 		0.139
(0.196) 		0.0151
(0.0323)
del 3p13 8 (4%) 183 0.00062
(0.00338) 		0.0457
(0.0819) 		0.066
(0.108) 		0.235
(0.294) 		0.0368
(0.0682) 		0.0484
(0.0841)
del 17q11 2 13 (7%) 178 1e-05
(0.000109) 		0.00512
(0.0137) 		0.156
(0.217) 		0.00658
(0.0158) 		0.135
(0.193) 		0.00383
(0.0106)
del 12p13 2 10 (5%) 181 3e-05
(0.000277) 		0.00158
(0.00575) 		0.196
(0.259) 		0.0732
(0.114) 		0.0695
(0.11) 		0.0101
(0.0224)
del 12q21 33 3 (2%) 188 0.00121
(0.00468) 		0.701
(0.765) 		0.188
(0.25) 		0.586
(0.659) 		0.0086
(0.0198) 		0.00611
(0.0153)
del 16q23 1 9 (5%) 182 0.00152
(0.0057) 		0.0226
(0.0467) 		0.331
(0.403) 		0.493
(0.563) 		0.0451
(0.0819) 		0.065
(0.108)
del 18p11 21 9 (5%) 182 2e-05
(2e-04) 		0.00387
(0.0106) 		0.381
(0.448) 		0.333
(0.403) 		0.214
(0.273) 		0.0318
(0.0625)
amp 11q23 3 17 (9%) 174 1e-05
(0.000109) 		0.00217
(0.00723) 		0.371
(0.444) 		0.201
(0.262) 		0.747
(0.8) 		0.184
(0.249)
amp 13q31 3 7 (4%) 184 0.0813
(0.125) 		0.00245
(0.00757) 		0.0674
(0.108) 		0.037
(0.0682) 		0.736
(0.795) 		0.0571
(0.0964)
amp 19p13 2 6 (3%) 185 0.0032
(0.0096) 		0.254
(0.314) 		0.856
(0.901) 		0.633
(0.696) 		0.893
(0.932) 		1
(1.00)
amp 20q11 21 3 (2%) 188 0.00656
(0.0158) 		0.211
(0.273)
del 20q13 13 4 (2%) 187 0.029
(0.058) 		0.056
(0.096) 		0.785
(0.834) 		0.588
(0.659) 		0.125
(0.184) 		0.41
(0.478)
del 9q21 32 5 (3%) 186 0.231
(0.292) 		0.465
(0.536) 		0.175
(0.242) 		0.602
(0.669) 		0.183
(0.249) 		0.106
(0.159)
'amp_1p33' versus 'CN_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0029

Table S1.  Gene #1: 'amp_1p33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
AMP PEAK 1(1P33) MUTATED 1 3 3 0
AMP PEAK 1(1P33) WILD-TYPE 147 11 24 2

Figure S1.  Get High-res Image Gene #1: 'amp_1p33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p33' versus 'METHLYATION_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.0076

Table S2.  Gene #1: 'amp_1p33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
AMP PEAK 1(1P33) MUTATED 0 7 0 0
AMP PEAK 1(1P33) WILD-TYPE 33 54 47 44

Figure S2.  Get High-res Image Gene #1: 'amp_1p33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1p33' versus 'MIRSEQ_CNMF'

P value = 0.00946 (Fisher's exact test), Q value = 0.021

Table S3.  Gene #1: 'amp_1p33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
AMP PEAK 1(1P33) MUTATED 0 3 0 4
AMP PEAK 1(1P33) WILD-TYPE 58 34 41 39

Figure S3.  Get High-res Image Gene #1: 'amp_1p33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_1p33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 0.084

Table S4.  Gene #1: 'amp_1p33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
AMP PEAK 1(1P33) MUTATED 0 3 4
AMP PEAK 1(1P33) WILD-TYPE 67 31 74

Figure S4.  Get High-res Image Gene #1: 'amp_1p33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_1q43' versus 'CN_CNMF'

P value = 0.00338 (Fisher's exact test), Q value = 0.0097

Table S5.  Gene #2: 'amp_1q43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
AMP PEAK 2(1Q43) MUTATED 2 2 2 1
AMP PEAK 2(1Q43) WILD-TYPE 146 12 25 1

Figure S5.  Get High-res Image Gene #2: 'amp_1q43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q43' versus 'METHLYATION_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.0076

Table S6.  Gene #2: 'amp_1q43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
AMP PEAK 2(1Q43) MUTATED 0 7 0 0
AMP PEAK 2(1Q43) WILD-TYPE 33 54 47 44

Figure S6.  Get High-res Image Gene #2: 'amp_1q43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.036 (Fisher's exact test), Q value = 0.068

Table S7.  Gene #2: 'amp_1q43' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
AMP PEAK 2(1Q43) MUTATED 0 0 0 7 0 0
AMP PEAK 2(1Q43) WILD-TYPE 16 13 14 48 26 42

Figure S7.  Get High-res Image Gene #2: 'amp_1q43' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1q43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.032

Table S8.  Gene #2: 'amp_1q43' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
AMP PEAK 2(1Q43) MUTATED 0 4 3
AMP PEAK 2(1Q43) WILD-TYPE 67 30 75

Figure S8.  Get High-res Image Gene #2: 'amp_1q43' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S9.  Gene #3: 'amp_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
AMP PEAK 3(11Q23.3) MUTATED 0 14 3 0
AMP PEAK 3(11Q23.3) WILD-TYPE 148 0 24 2

Figure S9.  Get High-res Image Gene #3: 'amp_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q23.3' versus 'METHLYATION_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0072

Table S10.  Gene #3: 'amp_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
AMP PEAK 3(11Q23.3) MUTATED 0 12 1 4
AMP PEAK 3(11Q23.3) WILD-TYPE 33 49 46 40

Figure S10.  Get High-res Image Gene #3: 'amp_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q31.3' versus 'METHLYATION_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.0076

Table S11.  Gene #4: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
AMP PEAK 4(13Q31.3) MUTATED 0 7 0 0
AMP PEAK 4(13Q31.3) WILD-TYPE 33 54 47 44

Figure S11.  Get High-res Image Gene #4: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.037 (Fisher's exact test), Q value = 0.068

Table S12.  Gene #4: 'amp_13q31.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
AMP PEAK 4(13Q31.3) MUTATED 0 0 0 7 0 0
AMP PEAK 4(13Q31.3) WILD-TYPE 16 13 14 48 26 42

Figure S12.  Get High-res Image Gene #4: 'amp_13q31.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.0096

Table S13.  Gene #5: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
AMP PEAK 5(19P13.2) MUTATED 1 1 4 0
AMP PEAK 5(19P13.2) WILD-TYPE 147 13 23 2

Figure S13.  Get High-res Image Gene #5: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 0.00656 (Fisher's exact test), Q value = 0.016

Table S14.  Gene #6: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
AMP PEAK 6(20Q11.21) MUTATED 0 0 3 0
AMP PEAK 6(20Q11.21) WILD-TYPE 148 14 24 2

Figure S14.  Get High-res Image Gene #6: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_21q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S15.  Gene #7: 'amp_21q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
AMP PEAK 7(21Q22.2) MUTATED 0 0 14 0
AMP PEAK 7(21Q22.2) WILD-TYPE 148 14 13 2

Figure S15.  Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_21q22.2' versus 'METHLYATION_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0031

Table S16.  Gene #7: 'amp_21q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
AMP PEAK 7(21Q22.2) MUTATED 0 11 2 0
AMP PEAK 7(21Q22.2) WILD-TYPE 33 50 45 44

Figure S16.  Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_21q22.2' versus 'MRNASEQ_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.0097

Table S17.  Gene #7: 'amp_21q22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 52 44
AMP PEAK 7(21Q22.2) MUTATED 10 1 0
AMP PEAK 7(21Q22.2) WILD-TYPE 60 51 44

Figure S17.  Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_21q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0365 (Fisher's exact test), Q value = 0.068

Table S18.  Gene #7: 'amp_21q22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
AMP PEAK 7(21Q22.2) MUTATED 0 0 1 9 0 1
AMP PEAK 7(21Q22.2) WILD-TYPE 16 13 13 46 26 41

Figure S18.  Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_21q22.2' versus 'MIRSEQ_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0058

Table S19.  Gene #7: 'amp_21q22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
AMP PEAK 7(21Q22.2) MUTATED 1 4 7 0
AMP PEAK 7(21Q22.2) WILD-TYPE 57 33 34 43

Figure S19.  Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p13' versus 'CN_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0034

Table S20.  Gene #8: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
DEL PEAK 2(3P13) MUTATED 2 0 6 0
DEL PEAK 2(3P13) WILD-TYPE 146 14 21 2

Figure S20.  Get High-res Image Gene #8: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 0.0457 (Fisher's exact test), Q value = 0.082

Table S21.  Gene #8: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
DEL PEAK 2(3P13) MUTATED 0 6 2 0
DEL PEAK 2(3P13) WILD-TYPE 33 55 45 44

Figure S21.  Get High-res Image Gene #8: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p13' versus 'MIRSEQ_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.068

Table S22.  Gene #8: 'del_3p13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
DEL PEAK 2(3P13) MUTATED 0 4 2 1
DEL PEAK 2(3P13) WILD-TYPE 58 33 39 42

Figure S22.  Get High-res Image Gene #8: 'del_3p13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0484 (Fisher's exact test), Q value = 0.084

Table S23.  Gene #8: 'del_3p13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
DEL PEAK 2(3P13) MUTATED 0 3 4
DEL PEAK 2(3P13) WILD-TYPE 67 31 74

Figure S23.  Get High-res Image Gene #8: 'del_3p13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_5q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S24.  Gene #9: 'del_5q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
DEL PEAK 3(5Q31.2) MUTATED 1 1 15 1
DEL PEAK 3(5Q31.2) WILD-TYPE 147 13 12 1

Figure S24.  Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S25.  Gene #9: 'del_5q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
DEL PEAK 3(5Q31.2) MUTATED 0 15 3 0
DEL PEAK 3(5Q31.2) WILD-TYPE 33 46 44 44

Figure S25.  Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q31.2' versus 'MRNASEQ_CNMF'

P value = 0.00535 (Fisher's exact test), Q value = 0.014

Table S26.  Gene #9: 'del_5q31.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 52 44
DEL PEAK 3(5Q31.2) MUTATED 13 2 1
DEL PEAK 3(5Q31.2) WILD-TYPE 57 50 43

Figure S26.  Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_5q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0038

Table S27.  Gene #9: 'del_5q31.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
DEL PEAK 3(5Q31.2) MUTATED 0 0 0 14 0 2
DEL PEAK 3(5Q31.2) WILD-TYPE 16 13 14 41 26 40

Figure S27.  Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0034

Table S28.  Gene #9: 'del_5q31.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
DEL PEAK 3(5Q31.2) MUTATED 1 10 3 3
DEL PEAK 3(5Q31.2) WILD-TYPE 57 27 38 40

Figure S28.  Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_5q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0047

Table S29.  Gene #9: 'del_5q31.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
DEL PEAK 3(5Q31.2) MUTATED 1 8 8
DEL PEAK 3(5Q31.2) WILD-TYPE 66 26 70

Figure S29.  Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7p12.1' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0016

Table S30.  Gene #10: 'del_7p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
DEL PEAK 4(7P12.1) MUTATED 7 0 8 1
DEL PEAK 4(7P12.1) WILD-TYPE 141 14 19 1

Figure S30.  Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7p12.1' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0023

Table S31.  Gene #10: 'del_7p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
DEL PEAK 4(7P12.1) MUTATED 0 13 1 2
DEL PEAK 4(7P12.1) WILD-TYPE 33 48 46 42

Figure S31.  Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0063

Table S32.  Gene #10: 'del_7p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 52 44
DEL PEAK 4(7P12.1) MUTATED 12 0 3
DEL PEAK 4(7P12.1) WILD-TYPE 58 52 41

Figure S32.  Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S33.  Gene #10: 'del_7p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
DEL PEAK 4(7P12.1) MUTATED 0 0 0 15 0 0
DEL PEAK 4(7P12.1) WILD-TYPE 16 13 14 40 26 42

Figure S33.  Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00568 (Fisher's exact test), Q value = 0.015

Table S34.  Gene #10: 'del_7p12.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
DEL PEAK 4(7P12.1) MUTATED 1 8 2 5
DEL PEAK 4(7P12.1) WILD-TYPE 57 29 39 38

Figure S34.  Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00684 (Fisher's exact test), Q value = 0.016

Table S35.  Gene #10: 'del_7p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
DEL PEAK 4(7P12.1) MUTATED 1 6 9
DEL PEAK 4(7P12.1) WILD-TYPE 66 28 69

Figure S35.  Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S36.  Gene #11: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
DEL PEAK 5(7Q34) MUTATED 9 2 11 2
DEL PEAK 5(7Q34) WILD-TYPE 139 12 16 0

Figure S36.  Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q34' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00094

Table S37.  Gene #11: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
DEL PEAK 5(7Q34) MUTATED 1 18 2 3
DEL PEAK 5(7Q34) WILD-TYPE 32 43 45 41

Figure S37.  Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q34' versus 'MRNASEQ_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.047

Table S38.  Gene #11: 'del_7q34' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 52 44
DEL PEAK 5(7Q34) MUTATED 14 2 4
DEL PEAK 5(7Q34) WILD-TYPE 56 50 40

Figure S38.  Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S39.  Gene #11: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
DEL PEAK 5(7Q34) MUTATED 1 1 0 18 0 0
DEL PEAK 5(7Q34) WILD-TYPE 15 12 14 37 26 42

Figure S39.  Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q34' versus 'MIRSEQ_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0039

Table S40.  Gene #11: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
DEL PEAK 5(7Q34) MUTATED 2 12 5 4
DEL PEAK 5(7Q34) WILD-TYPE 56 25 36 39

Figure S40.  Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0034

Table S41.  Gene #11: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
DEL PEAK 5(7Q34) MUTATED 2 10 11
DEL PEAK 5(7Q34) WILD-TYPE 65 24 67

Figure S41.  Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S42.  Gene #12: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
DEL PEAK 6(7Q34) MUTATED 9 2 11 2
DEL PEAK 6(7Q34) WILD-TYPE 139 12 16 0

Figure S42.  Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q34' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00096

Table S43.  Gene #12: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
DEL PEAK 6(7Q34) MUTATED 1 18 2 3
DEL PEAK 6(7Q34) WILD-TYPE 32 43 45 41

Figure S43.  Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q34' versus 'MRNASEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.046

Table S44.  Gene #12: 'del_7q34' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 52 44
DEL PEAK 6(7Q34) MUTATED 14 2 4
DEL PEAK 6(7Q34) WILD-TYPE 56 50 40

Figure S44.  Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S45.  Gene #12: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
DEL PEAK 6(7Q34) MUTATED 1 1 0 18 0 0
DEL PEAK 6(7Q34) WILD-TYPE 15 12 14 37 26 42

Figure S45.  Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q34' versus 'MIRSEQ_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0039

Table S46.  Gene #12: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
DEL PEAK 6(7Q34) MUTATED 2 12 5 4
DEL PEAK 6(7Q34) WILD-TYPE 56 25 36 39

Figure S46.  Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.0035

Table S47.  Gene #12: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
DEL PEAK 6(7Q34) MUTATED 2 10 11
DEL PEAK 6(7Q34) WILD-TYPE 65 24 67

Figure S47.  Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00028

Table S48.  Gene #14: 'del_12p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
DEL PEAK 10(12P13.2) MUTATED 2 0 7 1
DEL PEAK 10(12P13.2) WILD-TYPE 146 14 20 1

Figure S48.  Get High-res Image Gene #14: 'del_12p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.2' versus 'METHLYATION_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0057

Table S49.  Gene #14: 'del_12p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
DEL PEAK 10(12P13.2) MUTATED 0 9 1 0
DEL PEAK 10(12P13.2) WILD-TYPE 33 52 46 44

Figure S49.  Get High-res Image Gene #14: 'del_12p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.022

Table S50.  Gene #14: 'del_12p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
DEL PEAK 10(12P13.2) MUTATED 0 4 6
DEL PEAK 10(12P13.2) WILD-TYPE 67 30 72

Figure S50.  Get High-res Image Gene #14: 'del_12p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_12q21.33' versus 'CN_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0047

Table S51.  Gene #15: 'del_12q21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
DEL PEAK 11(12Q21.33) MUTATED 0 0 2 1
DEL PEAK 11(12Q21.33) WILD-TYPE 148 14 25 1

Figure S51.  Get High-res Image Gene #15: 'del_12q21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q21.33' versus 'MIRSEQ_CNMF'

P value = 0.0086 (Fisher's exact test), Q value = 0.02

Table S52.  Gene #15: 'del_12q21.33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
DEL PEAK 11(12Q21.33) MUTATED 0 3 0 0
DEL PEAK 11(12Q21.33) WILD-TYPE 58 34 41 43

Figure S52.  Get High-res Image Gene #15: 'del_12q21.33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_12q21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00611 (Fisher's exact test), Q value = 0.015

Table S53.  Gene #15: 'del_12q21.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
DEL PEAK 11(12Q21.33) MUTATED 0 3 0
DEL PEAK 11(12Q21.33) WILD-TYPE 67 31 78

Figure S53.  Get High-res Image Gene #15: 'del_12q21.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.0057

Table S54.  Gene #16: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
DEL PEAK 12(16Q23.1) MUTATED 3 0 6 0
DEL PEAK 12(16Q23.1) WILD-TYPE 145 14 21 2

Figure S54.  Get High-res Image Gene #16: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 0.047

Table S55.  Gene #16: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
DEL PEAK 12(16Q23.1) MUTATED 0 7 2 0
DEL PEAK 12(16Q23.1) WILD-TYPE 33 54 45 44

Figure S55.  Get High-res Image Gene #16: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.082

Table S56.  Gene #16: 'del_16q23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
DEL PEAK 12(16Q23.1) MUTATED 1 4 3 0
DEL PEAK 12(16Q23.1) WILD-TYPE 57 33 38 43

Figure S56.  Get High-res Image Gene #16: 'del_16q23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S57.  Gene #17: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
DEL PEAK 13(17P13.2) MUTATED 0 0 15 0
DEL PEAK 13(17P13.2) WILD-TYPE 148 14 12 2

Figure S57.  Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0017

Table S58.  Gene #17: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
DEL PEAK 13(17P13.2) MUTATED 0 12 3 0
DEL PEAK 13(17P13.2) WILD-TYPE 33 49 44 44

Figure S58.  Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.2' versus 'MRNASEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.024

Table S59.  Gene #17: 'del_17p13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 52 44
DEL PEAK 13(17P13.2) MUTATED 12 2 1
DEL PEAK 13(17P13.2) WILD-TYPE 58 50 43

Figure S59.  Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0016

Table S60.  Gene #17: 'del_17p13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
DEL PEAK 13(17P13.2) MUTATED 0 0 0 14 0 1
DEL PEAK 13(17P13.2) WILD-TYPE 16 13 14 41 26 41

Figure S60.  Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0047

Table S61.  Gene #17: 'del_17p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
DEL PEAK 13(17P13.2) MUTATED 0 5 10
DEL PEAK 13(17P13.2) WILD-TYPE 67 29 68

Figure S61.  Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S62.  Gene #18: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
DEL PEAK 14(17Q11.2) MUTATED 2 2 9 0
DEL PEAK 14(17Q11.2) WILD-TYPE 146 12 18 2

Figure S62.  Get High-res Image Gene #18: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00512 (Fisher's exact test), Q value = 0.014

Table S63.  Gene #18: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
DEL PEAK 14(17Q11.2) MUTATED 0 9 4 0
DEL PEAK 14(17Q11.2) WILD-TYPE 33 52 43 44

Figure S63.  Get High-res Image Gene #18: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00658 (Fisher's exact test), Q value = 0.016

Table S64.  Gene #18: 'del_17q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
DEL PEAK 14(17Q11.2) MUTATED 0 1 0 11 0 1
DEL PEAK 14(17Q11.2) WILD-TYPE 16 12 14 44 26 41

Figure S64.  Get High-res Image Gene #18: 'del_17q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00383 (Fisher's exact test), Q value = 0.011

Table S65.  Gene #18: 'del_17q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
DEL PEAK 14(17Q11.2) MUTATED 0 4 9
DEL PEAK 14(17Q11.2) WILD-TYPE 67 30 69

Figure S65.  Get High-res Image Gene #18: 'del_17q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_18p11.21' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S66.  Gene #19: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
DEL PEAK 15(18P11.21) MUTATED 1 0 8 0
DEL PEAK 15(18P11.21) WILD-TYPE 147 14 19 2

Figure S66.  Get High-res Image Gene #19: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_18p11.21' versus 'METHLYATION_CNMF'

P value = 0.00387 (Fisher's exact test), Q value = 0.011

Table S67.  Gene #19: 'del_18p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
DEL PEAK 15(18P11.21) MUTATED 0 8 0 1
DEL PEAK 15(18P11.21) WILD-TYPE 33 53 47 43

Figure S67.  Get High-res Image Gene #19: 'del_18p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.063

Table S68.  Gene #19: 'del_18p11.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
DEL PEAK 15(18P11.21) MUTATED 0 3 5
DEL PEAK 15(18P11.21) WILD-TYPE 67 31 73

Figure S68.  Get High-res Image Gene #19: 'del_18p11.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_20q13.13' versus 'CN_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.058

Table S69.  Gene #20: 'del_20q13.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
DEL PEAK 16(20Q13.13) MUTATED 1 0 3 0
DEL PEAK 16(20Q13.13) WILD-TYPE 147 14 24 2

Figure S69.  Get High-res Image Gene #20: 'del_20q13.13' versus Molecular Subtype #1: 'CN_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/LAML-TB/19782150/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/19785823/LAML-TB.transferedmergedcluster.txt

  • Number of patients = 191

  • Number of significantly focal cnvs = 20

  • Number of molecular subtypes = 6

  • 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.

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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